HEADER HYDROLASE 08-MAY-08 3D2A TITLE STRUCTURE OF 1-17A4, A THERMOSTABLE MUTANT OF BACILLUS SUBTILIS LIPASE TITLE 2 OBTAINED THROUGH DIRECTED EVOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: LIPASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TRIACYLGLYCEROL LIPASE; COMPND 5 EC: 3.1.1.3; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 GENE: LIPA, LIP, BSU02700; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET21B KEYWDS LIPASE, ALPHA/BETA HYDROLASE, STABILITY, DIRECTED EVOLUTION, KEYWDS 2 HYDROLASE, LIPID DEGRADATION, SECRETED EXPDTA X-RAY DIFFRACTION AUTHOR R.SANKARANARAYANAN,M.Z.KAMAL REVDAT 5 10-NOV-21 3D2A 1 SEQADV REVDAT 4 25-OCT-17 3D2A 1 REMARK REVDAT 3 24-FEB-09 3D2A 1 VERSN REVDAT 2 12-AUG-08 3D2A 1 JRNL REVDAT 1 03-JUN-08 3D2A 0 JRNL AUTH S.AHMAD,M.Z.KAMAL,R.SANKARANARAYANAN,N.M.RAO JRNL TITL THERMOSTABLE BACILLUS SUBTILIS LIPASES: IN VITRO EVOLUTION JRNL TITL 2 AND STRUCTURAL INSIGHT JRNL REF J.MOL.BIOL. V. 381 324 2008 JRNL REFN ISSN 0022-2836 JRNL PMID 18599073 JRNL DOI 10.1016/J.JMB.2008.05.063 REMARK 2 REMARK 2 RESOLUTION. 1.73 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.73 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 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) (%) : 91.7 REMARK 3 NUMBER OF REFLECTIONS : 18119 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 933 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 : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL 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 : 1357 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 143 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.21 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.46500 REMARK 3 B22 (A**2) : -0.33600 REMARK 3 B33 (A**2) : -1.12900 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 0.005 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.190 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 61.75 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3D2A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-MAY-08. REMARK 100 THE DEPOSITION ID IS D_1000047501. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 10.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : OSMIC MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18153 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.730 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.0 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.73 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.27900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2MM GLYCINE-NAOH, PH 10.0, SMALL REMARK 280 TUBES, TEMPERATURE 277K 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 19.00700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.42450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.97900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 41.42450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.00700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.97900 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 GLU A 2 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 -127.52 52.51 REMARK 500 LEU A 90 -140.35 -104.03 REMARK 500 ALA A 97 -62.95 -104.60 REMARK 500 ASN A 179 96.36 -166.86 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1T2N RELATED DB: PDB REMARK 900 RELATED ID: 1T4M RELATED DB: PDB REMARK 900 RELATED ID: 3D2B RELATED DB: PDB REMARK 900 RELATED ID: 3D2C RELATED DB: PDB DBREF 3D2A A 1 181 UNP P37957 LIP_BACSU 32 212 SEQADV 3D2A PRO A 114 UNP P37957 LEU 145 ENGINEERED MUTATION SEQADV 3D2A ASP A 132 UNP P37957 ALA 163 ENGINEERED MUTATION SEQADV 3D2A MET A 157 UNP P37957 ILE 188 ENGINEERED MUTATION SEQADV 3D2A TYR A 166 UNP P37957 ASN 197 ENGINEERED MUTATION 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 PRO 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 ASP 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 MET GLY LEU LEU TYR SER SER GLN VAL TYR SER LEU ILE SEQRES 14 A 181 LYS GLU GLY LEU ASN GLY GLY GLY GLN ASN THR ASN FORMUL 2 HOH *143(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 ASP A 72 N VAL A 7 SHEET 4 A 6 VAL A 96 LEU A 102 1 O LEU A 102 N ALA A 75 SHEET 5 A 6 LEU A 124 SER A 130 1 O ILE A 128 N THR A 101 SHEET 6 A 6 ARG A 147 ILE A 151 1 O VAL A 149 N SER A 127 CRYST1 38.014 57.958 82.849 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 0.026306 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017254 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012070 0.00000