HEADER HYDROLASE 05-MAR-01 1I6W TITLE THE CRYSTAL STRUCTURE OF BACILLUS SUBTILIS LIPASE: A MINIMAL TITLE 2 ALPHA/BETA HYDROLASE ENZYME COMPND MOL_ID: 1; COMPND 2 MOLECULE: LIPASE A; COMPND 3 CHAIN: A, B; COMPND 4 EC: 3.1.1.3; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 GENE: LIPA; SOURCE 5 EXPRESSION_SYSTEM: BACILLUS SUBTILIS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 1423; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BCL1051; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PMA5LIP KEYWDS ALPHA/BETA HYDROLASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR G.VAN POUDEROYEN,T.EGGERT,K.-E.JAEGER,B.W.DIJKSTRA REVDAT 5 07-FEB-24 1I6W 1 REMARK REVDAT 4 24-FEB-09 1I6W 1 VERSN REVDAT 3 01-APR-03 1I6W 1 JRNL REVDAT 2 06-JUN-01 1I6W 1 JRNL REVDAT 1 23-MAY-01 1I6W 0 JRNL AUTH G.VAN POUDEROYEN,T.EGGERT,K.E.JAEGER,B.W.DIJKSTRA JRNL TITL THE CRYSTAL STRUCTURE OF BACILLUS SUBTILIS LIPASE: A MINIMAL JRNL TITL 2 ALPHA/BETA HYDROLASE FOLD ENZYME. JRNL REF J.MOL.BIOL. V. 309 215 2001 JRNL REFN ISSN 0022-2836 JRNL PMID 11491291 JRNL DOI 10.1006/JMBI.2001.4659 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : CNS_TOPPAR:PROTEIN_REP.PARAM REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 81.0 REMARK 3 NUMBER OF REFLECTIONS : 41796 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : R-FREE REMARK 3 FREE R VALUE TEST SET SELECTION : 5% REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2099 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 41 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.51 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 116 REMARK 3 BIN R VALUE (WORKING SET) : 0.3344 REMARK 3 BIN FREE R VALUE : 0.3854 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 5 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2711 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 517 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.39 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.40 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.17 REMARK 3 ESD FROM SIGMAA (A) : 0.15 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.18 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.15 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.240 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.700 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : CNS ANISOTROPIC REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1I6W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-MAR-01. REMARK 100 THE DEPOSITION ID IS D_1000012979. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-DEC-99 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 10.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9393 REMARK 200 MONOCHROMATOR : SI111 OR SI311 CRYSTALS, LN2 REMARK 200 COOLED REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : CCP4 (TRUNCATE) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 689356 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 82.4 REMARK 200 DATA REDUNDANCY : 16.50 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 7.60000 REMARK 200 FOR THE DATA SET : 20.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 30.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 28.0000 REMARK 200 FOR SHELL : 2.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: DM REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, ETHANOL AMINE, SODIUM REMARK 280 SULPHATE, CADMIUM CHLORIDE, PH 10.0, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 19.81950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.87600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 41.60050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.87600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.81950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 41.60050 REMARK 290 SMTRY3 4 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 ALA A 1 REMARK 465 GLU A 2 REMARK 465 ALA B 1 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 77 -126.97 51.59 REMARK 500 LEU A 90 -142.40 -110.52 REMARK 500 ALA A 97 -66.90 -106.53 REMARK 500 ALA A 105 51.95 -90.62 REMARK 500 ASN A 179 78.66 -160.72 REMARK 500 THR A 180 33.53 -73.48 REMARK 500 SER B 16 33.77 -148.41 REMARK 500 SER B 77 -123.09 52.20 REMARK 500 LEU B 90 -148.29 -116.49 REMARK 500 ALA B 97 -67.03 -106.49 REMARK 500 ALA B 105 49.61 -87.23 REMARK 500 GLN B 121 108.58 -160.48 REMARK 500 TYR B 161 53.20 -142.65 REMARK 500 ASN B 179 91.17 -164.