10 20 30 40 50 60 70 80 1GGV - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE 27-SEP-00 1GGV
TITLE CRYSTAL STRUCTURE OF THE C123S MUTANT OF DIENELACTONE TITLE 2 HYDROLASE (DLH) BOUND WITH THE PMS MOIETY OF THE PROTEASE TITLE 3 INHIBITOR, PHENYLMETHYLSULFONYL FLUORIDE (PMSF)
COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIENELACTONE HYDROLASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.1.45; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS PUTIDA; SOURCE 3 ORGANISM_TAXID: 303; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR: LAMBDA TEMPERATURE SENSITIVE SOURCE 7 VECTOR SYSTEM (RSC, ANU); SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PAC27
KEYWDS ALPHA/BETA HYDROLASE FOLD, DIENELACTONE HYDROLASE, PMSF, KEYWDS 2 PSEUDOMONAS PUTIDA (PAC27)
EXPDTA X-RAY DIFFRACTION
AUTHOR A.ROBINSON,K.J.EDWARDS,P.D.CARR,J.D.BARTON,G.D.EWART, AUTHOR 2 D.L.OLLIS
REVDAT 3 24-FEB-09 1GGV 1 VERSN REVDAT 2 19-JUN-02 1GGV 1 CRYST1 SCALE1 SCALE2 SCALE3 REVDAT 1 13-DEC-00 1GGV 0
JRNL AUTH A.ROBINSON,K.J.EDWARDS,P.D.CARR,J.D.BARTON, JRNL AUTH 2 G.D.EWART,D.L.OLLIS JRNL TITL STRUCTURE OF THE C123S MUTANT OF DIENELACTONE JRNL TITL 2 HYDROLASE (DLH) BOUND WITH THE PMS MOIETY OF THE JRNL TITL 3 PROTEASE INHIBITOR PHENYLMETHYLSULFONYL FLUORIDE JRNL TITL 4 (PMSF). JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 56 1376 2000 JRNL REFN ISSN 0907-4449 JRNL PMID 11053834 JRNL DOI 10.1107/S0907444900010647
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 7.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 6459 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) : 0.151 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 : 2254 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 64 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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) : 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) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.51 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.24 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.29 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) : 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 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 1GGV COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-OCT-00. REMARK 100 THE RCSB ID CODE IS RCSB001500.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-DEC-94 REMARK 200 TEMPERATURE (KELVIN) : 277.0 REMARK 200 PH : 6.3 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 RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MANUFACTURER SUPPLIED (MSC) REMARK 200 DATA SCALING SOFTWARE : MSC REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12109 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 78.7 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.09 REMARK 200 COMPLETENESS FOR SHELL (%) : 65.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: X-PLOR REMARK 200 STARTING MODEL: DIENELACTONE HYDROLASE (WILD-TYPE) REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: (K+/NA+) PHOSPHATE, PMSF, PH 6.3, REMARK 280 VAPOR DIFFUSION/HANGING DROP, TEMPERATURE 291.0K
