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HEADER HYDROLASE 26-JAN-11 2Y6U
TITLE PEROXISOMAL ALPHA-BETA-HYDROLASE LPX1 (YOR084W) FROM
TITLE 2 SACCHAROMYCES CEREVISIAE (CRYSTAL FORM II)
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PEROXISOMAL MEMBRANE PROTEIN LPX1;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: LIPASE OF PEROXISOMES PROTEIN 1, LPX1-YOR084W;
COMPND 5 EC: 3.1.1.-;
COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE;
SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST;
SOURCE 4 ORGANISM_TAXID: 4932;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21;
SOURCE 8 EXPRESSION_SYSTEM_VARIANT: CODON PLUS RIL;
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET21D;
SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PST281
KEYWDS HYDROLASE, PUTATIVE ESTERASE, PUTATIVE LIPASE
EXPDTA X-RAY DIFFRACTION
AUTHOR S.THOMS,H.H.NIEMANN
REVDAT 1 13-JUL-11 2Y6U 0
JRNL AUTH S.THOMS,J.HOFHUIS,C.THOING,J.GARTNER,H.H.NIEMANN
JRNL TITL THE UNUSUAL EXTENDED C-TERMINAL HELIX OF THE PEROXISOMAL
JRNL TITL 2 ALPHA-BETA-HYDROLASE LPX1 IS INVOLVED IN DIMER CONTACTS BUT
JRNL TITL 3 DISPENSABLE FOR DIMERIZATION
JRNL REF J.STRUCT.BIOL. 2011
JRNL REFN ESSN 1095-8657
JRNL DOI 10.1016/J.JSB.2011.06.008
REMARK 2
REMARK 2 RESOLUTION. 1.90 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.5.0109
REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : NONE
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.88
REMARK 3 NUMBER OF REFLECTIONS : 41757
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING + TEST SET) : 0.15474
REMARK 3 R VALUE (WORKING SET) : 0.15343
REMARK 3 FREE R VALUE : 0.17900
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.0
REMARK 3 FREE R VALUE TEST SET COUNT : 2219
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 20
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.900
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.949
REMARK 3 REFLECTION IN BIN (WORKING SET) : 3006
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.84
REMARK 3 BIN R VALUE (WORKING SET) : 0.196
REMARK 3 BIN FREE R VALUE SET COUNT : 162
REMARK 3 BIN FREE R VALUE : 0.243
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 3070
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 6
REMARK 3 SOLVENT ATOMS : 280
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 25
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.025
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.04
REMARK 3 B22 (A**2) : -0.04
REMARK 3 B33 (A**2) : 0.05
REMARK 3 B12 (A**2) : -0.02
REMARK 3 B13 (A**2) : 0.00
REMARK 3 B23 (A**2) : 0.00
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.102
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.098
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.065
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.910
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.957
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3163 ; 0.027 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): 2164 ; 0.001 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4318 ; 2.018 ; 1.952
