HEADER HYDROLASE 23-JUL-22 7YKP TITLE CRYSTAL STRUCTURE OF A NOVEL ALPHA/BETA HYDROLASE FROM THERMOMONOSPORA TITLE 2 CURVATA WITH GLYCEROL COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRIACYLGLYCEROL LIPASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.1.3; COMPND 5 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,G.JIAN,U.T.BORNSCHEUER,R.WEI,W.LIU REVDAT 1 26-JUL-23 7YKP 0 JRNL AUTH X.HAN,G.JIAN,U.T.BORNSCHEUER,R.WEI,W.LIU JRNL TITL CRYSTAL STRUCTURE OF A NOVEL ALPHA/BETA HYDROLASE FROM JRNL TITL 2 THERMOMONOSPORA CURVATA WITH GLYCEROL JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.18 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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) : 1.18 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.31 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 3 NUMBER OF REFLECTIONS : 74649 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.158 REMARK 3 R VALUE (WORKING SET) : 0.158 REMARK 3 FREE R VALUE : 0.168 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 3740 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 25.3100 - 2.5400 0.99 7574 409 0.1485 0.1494 REMARK 3 2 2.5400 - 2.0200 0.99 7312 391 0.1516 0.1654 REMARK 3 3 2.0200 - 1.7600 0.98 7227 373 0.1533 0.1641 REMARK 3 4 1.7600 - 1.6000 0.97 7158 384 0.1530 0.1710 REMARK 3 5 1.6000 - 1.4900 0.96 7061 364 0.1541 0.1678 REMARK 3 6 1.4900 - 1.4000 0.96 7008 380 0.1681 0.1881 REMARK 3 7 1.4000 - 1.3300 0.96 6966 369 0.1730 0.1923 REMARK 3 8 1.3300 - 1.2700 0.96 6976 361 0.1808 0.1923 REMARK 3 9 1.2700 - 1.2200 0.95 6888 354 0.1907 0.2270 REMARK 3 10 1.2200 - 1.1800 0.93 6739 355 0.2136 0.2209 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) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.570 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.71 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 7YKP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-AUG-22. REMARK 100 THE DEPOSITION ID IS D_1300031107. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-NOV-20 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 : 74712 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.180 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 200 DATA REDUNDANCY : 8.461 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.3400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.18 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.25 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.4 REMARK 200 DATA REDUNDANCY IN SHELL : 7.89 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.130 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 (%): 40.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MPD, PEG 1500, NAAC, PH 8.0, VAPOR REMARK 280 DIFFUSION, 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 71.60500 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 71.60500 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 22.81500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 35.79000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 22.81500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 35.79000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 71.60500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 22.81500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 35.79000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 71.60500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 22.81500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 35.79000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.0 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 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 687 LIES ON A SPECIAL POSITION. 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 -6.88 78.96 REMARK 500 SER A 130 -125.24 66.96 REMARK 500 HIS A 184 -84.82 -119.22 REMARK 500 ASN A 205 15.59 59.82 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 839 DISTANCE = 6.11 ANGSTROMS DBREF 7YKP 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 HET GOL A 301 14 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL C3 H8 O3 FORMUL 3 HOH *439(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 LEU A 192 1 9 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 VAL A 83 N TYR A 43 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 2.04 CISPEP 1 CYS A 241 PRO A 242 0 -9.26 CISPEP 2 CYS A 257 PRO A 258 0 2.82 CRYST1 45.630 71.580 143.210 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 0.021915 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013970 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006983 0.00000