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 25.54000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.30500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.93000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 41.30500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.54000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.93000 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 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 MET A 1 CG SD CE REMARK 470 GLU A 4 CG CD OE1 OE2 REMARK 470 LYS A 25 CG CD CE NZ REMARK 470 ARG A 45 CD NE CZ NH1 NH2 REMARK 470 ASN A 154 CG OD1 ND2 REMARK 470 HIS A 172 CG ND1 CD2 CE1 NE2 REMARK 470 GLU A 199 CG CD OE1 OE2 REMARK 470 HIS A 202 CG ND1 CD2 CE1 NE2
REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ARG A 45 CG
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 ASN A 41 -165.54 -112.08 REMARK 500 TYR A 145 65.59 35.42 REMARK 500 GLN A 170 44.86 -104.69 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR A 197 0.07 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
DBREF 1GGV A 1 232 UNP P0A114 CLCD_PSEPU 1 232
SEQADV 1GGV ALA A 79 UNP P0A114 ARG 79 CONFLICT SEQADV 1GGV SEB A 123 UNP P0A114 CYS 123 SEE REMARK 999 SEQADV 1GGV ASN A 154 UNP P0A114 LYS 154 CONFLICT SEQADV 1GGV THR A 224 UNP P0A114 ARG 224 CONFLICT
SEQRES 1 A 232 MET LEU THR GLU GLY ILE SER ILE GLN SER TYR ASP GLY SEQRES 2 A 232 HIS THR PHE GLY ALA LEU VAL GLY SER PRO ALA LYS ALA SEQRES 3 A 232 PRO ALA PRO VAL ILE VAL ILE ALA GLN GLU ILE PHE GLY SEQRES 4 A 232 VAL ASN ALA PHE MET ARG GLU THR VAL SER TRP LEU VAL SEQRES 5 A 232 ASP GLN GLY TYR ALA ALA VAL CYS PRO ASP LEU TYR ALA SEQRES 6 A 232 ARG GLN ALA PRO GLY THR ALA LEU ASP PRO GLN ASP GLU SEQRES 7 A 232 ALA GLN ARG GLU GLN ALA TYR LYS LEU TRP GLN ALA PHE SEQRES 8 A 232 ASP MET GLU ALA GLY VAL GLY ASP LEU GLU ALA ALA ILE SEQRES 9 A 232 ARG TYR ALA ARG HIS GLN PRO TYR SER ASN GLY LYS VAL SEQRES 10 A 232 GLY LEU VAL GLY TYR SEB LEU GLY GLY ALA LEU ALA PHE SEQRES 11 A 232 LEU VAL ALA ALA LYS GLY TYR VAL ASP ARG ALA VAL GLY SEQRES 12 A 232 TYR TYR GLY VAL GLY LEU GLU LYS GLN LEU ASN LYS VAL SEQRES 13 A 232 PRO GLU VAL LYS HIS PRO ALA LEU PHE HIS MET GLY GLY SEQRES 14 A 232 GLN ASP HIS PHE VAL PRO ALA PRO SER ARG GLN LEU ILE SEQRES 15 A 232 THR GLU GLY PHE GLY ALA ASN PRO LEU LEU GLN VAL HIS SEQRES 16 A 232 TRP TYR GLU GLU ALA GLY HIS SER PHE ALA ARG THR SER SEQRES 17 A 232 SER SER GLY TYR VAL ALA SER ALA ALA ALA LEU ALA ASN SEQRES 18 A 232 GLU ARG THR LEU ASP PHE LEU ALA PRO LEU GLN
MODRES 1GGV SEB A 123 SER O-BENZYLSULFONYL-SERINE
HET SEB A 123 16
HETNAM SEB O-BENZYLSULFONYL-SERINE
FORMUL 1 SEB C10 H13 N O5 S FORMUL 2 HOH *64(H2 O)
HELIX 1 1 ASN A 41 GLN A 54 1 14 HELIX 2 2 ASP A 62 GLN A 67 5 6 HELIX 3 3 ASP A 77 PHE A 91 1 15 HELIX 4 4 ASP A 92 HIS A 109 1 18 HELIX 5 5 LEU A 124 GLY A 136 1 13 HELIX 6 6 GLY A 148 LEU A 153 5 6 HELIX 7 7 GLN A 152 VAL A 159 5 8 HELIX 8 8 PRO A 175 ASN A 189 1 15 HELIX 9 9 VAL A 213 ALA A 229 1 17 HELIX 10 10 PRO A 230 GLN A 232 5 3
SHEET 1 B 7 ALA A 18 GLY A 21 0 SHEET 2 B 7 ALA A 28 ALA A 34 0 SHEET 3 B 7 ALA A 57 PRO A 61 0 SHEET 4 B 7 SER A 113 TYR A 122 0 SHEET 5 B 7 ARG A 140 TYR A 144 0 SHEET 6 B 7 ALA A 163 GLY A 168 0 SHEET 7 B 7 LEU A 192 TYR A 197 0
LINK C TYR A 122 N SEB A 123 1555 1555 1.33 LINK C SEB A 123 N LEU A 124 1555 1555 1.33
CISPEP 1 ALA A 26 PRO A 27 0 -0.26
CRYST1 51.080 51.860 82.610 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 0.019577 0.000000 0.000000 0.00000
SCALE2 0.000000 0.019283 0.000000 0.00000
SCALE3 0.000000 0.000000 0.012105 0.00000