REMARK 3 BOND ANGLES OTHERS (DEGREES): 5293 ; 1.088 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 421 ;22.017 ; 5.285
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 157 ;34.353 ;23.885
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 543 ;14.205 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 25 ;17.857 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 483 ; 0.140 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3547 ; 0.010 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 646 ; 0.001 ; 0.020
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1916 ; 1.222 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 762 ; 0.393 ; 1.500
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3132 ; 2.030 ; 2.000
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1247 ; 2.932 ; 3.000
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1165 ; 4.345 ; 4.500
REMARK 3
REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 NCS RESTRAINTS STATISTICS
REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 8
REMARK 3
REMARK 3 TLS GROUP : 1
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 1 A 54
REMARK 3 ORIGIN FOR THE GROUP (A): -37.0282 -4.4623 8.7453
REMARK 3 T TENSOR
REMARK 3 T11: 0.0667 T22: 0.1706
REMARK 3 T33: 0.1665 T12: -0.0144
REMARK 3 T13: 0.0060 T23: 0.0125
REMARK 3 L TENSOR
REMARK 3 L11: 2.1773 L22: 3.6522
REMARK 3 L33: 2.3182 L12: 0.3618
REMARK 3 L13: 0.5202 L23: 1.3970
REMARK 3 S TENSOR
REMARK 3 S11: 0.0357 S12: 0.0852 S13: -0.2381
REMARK 3 S21: 0.2079 S22: -0.1496 S23: 0.5407
REMARK 3 S31: 0.2504 S32: -0.3709 S33: 0.1139
REMARK 3
REMARK 3 TLS GROUP : 2
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 55 A 137
REMARK 3 ORIGIN FOR THE GROUP (A): -31.4446 -3.5166 5.3957
REMARK 3 T TENSOR
REMARK 3 T11: 0.0154 T22: 0.1122
REMARK 3 T33: 0.0496 T12: 0.0015
REMARK 3 T13: -0.0124 T23: -0.0043
REMARK 3 L TENSOR
REMARK 3 L11: 2.4550 L22: 3.4397
REMARK 3 L33: 3.0669 L12: 0.1719
REMARK 3 L13: 0.1290 L23: 1.2115
REMARK 3 S TENSOR
REMARK 3 S11: 0.0005 S12: 0.2213 S13: -0.1772
REMARK 3 S21: -0.0528 S22: -0.0126 S23: 0.2372
REMARK 3 S31: 0.1391 S32: -0.2227 S33: 0.0121
REMARK 3
REMARK 3 TLS GROUP : 3
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 138 A 283
REMARK 3 ORIGIN FOR THE GROUP (A): -21.9590 6.2272 -0.2924
REMARK 3 T TENSOR
REMARK 3 T11: 0.1416 T22: 0.1528
REMARK 3 T33: 0.1032 T12: -0.0034
REMARK 3 T13: 0.0082 T23: 0.0251
REMARK 3 L TENSOR
REMARK 3 L11: 1.8989 L22: 1.6313
REMARK 3 L33: 2.8178 L12: -0.2958
REMARK 3 L13: 0.6350 L23: -0.2479
REMARK 3 S TENSOR
REMARK 3 S11: -0.0432 S12: 0.3874 S13: 0.3271
REMARK 3 S21: -0.2836 S22: -0.0156 S23: -0.0553
REMARK 3 S31: -0.4295 S32: 0.1285 S33: 0.0588
REMARK 3
REMARK 3 TLS GROUP : 4
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 284 A 316
REMARK 3 ORIGIN FOR THE GROUP (A): -10.5905 -7.7053 3.7526
REMARK 3 T TENSOR
REMARK 3 T11: 0.0410 T22: 0.1396
REMARK 3 T33: 0.0756 T12: 0.0412
REMARK 3 T13: 0.0127 T23: -0.0567
REMARK 3 L TENSOR
REMARK 3 L11: 5.3565 L22: 3.0915
