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HEADER HYDROLASE 08-MAY-08 3D2A
TITLE STRUCTURE OF 1-17A4, A THERMOSTABLE MUTANT OF BACILLUS
TITLE 2 SUBTILIS LIPASE 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 GENE: LIPA, LIP, BSU02700;
SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 5 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 7 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 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
JRNL TITL 2 EVOLUTION AND STRUCTURAL INSIGHT
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 1
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) : 0.004 ; 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. 3.1, 01-AUG-2007
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ.
REMARK 100 THE RCSB ID CODE IS RCSB047501.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : NULL
REMARK 200 TEMPERATURE (KELVIN) : 100.0
REMARK 200 PH : 10.00
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 : NULL
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 : HKL
REMARK 200 DATA SCALING SOFTWARE : HKL
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 1/2-X,-Y,1/2+Z
REMARK 290 3555 -X,1/2+Y,1/2-Z
REMARK 290 4555 1/2+X,1/2-Y,-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; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSEQI
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 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 257 DISTANCE = 5.93 ANGSTROMS
REMARK 525 HOH A 281 DISTANCE = 7.73 ANGSTROMS
REMARK 525 HOH A 291 DISTANCE = 5.07 ANGSTROMS
REMARK 525 HOH A 315 DISTANCE = 5.19 ANGSTROMS
REMARK 525 HOH A 323 DISTANCE = 5.39 ANGSTROMS
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
SEQADV 3D2A ASP A 132 UNP P37957 ALA 163 ENGINEERED
SEQADV 3D2A MET A 157 UNP P37957 ILE 188 ENGINEERED
SEQADV 3D2A TYR A 166 UNP P37957 ASN 197 ENGINEERED
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
TER 1358 ASN A 181
MASTER 268 0 0 10 6 0 0 6 1500 1 0 14
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