| content |
HEADER HYDROLASE 26-SEP-22 8GZD
TITLE CRYSTAL STRUCTURE OF A NOVEL ALPHA/BETA HYDROLASE FROM THERMOMONOSPORA
TITLE 2 CURVATA IN APO FORM
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: TRIACYLGLYCEROL LIPASE;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: ALPHA/BETA HYDROLASE;
COMPND 5 EC: 3.1.1.3;
COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: THERMOMONOSPORA CURVATA DSM 43183;
SOURCE 3 ORGANISM_TAXID: 471852;
SOURCE 4 GENE: TCUR_1278;
SOURCE 5 EXPRESSION_SYSTEM: TRICHODERMA REESEI QM6A;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 431241
KEYWDS PLASTIC, PET, DEGRADATION, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR X.HAN,J.GAO,U.T.BORNSCHEUER,R.WEI,W.LIU
REVDAT 1 27-DEC-23 8GZD 0
JRNL AUTH X.HAN,J.GAO,U.T.BORNSCHEUER,R.WEI,W.LIU
JRNL TITL CRYSTAL STRUCTURE OF A NOVEL ALPHA/BETA HYDROLASE FROM
JRNL TITL 2 THERMOMONOSPORA CURVATA IN APO FORM
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 2
REMARK 2 RESOLUTION. 1.10 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX 1.19.1_4122
REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN
REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE,
REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER,
REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY,
REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON,
REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI,
REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT
REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART
REMARK 3
REMARK 3 REFINEMENT TARGET : ML
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.10
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.19
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8
REMARK 3 NUMBER OF REFLECTIONS : 94909
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.183
REMARK 3 R VALUE (WORKING SET) : 0.182
REMARK 3 FREE R VALUE : 0.191
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 9163
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE
REMARK 3 1 26.1900 - 2.3700 1.00 17451 907 0.1574 0.1608
REMARK 3 2 2.3700 - 1.8800 1.00 17437 910 0.1534 0.1613
REMARK 3 3 1.8800 - 1.6400 1.00 17432 951 0.1577 0.1797
REMARK 3 4 1.6400 - 1.4900 1.00 17482 894 0.1566 0.1678
REMARK 3 5 1.4900 - 1.3900 1.00 17482 890 0.1763 0.1841
REMARK 3 6 1.3900 - 1.3000 1.00 17382 961 0.2214 0.2153
REMARK 3 7 1.3000 - 1.2400 1.00 17502 886 0.2232 0.2331
REMARK 3 8 1.2400 - 1.1800 1.00 17348 963 0.2387 0.2540
REMARK 3 9 1.1800 - 1.1400 1.00 17448 885 0.2938 0.2970
REMARK 3 10 1.1400 - 1.1000 0.98 17145 916 0.3790 0.3887
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL
REMARK 3 SOLVENT RADIUS : 1.11
REMARK 3 SHRINKAGE RADIUS : 0.90
REMARK 3 K_SOL : NULL
REMARK 3 B_SOL : NULL
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.150
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.950
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 7.99
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.18
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 TWINNING INFORMATION.
REMARK 3 FRACTION: NULL
REMARK 3 OPERATOR: NULL
REMARK 3
REMARK 3 DEVIATIONS FROM IDEAL VALUES.
REMARK 3 RMSD COUNT
REMARK 3 BOND : NULL NULL
REMARK 3 ANGLE : NULL NULL
REMARK 3 CHIRALITY : NULL NULL
REMARK 3 PLANARITY : NULL NULL
REMARK 3 DIHEDRAL : NULL NULL
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 NCS DETAILS
REMARK 3 NUMBER OF NCS GROUPS : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 8GZD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-OCT-22.
REMARK 100 THE DEPOSITION ID IS D_1300031108.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 19-JAN-21
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 8.0
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : BESSY
REMARK 200 BEAMLINE : 14.1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.0
REMARK 200 MONOCHROMATOR : GRAPHITE
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : XSCALE
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 94978
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100
REMARK 200 RESOLUTION RANGE LOW (A) : 26.190
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5
REMARK 200 DATA REDUNDANCY : 12.83
REMARK 200 R MERGE (I) : 0.18200
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : 11.2200
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.10
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.17
REMARK 200 COMPLETENESS FOR SHELL (%) : 96.9
REMARK 200 DATA REDUNDANCY IN SHELL : 11.42
REMARK 200 R MERGE FOR SHELL (I) : 1.83200
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 FOR SHELL : 1.830
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: 1JFR
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 40.10
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG4000, 20% GLYCEROL, 0.02 M EACH
REMARK 280 AMINO ACID, 0.1 M MES/IMIDAZOLE PH 6.5, PH 8.0, VAPOR DIFFUSION,
REMARK 280 SITTING DROP, TEMPERATURE 295K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,-Y,Z+1/2
REMARK 290 3555 -X,Y,-Z+1/2
REMARK 290 4555 X,-Y,-Z
REMARK 290 5555 X+1/2,Y+1/2,Z
REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2
REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2
REMARK 290 8555 X+1/2,-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 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 71.53950
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 71.53950
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 4 0.000000 -1.000000 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 22.78550
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 35.79500
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 22.78550
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 35.79500
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 71.53950
REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 22.78550
REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 35.79500
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 71.53950
REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 22.78550
REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 35.79500
REMARK 290 SMTRY3 8 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 375
REMARK 375 SPECIAL POSITION
REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS
REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL
REMARK 375 POSITIONS.
REMARK 375
REMARK 375 ATOM RES CSSEQI
REMARK 375 HOH A 567 LIES ON A SPECIAL POSITION.