REMARK 3 L33: 6.3397 L12: 0.8049
REMARK 3 L13: -0.3807 L23: 0.1002
REMARK 3 S TENSOR
REMARK 3 S11: 0.0258 S12: 0.2278 S13: 0.0133
REMARK 3 S21: -0.0911 S22: -0.0208 S23: -0.1605
REMARK 3 S31: 0.0374 S32: 0.3792 S33: -0.0050
REMARK 3
REMARK 3 TLS GROUP : 5
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 317 A 348
REMARK 3 ORIGIN FOR THE GROUP (A): -20.1730 -14.0208 -3.5877
REMARK 3 T TENSOR
REMARK 3 T11: 0.0948 T22: 0.1771
REMARK 3 T33: 0.1182 T12: 0.0179
REMARK 3 T13: 0.0056 T23: -0.1050
REMARK 3 L TENSOR
REMARK 3 L11: 3.3117 L22: 3.0491
REMARK 3 L33: 5.0939 L12: 0.4349
REMARK 3 L13: -0.7485 L23: -0.0217
REMARK 3 S TENSOR
REMARK 3 S11: -0.0643 S12: 0.4054 S13: -0.4264
REMARK 3 S21: -0.3048 S22: -0.0094 S23: -0.1252
REMARK 3 S31: 0.5581 S32: 0.1224 S33: 0.0737
REMARK 3
REMARK 3 TLS GROUP : 6
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 349 A 356
REMARK 3 ORIGIN FOR THE GROUP (A): -32.6812 -26.0021 19.8660
REMARK 3 T TENSOR
REMARK 3 T11: 0.9901 T22: 1.3119
REMARK 3 T33: 1.0034 T12: -0.1287
REMARK 3 T13: 0.0350 T23: 0.0166
REMARK 3 L TENSOR
REMARK 3 L11: 1.7967 L22: 4.4578
REMARK 3 L33: 0.0689 L12: 2.8258
REMARK 3 L13: 0.3425 L23: 0.5323
REMARK 3 S TENSOR
REMARK 3 S11: 0.2662 S12: -0.2612 S13: -0.2574
REMARK 3 S21: 0.1908 S22: -0.3356 S23: -0.4469
REMARK 3 S31: 0.0793 S32: -0.0478 S33: 0.0695
REMARK 3
REMARK 3 TLS GROUP : 7
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 357 A 376
REMARK 3 ORIGIN FOR THE GROUP (A): -30.3424 -24.7320 36.9585
REMARK 3 T TENSOR
REMARK 3 T11: 0.2685 T22: 0.0821
REMARK 3 T33: 0.1929 T12: -0.0451
REMARK 3 T13: 0.0164 T23: 0.0930
REMARK 3 L TENSOR
REMARK 3 L11: 21.0558 L22: 6.2058
REMARK 3 L33: 3.3985 L12: 3.4366
REMARK 3 L13: 2.3717 L23: 0.2505
REMARK 3 S TENSOR
REMARK 3 S11: 0.1364 S12: -0.0200 S13: -0.5760
REMARK 3 S21: 0.0730 S22: 0.0522 S23: -0.0088
REMARK 3 S31: 0.3392 S32: -0.0630 S33: -0.1887
REMARK 3
REMARK 3 TLS GROUP : 8
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 377 A 381
REMARK 3 ORIGIN FOR THE GROUP (A): -12.1012 -22.9028 39.6455
REMARK 3 T TENSOR
REMARK 3 T11: 0.5158 T22: 0.3141
REMARK 3 T33: 0.5725 T12: 0.0966
REMARK 3 T13: -0.1326 T23: 0.0302
REMARK 3 L TENSOR
REMARK 3 L11: 30.1350 L22: 3.4901
REMARK 3 L33: 10.4515 L12: -2.4376
REMARK 3 L13: 8.3774 L23: -5.8449
REMARK 3 S TENSOR
REMARK 3 S11: 1.0868 S12: -0.5199 S13: -1.7782
REMARK 3 S21: -0.3553 S22: -0.4039 S23: 0.2429
REMARK 3 S31: 0.7993 S32: 0.5684 S33: -0.6829
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : BABINET MODEL WITH MASK
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.40
REMARK 3 ION PROBE RADIUS : 0.80
REMARK 3 SHRINKAGE RADIUS : 0.80
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE
REMARK 3 RIDING POSITIONS.
REMARK 4
REMARK 4 2Y6U COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-JAN-11.
REMARK 100 THE PDBE ID CODE IS EBI-45782.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 26-FEB-09
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG
REMARK 200 BEAMLINE : X12
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.0332
