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HEADER HYDROLASE 27-FEB-04 1UXO
TITLE THE CRYSTAL STRUCTURE OF THE YDEN GENE PRODUCT FROM B.
TITLE 2 SUBTILIS
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: YDEN PROTEIN;
COMPND 3 FRAGMENT: RESIDUES 2-190;
COMPND 4 MUTATION: YES;
COMPND 5 CHAIN: A
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS
KEYWDS A/B HYDROLASE, ESTERASE
EXPDTA X-RAY DIFFRACTION
AUTHOR I.K.JANDA,Y.DEVEDJIEV,D.COOPER,M.CHRUSZCZ,U.DEREWENDA,
AUTHOR 2 A.GABRYS,W.MINOR,A.JOACHIMIAK,Z.S.DEREWENDA
REVDAT 2 08-JUN-04 1UXO 1 SEQRES
REVDAT 1 27-MAY-04 1UXO 0
JRNL AUTH I.K.JANDA,Y.DEVEDJIEV,D.COOPER,M.CHRUSZCZ,
JRNL AUTH 2 U.DEREWENDA,A.GABRYS,W.MINOR,A.JOACHIMIAK,
JRNL AUTH 3 Z.S.DEREWENDA
JRNL TITL HARVESTING THE HIGH-HANGING FRUIT: THE STRUCTURE OF
JRNL TITL 2 THE YDEN GENE PRODUCT FROM BACILLUS SUBTILIS AT 1.8
JRNL TITL 3 A RESOLUTION
JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 60 1101 2004
JRNL REFN ASTM ABCRE6 DK ISSN 0907-4449
REMARK 2
REMARK 2 RESOLUTION. 1.8 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC_5.1.24 24/04/2001
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) : 1.80
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.62
REMARK 3 DATA CUTOFF (SIGMA(F)) : NONE
REMARK 3 COMPLETENESS FOR RANGE (%) : 94.37
REMARK 3 NUMBER OF REFLECTIONS : 15495
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) : NULL
REMARK 3 R VALUE (WORKING SET) : 0.12520
REMARK 3 FREE R VALUE : 0.18070
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.3
REMARK 3 FREE R VALUE TEST SET COUNT : 1038
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 20
REMARK 3 BIN RESOLUTION RANGE HIGH : 1.800
REMARK 3 BIN RESOLUTION RANGE LOW : 1.847
REMARK 3 REFLECTION IN BIN (WORKING SET) : 707
REMARK 3 BIN R VALUE (WORKING SET) : 0.158
REMARK 3 BIN FREE R VALUE SET COUNT : 43
REMARK 3 BIN FREE R VALUE : 0.263
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 1497
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 16
REMARK 3 SOLVENT ATOMS : 292
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.413
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.71
REMARK 3 B22 (A**2) : 1.03
REMARK 3 B33 (A**2) : -0.33
REMARK 3 B12 (A**2) : 0.00
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): 0.375
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.116
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.068
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.196
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.972
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.951
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED (A): 1553 ; 0.019 ; 0.021
REMARK 3 BOND LENGTHS OTHERS (A): 1382 ; 0.002 ; 0.020
REMARK 3 BOND ANGLES REFINED (DEGREES): 2109 ; 1.621 ; 1.940
REMARK 3 BOND ANGLES OTHERS (DEGREES): 3230 ; 1.904 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 185 ; 5.271 ; 5.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 233 ; 0.108 ; 0.200
REMARK 3 GENERAL PLANES REFINED (A): 1713 ; 0.011 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): 314 ; 0.013 ; 0.020
REMARK 3 NON-BONDED CONTACTS REFINED (A): 330 ; 0.324 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1588 ; 0.252 ; 0.200
REMARK 3 NON-BONDED TORSION OTHERS (A): 860 ; 0.087 ; 0.200
REMARK 3 H-BOND (X...Y) REFINED (A): 230 ; 0.303 ; 0.200
REMARK 3 SYMMETRY VDW REFINED (A): 6 ; 0.046 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): 45 ; 0.304 ; 0.200
REMARK 3 SYMMETRY H-BOND REFINED (A): 30 ; 0.229 ; 0.200
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 MAIN-CHAIN BOND REFINED (A**2): 928 ; 1.395 ; 1.500
REMARK 3 MAIN-CHAIN ANGLE REFINED (A**2): 1503 ; 2.140 ; 2.000
REMARK 3 SIDE-CHAIN BOND REFINED (A**2): 625 ; 3.115 ; 3.000
REMARK 3 SIDE-CHAIN ANGLE REFINED (A**2): 606 ; 4.619 ; 4.500
REMARK 3
REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 RIGID-BOND RESTRAINTS (A**2): 1553 ; 1.761 ; 2.000
REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 1513 ; 2.534 ; 2.000
REMARK 3
REMARK 3 NCS RESTRAINTS STATISTICS
REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NONE
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NONE
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : BABINET MODEL PLUS 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
REMARK 3 THE RIDING POSITIONS
REMARK 4
REMARK 4 1UXO COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY EBI ON 1-MAR-2004.
