HEADER HYDROLASE 04-FEB-22 7R25 TITLE BACILLUS PUMILUS LIPASE A COMPND MOL_ID: 1; COMPND 2 MOLECULE: LIPASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS PUMILUS; SOURCE 3 ORGANISM_TAXID: 1408; SOURCE 4 GENE: L5; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: NICO21(DE3); SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET22B KEYWDS LIPASE, ESTERASE, APO, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR B.A.LUND REVDAT 2 31-JAN-24 7R25 1 REMARK REVDAT 1 25-MAY-22 7R25 0 JRNL AUTH B.A.LUND,L.SVALBERG,M.PURG,G.CHUKWU,M.WIDERSTEN,G.V.ISAKSEN, JRNL AUTH 2 B.O.BRANDSDAL,J.AQVIST JRNL TITL STRUCTURE AND MECHANISM OF A COLD-ADAPTED BACTERIAL LIPASE JRNL REF BIOCHEMISTRY V. 61 933 2022 JRNL REFN ISSN 0006-2960 JRNL DOI 10.1021/ACS.BIOCHEM.2C00087 REMARK 2 REMARK 2 RESOLUTION. 0.87 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20RC4_4425 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.87 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.07 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 81.8 REMARK 3 NUMBER OF REFLECTIONS : 103382 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.112 REMARK 3 R VALUE (WORKING SET) : 0.111 REMARK 3 FREE R VALUE : 0.133 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.030 REMARK 3 FREE R VALUE TEST SET COUNT : 2100 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 35.0700 - 2.1500 0.99 8367 174 0.1146 0.1480 REMARK 3 2 2.1500 - 1.7000 0.99 8201 170 0.1129 0.1211 REMARK 3 3 1.7000 - 1.4900 1.00 8254 171 0.1084 0.1285 REMARK 3 4 1.4900 - 1.3500 0.98 8081 168 0.1082 0.1194 REMARK 3 5 1.3500 - 1.2600 1.00 8238 170 0.1053 0.1320 REMARK 3 6 1.2600 - 1.1800 0.98 8084 168 0.0986 0.1217 REMARK 3 7 1.1800 - 1.1200 0.99 8160 169 0.0990 0.1075 REMARK 3 8 1.1200 - 1.0700 1.00 8222 171 0.0970 0.1050 REMARK 3 9 1.0700 - 1.0300 0.97 7988 165 0.1018 0.1233 REMARK 3 10 1.0300 - 1.0000 1.00 8193 170 0.1120 0.1220 REMARK 3 11 1.0000 - 0.9600 0.89 7327 152 0.1290 0.1480 REMARK 3 12 0.9600 - 0.9400 0.64 5229 108 0.1443 0.1830 REMARK 3 13 0.9400 - 0.9100 0.45 3692 77 0.1753 0.2000 REMARK 3 14 0.9100 - 0.8900 0.28 2314 48 0.2064 0.2376 REMARK 3 15 0.8900 - 0.8700 0.11 932 19 0.2499 0.3362 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.40 REMARK 3 SHRINKAGE RADIUS : 1.30 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.049 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.836 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 7.03 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.66 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 : 0.009 1498 REMARK 3 ANGLE : 1.027 2034 REMARK 3 CHIRALITY : 0.086 224 REMARK 3 PLANARITY : 0.011 269 REMARK 3 DIHEDRAL : 22.010 222 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 7R25 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-FEB-22. REMARK 100 THE DEPOSITION ID IS D_1292120794. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-MAR-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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) : 0.9184 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS 2019 REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 103387 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.870 REMARK 200 RESOLUTION RANGE LOW (A) : 35.070 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 81.8 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.02800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 30.4500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.87 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 3.