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : SCALA
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44068
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.90
REMARK 200 RESOLUTION RANGE LOW (A) : 48.00
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.0
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 200 DATA REDUNDANCY : 10.3
REMARK 200 R MERGE (I) : 0.12
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : 18.10
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8
REMARK 200 DATA REDUNDANCY IN SHELL : 4.4
REMARK 200 R MERGE FOR SHELL (I) : 0.50
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 FOR SHELL : 3.40
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASER
REMARK 200 STARTING MODEL: PDB ENTRY 2Y6V
REMARK 200
REMARK 200 REMARK: NONE
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 59
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.9
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: VAPOR DIFFUSION. DROP CONTAINED
REMARK 280 2.5 UL PROTEIN (2.0 MG/ML), 0.5 UL ADDITIVE (0.1 M UREA)
REMARK 280 AND 2 UL RESERVOIR (8 % PEG 8000, 0.1 M HEPES, PH 7.0)
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -Y,X-Y,Z+2/3
REMARK 290 3555 -X+Y,-X,Z+1/3
REMARK 290 4555 Y,X,-Z
REMARK 290 5555 X-Y,-Y,-Z+1/3
REMARK 290 6555 -X,-X+Y,-Z+2/3
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 83.68000
REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 41.84000
REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 41.84000
REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 83.68000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 6660 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 30700 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -44.4 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 41.84000
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 MET A 1
REMARK 465 GLU A 2
REMARK 465 ALA A 243
REMARK 465 SER A 244
REMARK 465 GLY A 245
REMARK 465 ASP A 246
REMARK 465 ASP A 247
REMARK 465 GLU A 248
REMARK 465 ASP A 249
REMARK 465 GLY A 250
REMARK 465 THR A 382
REMARK 465 THR A 383
REMARK 465 LYS A 384
REMARK 465 GLN A 385
REMARK 465 LYS A 386
REMARK 465 LEU A 387
REMARK 465 ALA A 388
REMARK 465 ALA A 389
REMARK 465 ALA A 390
REMARK 465 LEU A 391
REMARK 465 GLU A 392
REMARK 465 HIS A 393
REMARK 465 HIS A 394
REMARK 465 HIS A 395
REMARK 465 HIS A 396
REMARK 465 HIS A 397
REMARK 465 HIS A 398
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION
REMARK 500 GLU A 69 CG GLU A 69 CD 0.095
REMARK 500 ARG A 119 CZ ARG A 119 NH1 -0.079
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 ARG A 119 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES
REMARK 500 ARG A 119 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES
REMARK 500 MET A 269 CG - SD - CE ANGL. DEV. = 16.8 DEGREES
REMARK 500 ARG A 336 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES
REMARK 500 ARG A 336 NE - CZ - NH2 ANGL. DEV. = -5.0 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 MET A 63 -145.20 -110.40
REMARK 500 VAL A 76 114.98 -32.10
REMARK 500 ALA A 80 -91.42 -42.13