REMARK 375 HOH A 690 LIES ON A SPECIAL POSITION.
REMARK 375 HOH A 722 LIES ON A SPECIAL POSITION.
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 THR A 260
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 THR A 63 -6.57 75.61
REMARK 500 SER A 130 -120.79 63.56
REMARK 500 HIS A 184 -86.43 -119.80
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 719 DISTANCE = 5.89 ANGSTROMS
REMARK 525 HOH A 720 DISTANCE = 6.99 ANGSTROMS
REMARK 525 HOH A 721 DISTANCE = 7.21 ANGSTROMS
REMARK 525 HOH A 722 DISTANCE = 8.31 ANGSTROMS
DBREF 8GZD A 1 260 UNP D1A9G5 D1A9G5_THECD 30 289
SEQRES 1 A 260 ALA ASN PRO TYR GLN ARG GLY PRO ASP PRO THR GLU SER
SEQRES 2 A 260 LEU LEU ARG ALA ALA ARG GLY PRO PHE ALA VAL SER GLU
SEQRES 3 A 260 GLN SER VAL SER ARG LEU SER VAL SER GLY PHE GLY GLY
SEQRES 4 A 260 GLY ARG ILE TYR TYR PRO THR THR THR SER GLN GLY THR
SEQRES 5 A 260 PHE GLY ALA ILE ALA ILE SER PRO GLY PHE THR ALA SER
SEQRES 6 A 260 TRP SER SER LEU ALA TRP LEU GLY PRO ARG LEU ALA SER
SEQRES 7 A 260 HIS GLY PHE VAL VAL ILE GLY ILE GLU THR ASN THR ARG
SEQRES 8 A 260 LEU ASP GLN PRO ASP SER ARG GLY ARG GLN LEU LEU ALA
SEQRES 9 A 260 ALA LEU ASP TYR LEU THR GLN ARG SER SER VAL ARG ASN
SEQRES 10 A 260 ARG VAL ASP ALA SER ARG LEU ALA VAL ALA GLY HIS SER
SEQRES 11 A 260 MET GLY GLY GLY GLY THR LEU GLU ALA ALA LYS SER ARG
SEQRES 12 A 260 THR SER LEU LYS ALA ALA ILE PRO ILE ALA PRO TRP ASN
SEQRES 13 A 260 LEU ASP LYS THR TRP PRO GLU VAL ARG THR PRO THR LEU
SEQRES 14 A 260 ILE ILE GLY GLY GLU LEU ASP SER ILE ALA PRO VAL ALA
SEQRES 15 A 260 THR HIS SER ILE PRO PHE TYR ASN SER LEU THR ASN ALA
SEQRES 16 A 260 ARG GLU LYS ALA TYR LEU GLU LEU ASN ASN ALA SER HIS
SEQRES 17 A 260 PHE PHE PRO GLN PHE SER ASN ASP THR MET ALA LYS PHE
SEQRES 18 A 260 MET ILE SER TRP MET LYS ARG PHE ILE ASP ASP ASP THR
SEQRES 19 A 260 ARG TYR ASP GLN PHE LEU CYS PRO PRO PRO ARG ALA ILE
SEQRES 20 A 260 GLY ASP ILE SER ASP TYR ARG ASP THR CYS PRO HIS THR
FORMUL 2 HOH *422(H2 O)
HELIX 1 AA1 THR A 11 ALA A 17 1 7
HELIX 2 AA2 SER A 30 VAL A 34 5 5
HELIX 3 AA3 SER A 65 ALA A 70 5 6
HELIX 4 AA4 TRP A 71 SER A 78 1 8
HELIX 5 AA5 GLN A 94 ARG A 112 1 19
HELIX 6 AA6 VAL A 115 ASN A 117 5 3
HELIX 7 AA7 SER A 130 ARG A 143 1 14
HELIX 8 AA8 HIS A 184 SER A 191 1 8
HELIX 9 AA9 PHE A 209 PHE A 213 5 5
HELIX 10 AB1 ASN A 215 ASP A 231 1 17
HELIX 11 AB2 ASP A 233 LEU A 240 5 8
SHEET 1 AA1 6 VAL A 24 VAL A 29 0
SHEET 2 AA1 6 GLY A 40 PRO A 45 -1 O TYR A 44 N SER A 25
SHEET 3 AA1 6 VAL A 82 ILE A 86 -1 O GLY A 85 N ARG A 41
SHEET 4 AA1 6 PHE A 53 SER A 59 1 N ILE A 56 O ILE A 84
SHEET 5 AA1 6 VAL A 119 HIS A 129 1 O ASP A 120 N PHE A 53
SHEET 6 AA1 6 ALA A 148 ILE A 152 1 O ILE A 152 N GLY A 128
SHEET 1 AA2 3 THR A 168 GLY A 173 0
SHEET 2 AA2 3 LYS A 198 LEU A 203 1 O LEU A 203 N GLY A 172
SHEET 3 AA2 3 ILE A 250 ASP A 255 -1 O ASP A 252 N GLU A 202
SSBOND 1 CYS A 241 CYS A 257 1555 1555 2.02
CISPEP 1 CYS A 241 PRO A 242 0 -12.45
CISPEP 2 CYS A 257 PRO A 258 0 0.17
CRYST1 45.571 71.590 143.079 90.00 90.00 90.00 C 2 2 21 8
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 0.021944 0.000000 0.000000 0.00000
SCALE2 0.000000 0.013968 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006989 0.00000
TER 2006 HIS A 259
MASTER 267 0 0 11 9 0 0 6 2418 1 2 20
END |