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HEADER HYDROLASE 12-MAY-15 4ZRE
TITLE CRYSTAL STRUCTURE OF SMG1 F278D MUTANT
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: LIP1, SECRETORY LIPASE (FAMILY 3);
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: UNP RESIDUES 20-304;
COMPND 5 ENGINEERED: YES;
COMPND 6 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: MALASSEZIA GLOBOSA;
SOURCE 3 ORGANISM_COMMON: DANDRUFF-ASSOCIATED FUNGUS;
SOURCE 4 ORGANISM_TAXID: 425265;
SOURCE 5 STRAIN: ATCC MYA-4612 / CBS 7966;
SOURCE 6 GENE: MGL_0797;
SOURCE 7 EXPRESSION_SYSTEM: KOMAGATAELLA PASTORIS;
SOURCE 8 EXPRESSION_SYSTEM_TAXID: 4922;
SOURCE 9 EXPRESSION_SYSTEM_STRAIN: X33
KEYWDS MONO- AND DIACYLGLYCEROL LIPASE, SECRETORY LIPASE (FAMILY 3),
KEYWDS 2 HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR J.XU,H.XU,S.HOU,J.LIU
REVDAT 1 23-SEP-15 4ZRE 0
JRNL AUTH S.GUO,J.XU,I.V.PAVLIDIS,D.LAN,U.T.BORNSCHEUER,J.LIU,Y.WANG
JRNL TITL STRUCTURE OF PRODUCT-BOUND SMG1 LIPASE: ACTIVE SITE GATING
JRNL TITL 2 IMPLICATIONS
JRNL REF FEBS J. 2015
JRNL REFN ISSN 1742-464X
JRNL DOI 10.1111/FEBS.13513
REMARK 2
REMARK 2 RESOLUTION. 2.00 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC
REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.40
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7
REMARK 3 NUMBER OF REFLECTIONS : 15678
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE
REMARK 3 FREE R VALUE TEST SET SELECTION : NULL
REMARK 3 R VALUE (WORKING + TEST SET) : NULL
REMARK 3 R VALUE (WORKING SET) : 0.157
REMARK 3 FREE R VALUE : 0.205
REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT : NULL
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2188
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 40
REMARK 3 SOLVENT ATOMS : 193
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 9.97
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): NULL
REMARK 3 ESU BASED ON FREE R VALUE (A): NULL
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA
REMARK 3 BOND LENGTH (A) : NULL ; NULL
REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL
REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL
REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL
REMARK 3
REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL
REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL
REMARK 3
REMARK 3 NON-BONDED CONTACT RESTRAINTS.
REMARK 3 SINGLE TORSION (A) : NULL ; NULL
REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL
REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL
REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL
REMARK 3
REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS.
REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL
REMARK 3 PLANAR (DEGREES) : NULL ; NULL
REMARK 3 STAGGERED (DEGREES) : NULL ; NULL
REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 4ZRE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-MAY-15.