REMARK 100 THE EBI ID CODE IS EBI-14327.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 15-OCT-2003
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 4.6
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS BEAMLINE 22-ID
REMARK 200 BEAMLINE : 22-ID
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.97920,0.97931,0.97546
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : NULL
REMARK 200 DETECTOR MANUFACTURER : NULL
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL2000
REMARK 200 DATA SCALING SOFTWARE : HKL2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31784
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.70
REMARK 200 RESOLUTION RANGE LOW (A) : 50.0
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NONE
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8
REMARK 200 DATA REDUNDANCY : 3.5
REMARK 200 R MERGE (I) : 0.82
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : 13.9
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.83
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.91
REMARK 200 COMPLETENESS FOR SHELL (%) : 65.8
REMARK 200 DATA REDUNDANCY IN SHELL : 2.3
REMARK 200 R MERGE FOR SHELL (I) : 0.22
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 FOR SHELL : 4.3
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: MAD
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER
REMARK 200 SOFTWARE USED: SHELXD, SHARP
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 40.7
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.1
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 8000, 0.05 M KH2PO4,
REMARK 280 PH 4.6
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 1/2-X,-Y,1/2+Z
REMARK 290 3555 -X,1/2+Y,1/2-Z
REMARK 290 4555 1/2+X,1/2-Y,-Z
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 -1.000000 0.000000 0.000000 18.06400
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.57550
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.98550
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 46.57550
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.06400
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.98550
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT
REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR
REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).
REMARK 300
REMARK 300 QUATERNARY STRUCTURE FOR THIS ENTRY: MONOMERIC
REMARK 350
REMARK 350 GENERATING THE BIOMOLECULE
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 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 400
REMARK 400 COMPOUND
REMARK 400 ENGINEERED MUTATION LYS 88 ALA AND GLN 89 ALA IN CHAIN A
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 GLY A -1
REMARK 465 ARG A 0
REMARK 465 GLY A 1
REMARK 465 GLU A 188
REMARK 465 THR A 189
REMARK 465 ARG A 190
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500
REMARK 500 O HOH Z 40 O HOH Z 87 2.19
REMARK 500 O HOH Z 167 O HOH Z 181 2.01
