HEADER HYDROLASE 01-NOV-19 6L7N TITLE CRYSTAL STRUCTURE OF A FUNGAL LIPASES COMPND MOL_ID: 1; COMPND 2 MOLECULE: LIPASE, CLASS 3; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PENICILLIUM ROQUEFORTI FM164; SOURCE 3 ORGANISM_TAXID: 1365484; SOURCE 4 STRAIN: FM164; SOURCE 5 GENE: PROQFM164_S02G000904; SOURCE 6 EXPRESSION_SYSTEM: PICHIA KUDRIAVZEVII; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4909 KEYWDS LIPASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.H.WANG,H.YUAN,D.M.LAN,X.H.LIU REVDAT 2 22-NOV-23 6L7N 1 REMARK REVDAT 1 04-NOV-20 6L7N 0 JRNL AUTH Y.H.WANG,H.YUAN,D.M.LAN,X.H.LIU JRNL TITL CRYSTAL STRUCTURE OF A FUNGAL LIPASES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.6 REMARK 3 NUMBER OF REFLECTIONS : 18008 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.190 REMARK 3 FREE R VALUE TEST SET COUNT : 934 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 10.0000 - 3.4400 0.92 2509 132 0.1645 0.1966 REMARK 3 2 3.4400 - 2.7300 0.97 2661 139 0.1694 0.2130 REMARK 3 3 2.7300 - 2.3900 0.97 2653 116 0.1796 0.2151 REMARK 3 4 2.3900 - 2.1700 0.82 2252 122 0.1812 0.2412 REMARK 3 5 2.1700 - 2.0100 0.94 2540 162 0.1749 0.2321 REMARK 3 6 2.0100 - 1.8900 0.75 2065 113 0.2041 0.3096 REMARK 3 7 1.8900 - 1.8000 0.89 2394 150 0.1998 0.2925 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.224 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.376 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.31 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.58 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 : 0.008 2132 REMARK 3 ANGLE : 0.888 2918 REMARK 3 CHIRALITY : 0.055 322 REMARK 3 PLANARITY : 0.006 378 REMARK 3 DIHEDRAL : 8.171 1658 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 6L7N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-NOV-19. REMARK 100 THE DEPOSITION ID IS D_1300014344. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAY-19 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 : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19035 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 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 (%) : 94.3 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.03900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.10000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 12.26 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: 1DT3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 26% PEG 1500, 0.1 M SODIUM ACETATE PH REMARK 280 4.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,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 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 GLU A -1 REMARK 465 PHE A 0 REMARK 465 ASN A 271 REMARK 465 ASP A 272 REMARK 465 GLY A 273 REMARK 465 ARG A 274 REMARK 465 PRO A 275 REMARK 465 PHE A 276 REMARK 465 LYS A 277 REMARK 465 ARG A 278 REMARK 465 VAL A 279 REMARK 465 VAL A 280 REMARK 465 ASP A 281 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 O HOH A 566 O HOH A 588 1.82 REMARK 500 O HOH A 454 O HOH A 464 1.87 REMARK 500 O HOH A 309 O HOH A 436 1.89 REMARK 500 O HOH A 344 O HOH A 480 2.03 REMARK 500 O HOH A 366 O HOH A 512 2.05 REMARK 500 O HOH A 492 O HOH A 550 2.08 REMARK 500 O HOH A 329 O HOH A 507 2.09 REMARK 500 O HOH A 471 O HOH A 585 2.10 REMARK 500 NE2 HIS A 184 O HOH A 301 2.11 REMARK 500 OD2 ASP A 109 O HOH A 302 2.13 REMARK 500 NE2 GLN A 9 O HOH A 303 2.16 REMARK 500 O HOH A 425 O HOH A 582 2.17 REMARK 500 O HOH A 338 O HOH A 376 2.17 REMARK 500 OH TYR A 97 O MET A 209 2.17 REMARK 500 O PHE A 95 O HOH A 304 2.18 REMARK 500 O THR A 227 O HOH A 305 2.18 REMARK 500 OE1 GLU A 74 O HOH A 306 2.19 REMARK 500 O HOH A 325 O HOH