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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 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
TER 2911 HIS A 186
MASTER 252 0 3 10 6 0 0 6 1674 1 33 15
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