HEADER HYDROLASE 19-DEC-01 1ISP TITLE CRYSTAL STRUCTURE OF BACILLUS SUBTILIS LIPASE AT 1.3A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: LIPASE; COMPND 3 CHAIN: A; 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 MEGATERIUM; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 1404; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: WH320; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PWSL1 KEYWDS ALPHA/BETA HYDROLASE FOLD, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR K.KAWASAKI,H.KONDO,M.SUZUKI,S.OHGIYA,S.TSUDA REVDAT 3 13-JUL-11 1ISP 1 VERSN REVDAT 2 24-FEB-09 1ISP 1 VERSN REVDAT 1 19-DEC-02 1ISP 0 JRNL AUTH K.KAWASAKI,H.KONDO,M.SUZUKI,S.OHGIYA,S.TSUDA JRNL TITL ALTERNATE CONFORMATIONS OBSERVED IN CATALYTIC SERINE OF JRNL TITL 2 BACILLUS SUBTILIS LIPASE DETERMINED AT 1.3 A RESOLUTION. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 58 1168 2002 JRNL REFN ISSN 0907-4449 JRNL PMID 12077437 JRNL DOI 10.1107/S090744490200714X REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.192 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 2.992 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1330 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 44447 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1351 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 151 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.029 REMARK 3 ANGLE DISTANCES (A) : NULL REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1ISP COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-DEC-01. REMARK 100 THE RCSB ID CODE IS RCSB005239. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-NOV-00 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-6A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : BENT SI 111 REMARK 200 OPTICS : BENT PLANE FUSED QUARTZ REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUAMTUM 4R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44447 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.06800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 79.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.31500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, GLYCEROL, PH 8.7, VAPOR REMARK 280 DIFFUSION, HANGING 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 19.10000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.14500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.22500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 41.14500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.10000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.22500 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: 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 ALA A 1 REMARK 465 ASN A 181 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PHE A 17 CB - CG - CD1 ANGL. DEV. = 4.9 DEGREES REMARK 500 ASP A 40 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 ARG A 57 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES 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 SER A 77 -128.88 60.92 REMARK 500 LEU A 90 -142.29 -110.59 REMARK 500 ALA A 97 -64.42 -107.73 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 431 DISTANCE = 6.63 ANGSTROMS REMARK 525 HOH A 451 DISTANCE = 5.73 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 200 DBREF 1ISP A 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 HET GOL A 200 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL C3 H8 O3 FORMUL 3 HOH *151(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 SHEET 1 A 6 LEU A 36 ALA A 38 0 SHEET 2 A 6 VAL A 6 VAL A 9 1 N VAL A 6 O TYR A 37 SHEET 3 A 6 VAL A 71 HIS A 76 1 O HIS A 76 N VAL A 9 SHEET 4 A 6 VAL A 96 LEU A 102 1 O VAL A 100 N ILE A 73 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 VAL A 149 N SER A 127 SITE 1 AC1 10 GLY A 11 ILE A 12 GLY A 14 ASN A 18 SITE 2 AC1 10 HIS A 76 SER A 77 ILE A 157 LEU A 160 SITE 3 AC1 10 HOH A 316 HOH A 417 CRYST1 38.200 58.450 82.290 90.00 90.00 90.00 P 21 21 21 4 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 0.026178 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017109 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012152 0.00000 MASTER 244 0 1 10 6 0 3 6 0 0 0 14 END