A 544 2.19 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 ALA A 58 -159.95 -167.98 REMARK 500 ASP A 92 -2.30 -144.33 REMARK 500 SER A 145 -142.95 62.69 REMARK 500 ALA A 177 -173.46 -170.03 REMARK 500 THR A 197 -113.83 33.82 REMARK 500 ASP A 199 123.26 -39.02 REMARK 500 PHE A 263 -53.50 71.24 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 592 DISTANCE = 6.03 ANGSTROMS REMARK 525 HOH A 593 DISTANCE = 6.49 ANGSTROMS REMARK 525 HOH A 594 DISTANCE = 7.12 ANGSTROMS DBREF 6L7N A 1 279 UNP W6Q990 W6Q990_PENRF 27 305 SEQADV 6L7N GLU A -1 UNP W6Q990 EXPRESSION TAG SEQADV 6L7N PHE A 0 UNP W6Q990 EXPRESSION TAG SEQADV 6L7N VAL A 280 UNP W6Q990 EXPRESSION TAG SEQADV 6L7N ASP A 281 UNP W6Q990 EXPRESSION TAG SEQRES 1 A 283 GLU PHE ASP VAL SER THR SER GLU LEU ASN GLN PHE ASP SEQRES 2 A 283 PHE TRP VAL GLN TYR ALA ALA ALA ALA TYR TYR ALA ASP SEQRES 3 A 283 ASP TYR THR ALA GLN VAL GLY ALA LYS ILE SER CYS SER SEQRES 4 A 283 LYS GLY ASN CYS PRO GLN VAL GLU GLU ALA GLY ALA THR SEQRES 5 A 283 VAL PHE TYR ASP PHE SER ASN ALA THR ILE THR ASP THR SEQRES 6 A 283 SER GLY PHE ILE ALA VAL ASP HIS ALA ASN GLU ALA VAL SEQRES 7 A 283 VAL LEU SER PHE ARG GLY SER TYR SER VAL ARG ASN TRP SEQRES 8 A 283 VAL SER ASP ALA ILE PHE VAL TYR THR ASN PRO ASP LEU SEQRES 9 A 283 CYS ASP GLY CYS LEU ALA ASP LEU GLY PHE TRP GLY SER SEQRES 10 A 283 TRP VAL LEU VAL ARG ASP ASP ILE ILE LYS GLU LEU LYS SEQRES 11 A 283 GLU ALA VAL SER GLN ASN PRO GLY TYR GLU LEU ALA VAL SEQRES 12 A 283 VAL GLY HIS SER LEU GLY ALA ALA VAL ALA THR LEU ALA SEQRES 13 A 283 VAL ALA ASP LEU ARG GLY LYS GLY TYR PRO SER ALA LYS SEQRES 14 A 283 LEU TYR ALA TYR ALA SER PRO ARG VAL ALA ASN VAL PRO SEQRES 15 A 283 LEU ALA LYS HIS ILE THR ALA GLN GLY ASN ASN TYR ARG SEQRES 16 A 283 PHE THR HIS THR ASP ASP PRO VAL PRO LYS LEU PRO LEU SEQRES 17 A 283 LEU ALA MET GLY TYR VAL HIS ILE SER PRO GLU TYR TRP SEQRES 18 A 283 ILE THR SER PRO ASN ASN VAL THR VAL GLY ALA SER ASP SEQRES 19 A 283 ILE LYS VAL ILE ASP GLY ASP ILE SER PHE ALA GLY ASN SEQRES 20 A 283 THR GLY THR GLY LEU PRO SER LEU GLU ASP PHE GLU ALA SEQRES 21 A 283 HIS LYS TRP TYR PHE MET LYS THR ASP ALA GLY LYS ASN SEQRES 22 A 283 ASP GLY ARG PRO PHE LYS ARG VAL VAL ASP FORMUL 2 HOH *294(H2 O) HELIX 1 AA1 SER A 3 TYR A 21 1 19 HELIX 2 AA2 TYR A 22 THR A 27 1 6 HELIX 3 AA3 CYS A 41 ALA A 47 1 7 HELIX 4 AA4 SER A 85 ALA A 93 1 9 HELIX 5 AA5 LEU A 110 ASN A 134 1 25 HELIX 6 AA6 SER A 145 GLY A 160 1 16 HELIX 7 AA7 VAL A 179 GLY A 189 1 11 HELIX 8 AA8 PRO A 200 LEU A 204 5 5 HELIX 9 AA9 LEU A 206 MET A 209 5 4 HELIX 10 AB1 GLY A 229 SER A 231 5 3 HELIX 11 AB2 ALA A 243 THR A 248 1 6 HELIX 12 AB3 SER A 252 LYS A 260 5 9 SHEET 1 AA1 8 THR A 50 PHE A 55 0 SHEET 2 AA1 8 SER A 64 ASP A 70 -1 O ILE A 67 N PHE A 52 SHEET 3 AA1 8 ALA A 75 ARG A 81 -1 O ALA A 75 N ASP A 70 SHEET 4 AA1 8 GLU A 138 HIS A 144 1 O GLU A 138 N VAL A 76 SHEET 5 AA1 8 LYS A 167 TYR A 171 1 O LYS A 167 N LEU A 139 SHEET 6 AA1 8 ASN A 191 HIS A 196 1 O TYR A 192 N LEU A 168 SHEET 7 AA1 8 GLU A 217 ILE A 220 1 O ILE A 220 N THR A 195 SHEET 8 AA1 8 ILE A 233 ILE A 236 -1 O LYS A 234 N TRP A 219 SHEET 1 AA2 2 TYR A 97 THR A 98 0 SHEET 2 AA2 2 ALA A 108 ASP A 109 -1 O ALA A 108 N THR A 98 SHEET 1 AA3 2 ALA A 177 ASN A 178 0 SHEET 2 AA3 2 TYR A 211 VAL A 212 -1 O VAL A 212 N ALA A 177 SSBOND 1 CYS A 36 CYS A 41 1555 1555 2.04 SSBOND 2 CYS A 103 CYS A 106 1555 1555 2.02 CISPEP 1 LEU A 204 PRO A 205 0 -11.57 CISPEP 2 SER A 215 PRO A 216 0 -1.83 CRYST1 33.247 44.928 46.025 109.22 101.36 112.10 P 1 1 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 0.030078 0.012213 0.012796 0.00000 SCALE2 0.000000 0.024023 0.011903 0.00000 SCALE3 0.000000 0.000000 0.024733 0.00000