REMARK 100 THE DEPOSITION ID IS D_1000209758.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 06-JUN-14
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 5.3
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : N
REMARK 200 RADIATION SOURCE : SEALED TUBE
REMARK 200 BEAMLINE : NULL
REMARK 200 X-RAY GENERATOR MODEL : OXFORD DIFFRACTION ENHANCE ULTRA
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.54056
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : OXFORD RUBY CCD
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSALISPRO
REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.2.8
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16530
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000
REMARK 200 RESOLUTION RANGE LOW (A) : 18.410
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8
REMARK 200 DATA REDUNDANCY : 5.100
REMARK 200 R MERGE (I) : 0.13400
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : 12.3000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05
REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8
REMARK 200 DATA REDUNDANCY IN SHELL : 3.70
REMARK 200 R MERGE FOR SHELL (I) : 0.33100
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 FOR SHELL : 3.500
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: MOLREP
REMARK 200 STARTING MODEL: 3UUE
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 38.37
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS PH5.3, 20% PEG 3350,
REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,Y+1/2,-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 0.00000
REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 36.61950
REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000
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: MONOMERIC
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 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 SER A 20
REMARK 465 SER A 21
REMARK 465 ILE A 22
REMARK 465 TYR A 23
REMARK 465 ALA A 24
REMARK 465 ARG A 25
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 ASN A 62 116.00 -39.25
REMARK 500 TYR A 79 -74.86 -112.86
REMARK 500 SER A 171 -127.18 63.02
REMARK 500 ASP A 245 134.60 82.43
REMARK 500 GLN A 282 36.76 -97.59
REMARK 500 HIS A 287 3.79 82.00
REMARK 500 ILE A 290 78.88 -108.20
REMARK 500 ALA A 292 -142.73 69.09
REMARK 500
REMARK 500 REMARK: NULL
REMARK 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525 M RES CSSEQI
REMARK 525 HOH A 793 DISTANCE = 6.45 ANGSTROMS
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 504
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for Poly-Saccharide residues NAG A
REMARK 800 501 through BMA A 503 bound to ASN A 253
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 4ZRD RELATED DB: PDB
DBREF 4ZRE A 20 304 UNP A8PUY1 A8PUY1_MALGO 20 304
SEQADV 4ZRE ASP A 278 UNP A8PUY1 PHE 278 ENGINEERED MUTATION
SEQRES 1 A 285 SER SER ILE TYR ALA ARG GLY ARG GLY GLY SER SER THR
SEQRES 2 A 285 ASP GLN PRO VAL ALA ASN PRO TYR ASN THR LYS GLU ILE
SEQRES 3 A 285 SER LEU ALA ALA GLY LEU VAL GLN GLN THR TYR CYS ASP
SEQRES 4 A 285 SER THR GLU ASN GLY LEU LYS ILE GLY ASP SER GLU LEU
SEQRES 5 A 285 LEU TYR THR MET GLY GLU GLY TYR ALA ARG GLN ARG VAL
SEQRES 6 A 285 ASN ILE TYR HIS SER PRO SER LEU GLY ILE ALA VAL ALA
SEQRES 7 A 285 ILE GLU GLY THR ASN LEU PHE SER LEU ASN SER ASP LEU