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 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500
REMARK 500 SER A 71 -116.81 55.19
REMARK 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES ARE GIVEN CHAIN IDENTIFIERS TO
REMARK 525 INDICATE THE PROTEIN CHAIN TO WHICH THEY ARE MOST CLOSELY
REMARK 525 ASSOCIATED WITH:
REMARK 525 PROTEIN CHAIN SOLVENT CHAIN
REMARK 525 A Z
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 ALA A 88, MUTAGENESIS FOR CRYSTALLIZATION
REMARK 999 ALA A 89, MUTAGENESIS FOR CRYSTALLIZATION
DBREF 1UXO A -1 1 PDB 1UXO 1UXO -1 1
DBREF 1UXO A 2 190 UNP P96671 P96671 2 190
SEQADV 1UXO ALA A 88 UNP P96671 LYS 88 ENGINEERED MUTATION
SEQADV 1UXO ALA A 89 UNP P96671 GLN 89 ENGINEERED MUTATION
SEQRES 1 A 192 GLY ARG GLY THR LYS GLN VAL TYR ILE ILE HIS GLY TYR
SEQRES 2 A 192 ARG ALA SER SER THR ASN HIS TRP PHE PRO TRP LEU LYS
SEQRES 3 A 192 LYS ARG LEU LEU ALA ASP GLY VAL GLN ALA ASP ILE LEU
SEQRES 4 A 192 ASN MSE PRO ASN PRO LEU GLN PRO ARG LEU GLU ASP TRP
SEQRES 5 A 192 LEU ASP THR LEU SER LEU TYR GLN HIS THR LEU HIS GLU
SEQRES 6 A 192 ASN THR TYR LEU VAL ALA HIS SER LEU GLY CYS PRO ALA
SEQRES 7 A 192 ILE LEU ARG PHE LEU GLU HIS LEU GLN LEU ARG ALA ALA
SEQRES 8 A 192 LEU GLY GLY ILE ILE LEU VAL SER GLY PHE ALA LYS SER
SEQRES 9 A 192 LEU PRO THR LEU GLN MSE LEU ASP GLU PHE THR GLN GLY
SEQRES 10 A 192 SER PHE ASP HIS GLN LYS ILE ILE GLU SER ALA LYS HIS
SEQRES 11 A 192 ARG ALA VAL ILE ALA SER LYS ASP ASP GLN ILE VAL PRO
SEQRES 12 A 192 PHE SER PHE SER LYS ASP LEU ALA GLN GLN ILE ASP ALA
SEQRES 13 A 192 ALA LEU TYR GLU VAL GLN HIS GLY GLY HIS PHE LEU GLU
SEQRES 14 A 192 ASP GLU GLY PHE THR SER LEU PRO ILE VAL TYR ASP VAL
SEQRES 15 A 192 LEU THR SER TYR PHE SER LYS GLU THR ARG
MODRES 1UXO MSE A 39 MET SELENOMETHIONINE
MODRES 1UXO MSE A 108 MET SELENOMETHIONINE
HET MSE A 39 8
HET MSE A 108 8
HETNAM MSE SELENOMETHIONINE
FORMUL 2 MSE 2(C5 H11 N1 O2 SE1)
FORMUL 3 HOH *292(H2 O1)
HELIX 1 1 TRP A 19 ASP A 30 1 12
HELIX 2 2 ARG A 46 LEU A 56 1 11
HELIX 3 3 TYR A 57 LEU A 61 5 5
HELIX 4 4 LEU A 72 HIS A 83 1 12
HELIX 5 5 LEU A 106 THR A 113 5 8
HELIX 6 6 ASP A 118 SER A 125 1 8
HELIX 7 7 PRO A 141 ILE A 152 1 12
HELIX 8 8 LEU A 166 GLY A 170 5 5
HELIX 9 9 LEU A 174 LYS A 187 1 14
SHEET 1 AA 6 GLN A 33 LEU A 37 0
SHEET 2 AA 6 GLN A 4 ILE A 8 1 O VAL A 5 N ASP A 35
SHEET 3 AA 6 THR A 65 HIS A 70 1 O TYR A 66 N TYR A 6
SHEET 4 AA 6 LEU A 90 VAL A 96 1 N GLY A 91 O THR A 65
SHEET 5 AA 6 ALA A 126 SER A 134 1 N LYS A 127 O LEU A 90
SHEET 6 AA 6 ALA A 155 VAL A 159 1 O ALA A 155 N VAL A 131
LINK C ASN A 38 N MSE A 39 1555 1555
LINK C MSE A 39 N PRO A 40 1555 1555
LINK C GLN A 107 N MSE A 108 1555 1555
LINK C MSE A 108 N LEU A 109 1555 1555
CRYST1 36.128 53.971 93.151 90.00 90.00 90.00 P 21 21 21 4
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 0.027679 0.000000 0.000000 0.00000
SCALE2 0.000000 0.018528 0.000000 0.00000
SCALE3 0.000000 0.000000 0.010735 0.00000
MASTER 268 0 2 9 6 0 0 6 1803 1 20 15
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