REMARK 500 SER A 134 -15.75 -43.83
REMARK 500 SER A 145 -122.02 64.07
REMARK 500 GLN A 158 83.18 -154.13
REMARK 500 LEU A 161 -63.17 -99.27
REMARK 500 VAL A 172 -58.96 -125.22
REMARK 500 HIS A 228 130.79 -39.95
REMARK 500 PRO A 252 156.43 -45.48
REMARK 500 PHE A 272 -17.68 -140.48
REMARK 500 GLN A 351 62.84 101.39
REMARK 500 GLN A 357 66.59 -101.73
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1382
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2Y6V RELATED DB: PDB
REMARK 900 PEROXISOMAL ALPHA-BETA-HYDROLASE LPX1 (YOR084W)
REMARK 900 FROM SACCHAROMYCES CEREVISIAE (CRYSTAL FORM I)
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 C-TERMINAL ELEVEN RESIDUES ARE CLONING ARTEFACT (AAALE)
REMARK 999 AND HEXA-HISTIDINE TAG.
DBREF 2Y6U A 1 387 UNP Q12405 LPX1_YEAST 1 387
SEQADV 2Y6U ALA A 388 UNP Q12405 EXPRESSION TAG
SEQADV 2Y6U ALA A 389 UNP Q12405 EXPRESSION TAG
SEQADV 2Y6U ALA A 390 UNP Q12405 EXPRESSION TAG
SEQADV 2Y6U LEU A 391 UNP Q12405 EXPRESSION TAG
SEQADV 2Y6U GLU A 392 UNP Q12405 EXPRESSION TAG
SEQADV 2Y6U HIS A 393 UNP Q12405 EXPRESSION TAG
SEQADV 2Y6U HIS A 394 UNP Q12405 EXPRESSION TAG
SEQADV 2Y6U HIS A 395 UNP Q12405 EXPRESSION TAG
SEQADV 2Y6U HIS A 396 UNP Q12405 EXPRESSION TAG
SEQADV 2Y6U HIS A 397 UNP Q12405 EXPRESSION TAG
SEQADV 2Y6U HIS A 398 UNP Q12405 EXPRESSION TAG
SEQRES 1 A 398 MET GLU GLN ASN ARG PHE LYS LYS GLU THR LYS THR CME
SEQRES 2 A 398 SER ALA SER TRP PRO ARG ALA PRO GLN SER THR LEU CSO
SEQRES 3 A 398 ALA THR ASP ARG LEU GLU LEU THR TYR ASP VAL TYR THR
SEQRES 4 A 398 SER ALA GLU ARG GLN ARG ARG SER ARG THR ALA THR ARG
SEQRES 5 A 398 LEU ASN LEU VAL PHE LEU HIS GLY SER GLY MET SER LYS
SEQRES 6 A 398 VAL VAL TRP GLU TYR TYR LEU PRO ARG LEU VAL ALA ALA
SEQRES 7 A 398 ASP ALA GLU GLY ASN TYR ALA ILE ASP LYS VAL LEU LEU
SEQRES 8 A 398 ILE ASP GLN VAL ASN HIS GLY ASP SER ALA VAL ARG ASN
SEQRES 9 A 398 ARG GLY ARG LEU GLY THR ASN PHE ASN TRP ILE ASP GLY
SEQRES 10 A 398 ALA ARG ASP VAL LEU LYS ILE ALA THR CSO GLU LEU GLY
SEQRES 11 A 398 SER ILE ASP SER HIS PRO ALA LEU ASN VAL VAL ILE GLY
SEQRES 12 A 398 HIS SER MET GLY GLY PHE GLN ALA LEU ALA CYS ASP VAL
SEQRES 13 A 398 LEU GLN PRO ASN LEU PHE HIS LEU LEU ILE LEU ILE GLU
SEQRES 14 A 398 PRO VAL VAL ILE THR ARG LYS ALA ILE GLY ALA GLY ARG
SEQRES 15 A 398 PRO GLY LEU PRO PRO ASP SER PRO GLN ILE PRO GLU ASN
SEQRES 16 A 398 LEU TYR ASN SER LEU ARG LEU LYS THR CSO ASP HIS PHE
SEQRES 17 A 398 ALA ASN GLU SER GLU TYR VAL LYS TYR MET ARG ASN GLY
SEQRES 18 A 398 SER PHE PHE THR ASN ALA HIS SER GLN ILE LEU GLN ASN
SEQRES 19 A 398 ILE ILE ASP PHE GLU ARG THR LYS ALA SER GLY ASP ASP
SEQRES 20 A 398 GLU ASP GLY GLY PRO VAL ARG THR LYS MET GLU GLN ALA
SEQRES 21 A 398 GLN ASN LEU LEU CYS TYR MET ASN MET GLN THR PHE ALA
SEQRES 22 A 398 PRO PHE LEU ILE SER ASN VAL LYS PHE VAL ARG LYS ARG
SEQRES 23 A 398 THR ILE HIS ILE VAL GLY ALA ARG SER ASN TRP CSO PRO
SEQRES 24 A 398 PRO GLN ASN GLN LEU PHE LEU GLN LYS THR LEU GLN ASN
SEQRES 25 A 398 TYR HIS LEU ASP VAL ILE PRO GLY GLY SER HIS LEU VAL
SEQRES 26 A 398 ASN VAL GLU ALA PRO ASP LEU VAL ILE GLU ARG ILE ASN