SEQRES 8 A 285 HIS ASP ALA LYS PHE TRP GLN GLU ASP PRO ASN GLU ARG
SEQRES 9 A 285 TYR ILE GLN TYR TYR PRO LYS GLY THR LYS LEU MET HIS
SEQRES 10 A 285 GLY PHE GLN GLN ALA TYR ASN ASP LEU MET ASP ASP ILE
SEQRES 11 A 285 PHE THR ALA VAL LYS LYS TYR LYS LYS GLU LYS ASN GLU
SEQRES 12 A 285 LYS ARG VAL THR VAL ILE GLY HIS SER LEU GLY ALA ALA
SEQRES 13 A 285 MET GLY LEU LEU CYS ALA MET ASP ILE GLU LEU ARG MET
SEQRES 14 A 285 ASP GLY GLY LEU TYR LYS THR TYR LEU PHE GLY LEU PRO
SEQRES 15 A 285 ARG LEU GLY ASN PRO THR PHE ALA SER PHE VAL ASP GLN
SEQRES 16 A 285 LYS ILE GLY ASP LYS PHE HIS SER ILE ILE ASN GLY ARG
SEQRES 17 A 285 ASP TRP VAL PRO THR VAL PRO PRO ARG ALA LEU GLY TYR
SEQRES 18 A 285 GLN HIS PRO SER ASP TYR VAL TRP ILE TYR PRO GLY ASN
SEQRES 19 A 285 SER THR SER ALA LYS LEU TYR PRO GLY GLN GLU ASN VAL
SEQRES 20 A 285 HIS GLY ILE LEU THR VAL ALA ARG GLU PHE ASN ASP ASP
SEQRES 21 A 285 ASP HIS GLN GLY ILE TYR PHE HIS THR GLN ILE GLY ALA
SEQRES 22 A 285 VAL MET GLY GLU CYS PRO ALA GLN VAL GLY ALA HIS
HET NAG A 501 14
HET NAG A 502 14
HET BMA A 503 11
HET CL A 504 1
HETNAM NAG N-ACETYL-D-GLUCOSAMINE
HETNAM BMA BETA-D-MANNOSE
HETNAM CL CHLORIDE ION
FORMUL 2 NAG 2(C8 H15 N O6)
FORMUL 2 BMA C6 H12 O6
FORMUL 3 CL CL 1-
FORMUL 4 HOH *193(H2 O)
HELIX 1 AA1 ASN A 41 GLN A 54 1 14
HELIX 2 AA2 THR A 55 CYS A 57 5 3
HELIX 3 AA3 ASP A 112 PHE A 115 5 4
HELIX 4 AA4 TYR A 124 TYR A 128 5 5
HELIX 5 AA5 HIS A 136 ASP A 144 1 9
HELIX 6 AA6 LEU A 145 LYS A 160 1 16
HELIX 7 AA7 SER A 171 MET A 188 1 18
HELIX 8 AA8 ASN A 205 GLY A 217 1 13
HELIX 9 AA9 TRP A 229 VAL A 233 5 5
HELIX 10 AB1 PRO A 235 GLY A 239 5 5
HELIX 11 AB2 GLY A 268 VAL A 272 5 5
HELIX 12 AB3 GLY A 291 GLY A 295 5 5
SHEET 1 AA110 VAL A 36 ALA A 37 0
SHEET 2 AA110 ALA A 257 TYR A 260 -1 O LEU A 259 N VAL A 36
SHEET 3 AA110 TYR A 246 ILE A 249 -1 N TYR A 246 O TYR A 260
SHEET 4 AA110 PHE A 220 ASN A 225 1 N ILE A 224 O ILE A 249
SHEET 5 AA110 LYS A 194 PHE A 198 1 N LEU A 197 O HIS A 221
SHEET 6 AA110 VAL A 165 HIS A 170 1 N GLY A 169 O PHE A 198
SHEET 7 AA110 GLY A 93 ILE A 98 1 N VAL A 96 O THR A 166
SHEET 8 AA110 VAL A 84 SER A 89 -1 N ASN A 85 O ALA A 97
SHEET 9 AA110 SER A 69 MET A 75 -1 N LEU A 72 O ILE A 86
SHEET 10 AA110 LYS A 65 ILE A 66 -1 N ILE A 66 O SER A 69
SHEET 1 AA2 2 GLN A 117 GLU A 118 0
SHEET 2 AA2 2 LEU A 134 MET A 135 -1 O LEU A 134 N GLU A 118
SHEET 1 AA3 2 ILE A 284 TYR A 285 0
SHEET 2 AA3 2 THR A 288 GLN A 289 -1 O THR A 288 N TYR A 285
SSBOND 1 CYS A 57 CYS A 297 1555 1555 2.04
LINK ND2 ASN A 253 C1 NAG A 501 1555 1555 1.46
LINK O4 NAG A 501 C1 NAG A 502 1555 1555 1.42
LINK O4 NAG A 502 C1 BMA A 503 1555 1555 1.42
CISPEP 1 VAL A 233 PRO A 234 0 -12.10
CISPEP 2 TYR A 250 PRO A 251 0 1.84
CISPEP 3 CYS A 297 PRO A 298 0 -8.32
SITE 1 AC1 5 GLU A 77 TYR A 79 ALA A 80 ARG A 81
SITE 2 AC1 5 HOH A 681
SITE 1 AC2 13 GLU A 122 ARG A 123 ASN A 253 ASP A 279
SITE 2 AC2 13 ASP A 280 GLN A 282 GLY A 283 GLN A 289
SITE 3 AC2 13 GLY A 291 HOH A 620 HOH A 658 HOH A 675
SITE 4 AC2 13 HOH A 743
CRYST1 39.740 73.239 44.919 90.00 108.51 90.00 P 1 21 1 2
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 0.025163 0.000000 0.008423 0.00000
SCALE2 0.000000 0.013654 0.000000 0.00000
SCALE3 0.000000 0.000000 0.023476 0.00000
TER 2194 HIS A 304
MASTER 243 0 4 12 14 0 6 6 2421 1 42 22
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