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.44470 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.150 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.2 REMARK 200 STARTING MODEL: 1ISP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES PH 6.5 18-22 % PEG 4000 0.1 REMARK 280 -0.5 M LITHIUM CITRATE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 27.34850 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 MET A 1 REMARK 465 ALA A 2 REMARK 465 HIS A 187 REMARK 465 HIS A 188 REMARK 465 HIS A 189 REMARK 465 HIS A 190 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 3 CG CD OE1 OE2 REMARK 470 HIS A 186 CG ND1 CD2 CE1 NE2 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 SER A 78 -129.71 58.39 REMARK 500 SER A 78 -120.59 58.97 REMARK 500 LEU A 91 -143.50 -115.40 REMARK 500 GLU A 98 -73.61 -109.00 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 570 DISTANCE = 6.15 ANGSTROMS REMARK 525 HOH A 571 DISTANCE = 6.47 ANGSTROMS REMARK 525 HOH A 572 DISTANCE = 6.81 ANGSTROMS REMARK 525 HOH A 573 DISTANCE = 7.22 ANGSTROMS DBREF 7R25 A 2 182 UNP W8FKE7 W8FKE7_BACPU 35 215 SEQADV 7R25 MET A 1 UNP W8FKE7 INITIATING METHIONINE SEQADV 7R25 LEU A 183 UNP W8FKE7 EXPRESSION TAG SEQADV 7R25 GLU A 184 UNP W8FKE7 EXPRESSION TAG SEQADV 7R25 HIS A 185 UNP W8FKE7 EXPRESSION TAG SEQADV 7R25 HIS A 186 UNP W8FKE7 EXPRESSION TAG SEQADV 7R25 HIS A 187 UNP W8FKE7 EXPRESSION TAG SEQADV 7R25 HIS A 188 UNP W8FKE7 EXPRESSION TAG SEQADV 7R25 HIS A 189 UNP W8FKE7 EXPRESSION TAG SEQADV 7R25 HIS A 190 UNP W8FKE7 EXPRESSION TAG SEQRES 1 A 190 MET ALA GLU HIS ASN PRO VAL VAL MET VAL HIS GLY MET SEQRES 2 A 190 GLY GLY ALA SER TYR ASN PHE ALA SER ILE LYS SER TYR SEQRES 3 A 190 LEU VAL THR GLN GLY TRP ASP ARG ASN GLN LEU PHE ALA SEQRES 4 A 190 ILE ASP PHE ILE ASP LYS THR GLY ASN ASN ARG ASN ASN SEQRES 5 A 190 GLY PRO ARG LEU SER ARG PHE VAL LYS ASP VAL LEU GLY SEQRES 6 A 190 LYS THR GLY ALA LYS LYS VAL ASP ILE VAL ALA HIS SER SEQRES 7 A 190 MET GLY GLY ALA ASN THR LEU TYR TYR ILE LYS ASN LEU SEQRES 8 A 190 ASP GLY GLY ASP LYS ILE GLU ASN VAL VAL THR LEU GLY SEQRES 9 A 190 GLY ALA ASN GLY LEU VAL SER LEU ARG ALA LEU PRO GLY SEQRES 10 A 190 THR ASP PRO ASN GLN LYS ILE LEU TYR THR SER VAL TYR SEQRES 11 A 190 SER SER ALA ASP MET ILE VAL VAL ASN SER LEU SER ARG SEQRES 12 A 190 LEU ILE GLY ALA ARG ASN VAL LEU ILE HIS GLY VAL GLY SEQRES 13 A 190 HIS ILE SER LEU LEU ALA SER SER GLN VAL LYS GLY TYR SEQRES 14 A 190 ILE LYS GLU GLY LEU ASN GLY GLY GLY GLN ASN THR ASN SEQRES 15 A 190 LEU GLU HIS HIS HIS HIS HIS HIS HET CIT A 201 18 HET PO4 A 202 5 HET PPI A 203 10 HETNAM CIT CITRIC ACID HETNAM PO4 PHOSPHATE ION HETNAM PPI PROPANOIC ACID FORMUL 2 CIT C6 H8 O7 FORMUL 3 PO4 O4 P 3- FORMUL 4 PPI C3 H6 O2 FORMUL 5 HOH *273(H2 O) HELIX 1 AA1 ALA A 16 ASN A 19 5 4 HELIX 2 AA2 PHE A 20 GLN A 30 1 11 HELIX 3 AA3 ASP A 33 ASN A 35 5 3 HELIX 4 AA4 ASN A 48 GLY A 68 1 21 HELIX 5 AA5 MET A 79 LEU A 91 1 13 HELIX 6 AA6 ASP A 92 ASP A 95 5 4 HELIX 7 AA7 ALA A 106 VAL A 110 5 5 HELIX 8 AA8 VAL A 138 ARG A 143 1 6 HELIX 9 AA9 ILE A 158 ALA A 162 5 5 HELIX 10 AB1 SER A 163 ASN A 175 1 13 SHEET 1 AA1 6 LEU A 37 ALA A 39 0 SHEET 2 AA1 6 VAL A 7 VAL A 10 1 N VAL A 7 O PHE A 38 SHEET 3 AA1 6 VAL A 72 HIS A 77 1 O ASP A 73 N VAL A 8 SHEET 4 AA1 6 ILE A 97 LEU A 103 1 O ASN A 99 N ILE A 74 SHEET 5 AA1 6 LEU A 125 SER A 131 1 O LEU A 125 N VAL A 100 SHEET 6 AA1 6 ARG A 148 ILE A 152 1 O VAL A 150 N SER A 128 CRYST1 35.109 54.697 40.970 90.00 92.72 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 0.028483 0.000000 0.001353 0.00000 SCALE2 0.000000 0.018283 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024436 0.00000