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD B 518 DBREF 1I6W A 1 181 UNP P37957 LIP_BACSU 32 212 DBREF 1I6W B 1 181 UNP P37957 LIP_BACSU 32 212 SEQRES 1 A 181 ALA GLU HIS ASN PRO VAL VAL MET VAL HIS GLY ILE GLY SEQRES 2 A 181 GLY ALA SER PHE ASN PHE ALA GLY ILE LYS SER TYR LEU SEQRES 3 A 181 VAL SER GLN GLY TRP SER ARG ASP LYS LEU TYR ALA VAL SEQRES 4 A 181 ASP PHE TRP ASP LYS THR GLY THR ASN TYR ASN ASN GLY SEQRES 5 A 181 PRO VAL LEU SER ARG PHE VAL GLN LYS VAL LEU ASP GLU SEQRES 6 A 181 THR GLY ALA LYS LYS VAL ASP ILE VAL ALA HIS SER MET SEQRES 7 A 181 GLY GLY ALA ASN THR LEU TYR TYR ILE LYS ASN LEU ASP SEQRES 8 A 181 GLY GLY ASN LYS VAL ALA ASN VAL VAL THR LEU GLY GLY SEQRES 9 A 181 ALA ASN ARG LEU THR THR GLY LYS ALA LEU PRO GLY THR SEQRES 10 A 181 ASP PRO ASN GLN LYS ILE LEU TYR THR SER ILE TYR SER SEQRES 11 A 181 SER ALA ASP MET ILE VAL MET ASN TYR LEU SER ARG LEU SEQRES 12 A 181 ASP GLY ALA ARG ASN VAL GLN ILE HIS GLY VAL GLY HIS SEQRES 13 A 181 ILE GLY LEU LEU TYR SER SER GLN VAL ASN SER LEU ILE SEQRES 14 A 181 LYS GLU GLY LEU ASN GLY GLY GLY GLN ASN THR ASN SEQRES 1 B 181 ALA GLU HIS ASN PRO VAL VAL MET VAL HIS GLY ILE GLY SEQRES 2 B 181 GLY ALA SER PHE ASN PHE ALA GLY ILE LYS SER TYR LEU SEQRES 3 B 181 VAL SER GLN GLY TRP SER ARG ASP LYS LEU TYR ALA VAL SEQRES 4 B 181 ASP PHE TRP ASP LYS THR GLY THR ASN TYR ASN ASN GLY SEQRES 5 B 181 PRO VAL LEU SER ARG PHE VAL GLN LYS VAL LEU ASP GLU SEQRES 6 B 181 THR GLY ALA LYS LYS VAL ASP ILE VAL ALA HIS SER MET SEQRES 7 B 181 GLY GLY ALA ASN THR LEU TYR TYR ILE LYS ASN LEU ASP SEQRES 8 B 181 GLY GLY ASN LYS VAL ALA ASN VAL VAL THR LEU GLY GLY SEQRES 9 B 181 ALA ASN ARG LEU THR THR GLY LYS ALA LEU PRO GLY THR SEQRES 10 B 181 ASP PRO ASN GLN LYS ILE LEU TYR THR SER ILE TYR SER SEQRES 11 B 181 SER ALA ASP MET ILE VAL MET ASN TYR LEU SER ARG LEU SEQRES 12 B 181 ASP GLY ALA ARG ASN VAL GLN ILE HIS GLY VAL GLY HIS SEQRES 13 B 181 ILE GLY LEU LEU TYR SER SER GLN VAL ASN SER LEU ILE SEQRES 14 B 181 LYS GLU GLY LEU ASN GLY GLY GLY GLN ASN THR ASN HET CD B 518 1 HETNAM CD CADMIUM ION FORMUL 3 CD CD 2+ FORMUL 4 HOH *517(H2 O) HELIX 1 1 ALA A 15 ASN A 18 5 4 HELIX 2 2 PHE A 19 GLN A 29 1 11 HELIX 3 3 SER A 32 ASP A 34 5 3 HELIX 4 4 THR A 47 GLY A 67 1 21 HELIX 5 5 MET A 78 LEU A 90 1 13 HELIX 6 6 ASP A 91 ASN A 94 5 4 HELIX 7 7 ALA A 105 THR A 109 5 5 HELIX 8 8 MET A 137 ARG A 142 1 6 HELIX 9 9 HIS A 156 TYR A 161 5 6 HELIX 10 10 SER A 162 ASN A 174 1 13 HELIX 11 11 PHE B 19 GLN B 29 1 11 HELIX 12 12 SER B 32 ASP B 34 5 3 HELIX 13 13 THR B 47 GLY B 67 1 21 HELIX 14 14 MET B 78 LEU B 90 1 13 HELIX 15 15 ASP B 91 ASN B 94 5 4 HELIX 16 16 ALA B 105 THR B 109 5 5 HELIX 17 17 MET B 137 SER B 141 5 5 HELIX 18 18 HIS B 156 TYR B 161 5 6 HELIX 19 19 SER B 162 ASN B 174 1 13 SHEET 1 A 6 LEU A 36 ALA A 38 0 SHEET 2 A 6 VAL A 6 VAL A 9 1 O VAL A 6 N TYR A 37 SHEET 3 A 6 VAL A 71 HIS A 76 1 O ASP A 72 N VAL A 7 SHEET 4 A 6 VAL A 96 LEU A 102 1 N ALA A 97 O VAL A 71 SHEET 5 A 6 LEU A 124 SER A 130 1 O LEU A 124 N VAL A 99 SHEET 6 A 6 ARG A 147 ILE A 151 1 O ARG A 147 N SER A 127 SHEET 1 B 6 LEU B 36 ALA B 38 0 SHEET 2 B 6 VAL B 6 VAL B 9 1 O VAL B 6 N TYR B 37 SHEET 3 B 6 VAL B 71 HIS B 76 1 O ASP B 72 N VAL B 7 SHEET 4 B 6 VAL B 96 LEU B 102 1 N ALA B 97 O VAL B 71 SHEET 5 B 6 LEU B 124 SER B 130 1 O LEU B 124 N VAL B 99 SHEET 6 B 6 ARG B 147 ILE B 151 1 O ARG B 147 N SER B 127 LINK CD CD B 518 O HOH B 748 1555 1555 2.65 SITE 1 AC1 1 HOH B 748 CRYST1 39.639 83.201 95.752 90.00 90.00 90.00 P 21 21 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 0.025228 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012019 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010444 0.00000