SEQRES 27 A 398 HIS HIS ILE HIS GLU PHE VAL LEU THR SER PRO LEU GLN
SEQRES 28 A 398 SER SER HIS ILE PRO GLN LEU THR LEU GLU GLU ARG ALA
SEQRES 29 A 398 VAL MET PHE ASP ARG ALA PHE ASP SER PHE LYS ASN GLU
SEQRES 30 A 398 ALA LEU VAL LYS THR THR LYS GLN LYS LEU ALA ALA ALA
SEQRES 31 A 398 LEU GLU HIS HIS HIS HIS HIS HIS
MODRES 2Y6U CME A 13 CYS S,S-(2-HYDROXYETHYL)THIOCYSTEINE
MODRES 2Y6U CSO A 26 CYS S-HYDROXYCYSTEINE
MODRES 2Y6U CSO A 127 CYS S-HYDROXYCYSTEINE
MODRES 2Y6U CSO A 205 CYS S-HYDROXYCYSTEINE
MODRES 2Y6U CSO A 298 CYS S-HYDROXYCYSTEINE
HET CME A 13 10
HET CSO A 26 7
HET CSO A 127 11
HET CSO A 205 7
HET CSO A 298 11
HET GOL A1382 6
HETNAM CME S,S-(2-HYDROXYETHYL)THIOCYSTEINE
HETNAM CSO S-HYDROXYCYSTEINE
HETNAM GOL GLYCEROL
HETSYN GOL GLYCERIN
FORMUL 2 CME C5 H11 N O3 S2
FORMUL 3 CSO 4(C3 H7 N O3 S)
FORMUL 4 GOL C3 H8 O3
FORMUL 5 HOH *280(H2 O)
HELIX 1 1 SER A 64 LEU A 75 5 12
HELIX 2 2 HIS A 97 ASN A 104 1 8
HELIX 3 3 ASN A 113 LEU A 129 1 17
HELIX 4 4 SER A 145 GLN A 158 1 14
HELIX 5 5 PRO A 193 LYS A 203 1 11
HELIX 6 6 ASN A 210 GLY A 221 1 12
HELIX 7 7 HIS A 228 GLU A 239 1 12
HELIX 8 8 GLU A 258 CYS A 265 1 8
HELIX 9 9 ASN A 268 THR A 271 5 4
HELIX 10 10 PHE A 272 VAL A 280 1 9
HELIX 11 11 LYS A 281 VAL A 283 5 3
HELIX 12 12 PRO A 299 LEU A 310 1 12
HELIX 13 13 LEU A 324 ALA A 329 1 6
HELIX 14 14 ALA A 329 SER A 348 1 20
HELIX 15 15 THR A 359 LEU A 379 1 21
SHEET 1 AA 8 PHE A 6 SER A 14 0
SHEET 2 AA 8 GLU A 32 SER A 40 -1 O LEU A 33 N CME A 13
SHEET 3 AA 8 TYR A 84 ILE A 92 -1 O ASP A 87 N SER A 40
SHEET 4 AA 8 THR A 51 LEU A 58 1 O THR A 51 N ALA A 85
SHEET 5 AA 8 ALA A 137 HIS A 144 1 O LEU A 138 N ASN A 54
SHEET 6 AA 8 LEU A 164 ILE A 168 1 O LEU A 164 N VAL A 141
SHEET 7 AA 8 ARG A 286 GLY A 292 1 O ARG A 286 N LEU A 165
SHEET 8 AA 8 TYR A 313 ILE A 318 1 O HIS A 314 N HIS A 289
SHEET 1 AB 3 HIS A 207 PHE A 208 0
SHEET 2 AB 3 VAL A 253 THR A 255 -1 O VAL A 253 N PHE A 208
SHEET 3 AB 3 ARG A 240 THR A 241 -1 O THR A 241 N ARG A 254
LINK C THR A 12 N CME A 13 1555 1555 1.31
LINK C CME A 13 N SER A 14 1555 1555 1.31
LINK C LEU A 25 N CSO A 26 1555 1555 1.34
LINK C CSO A 26 N ALA A 27 1555 1555 1.33
LINK C THR A 126 N CSO A 127 1555 1555 1.32
LINK C CSO A 127 N GLU A 128 1555 1555 1.32
LINK C THR A 204 N CSO A 205 1555 1555 1.35
LINK C CSO A 205 N ASP A 206 1555 1555 1.31
LINK C TRP A 297 N CSO A 298 1555 1555 1.32
LINK C CSO A 298 N PRO A 299 1555 1555 1.38
CISPEP 1 TRP A 17 PRO A 18 0 -3.44
CISPEP 2 HIS A 135 PRO A 136 0 -1.47
CISPEP 3 ALA A 180 GLY A 181 0 23.49
CISPEP 4 LEU A 350 GLN A 351 0 10.68
SITE 1 AC1 10 THR A 204 CSO A 205 TYR A 217 MET A 218
SITE 2 AC1 10 PHE A 224 GLU A 239 ASN A 262 HOH A2163
SITE 3 AC1 10 HOH A2184 HOH A2194
CRYST1 87.156 87.156 125.520 90.00 90.00 120.00 P 32 2 1 6
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.011474 0.006624 0.000000 0.00000
SCALE2 0.000000 0.013249 0.000000 0.00000
SCALE3 0.000000 0.000000 0.007967 0.00000
TER 3071 LYS A 381
MASTER 510 0 6 15 11 0 3 6 3356 1 62 31
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