HEADER HYDROLASE 12-MAY-99 1QH9 TITLE ENZYME-PRODUCT COMPLEX OF L-2-HALOACID DEHALOGENASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2-HALOACID DEHALOGENASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.8.1.2; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: COMPLEXED WITH D-LACTATE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS SP.; SOURCE 3 ORGANISM_TAXID: 66693; SOURCE 4 STRAIN: YL; SOURCE 5 GENE: DEX YL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PKK223-3; SOURCE 9 EXPRESSION_SYSTEM_GENE: DEX YL KEYWDS DEHALOGENASE, ENZYME-PRODUCT COMPLEX, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.-F.LI,Y.HATA,T.FUJII,T.KURIHARA,N.ESAKI REVDAT 4 15-NOV-23 1QH9 1 REMARK ATOM REVDAT 3 13-JUL-11 1QH9 1 VERSN REVDAT 2 24-FEB-09 1QH9 1 VERSN REVDAT 1 24-MAY-00 1QH9 0 JRNL AUTH Y.-F.LI,Y.HATA,T.FUJII,T.KURIHARA,N.ESAKI JRNL TITL THE STRUCTURE OF L-2-HALOACID DEHALOGENASE COMPLEXED WITH A JRNL TITL 2 REACTION PRODUCT REVEALS THE MECHANISM OF INTERMEDIATE JRNL TITL 3 HYDROLYSIS IN DEHALOGENASE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH T.HISANO,Y.HATA,T.FUJII,J.-Q.LIU,T.KURIHARA,N.ESAKI,K.SODA REMARK 1 TITL CRYSTAL STRUCTURE OF L-2-HALOACID DEHALOGENASE FROM REMARK 1 TITL 2 PSEUDOMONAS SP. YL. AN ALPHA/BETA HYDROLASE STRUCTURE THAT REMARK 1 TITL 3 IS DIFFERENT FROM THE ALPHA/BETA HYDROLASE FOLD REMARK 1 REF J.BIOL.CHEM. V. 271 20322 1996 REMARK 1 REFN ISSN 0021-9258 REMARK 1 DOI 10.1074/JBC.271.34.20322 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 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) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 100000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.1000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 91.0 REMARK 3 NUMBER OF REFLECTIONS : 7553 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.287 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 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 : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.61 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 79.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 740 REMARK 3 BIN R VALUE (WORKING SET) : 0.2890 REMARK 3 BIN FREE R VALUE : 0.3560 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 : 1741 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 16 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.30 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) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.080 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 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : PARA.DLA REMARK 3 PARAMETER FILE 3 : PARA.WATER REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : TOPO.DLA REMARK 3 TOPOLOGY FILE 3 : TOPO.WATER REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1QH9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-MAY-99. REMARK 100 THE DEPOSITION ID IS D_1000001048. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : JAN-98 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 5.5 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 RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : PROCESS REMARK 200 DATA SCALING SOFTWARE : PROCESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8320 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 48.630 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.07980 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.1 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 5.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 45.90500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.38000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 45.90500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 31.38000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 2970 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 63.77382 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 43.05667 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 MET A 1 REMARK 465 ASP A 2 REMARK 465 THR A 224 REMARK 465 ALA A 225 REMARK 465 ALA A 226 REMARK 465 GLY A 227 REMARK 465 LYS A 228 REMARK 465 ALA A 229 REMARK 465 GLU A 230 REMARK 465 LYS A 231 REMARK 465 GLY A 232 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 TYR A 3 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 HIS A 19 CG ND1 CD2 CE1 NE2 REMARK 470 ARG A 82 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 105 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 223 CA C O CB CG CD OE1 REMARK 470 GLU A 223 OE2 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 LEU A 11 -67.03 -103.02 REMARK 500 ARG A 56 75.55 -118.58 REMARK 500 ARG A 93 29.48 -140.42 REMARK 500 ASP A 136 10.25 -67.37 REMARK 500 PRO A 152 33.27 -86.17 REMARK 500 GLU A 203 56.12 -105.51 REMARK 500 PHE A 222 -154.06 -114.67 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 LAC A 300 DBREF 1QH9 A 1 232 UNP Q53464 HAD_PSEUY 1 232 SEQRES 1 A 232 MET ASP TYR ILE LYS GLY ILE ALA PHE ASP LEU TYR GLY SEQRES 2 A 232 THR LEU PHE ASP VAL HIS SER VAL VAL GLY ARG CYS ASP SEQRES 3 A 232 GLU ALA PHE PRO GLY ARG GLY ARG GLU ILE SER ALA LEU SEQRES 4 A 232 TRP ARG GLN LYS GLN LEU GLU TYR THR TRP LEU ARG SER SEQRES 5 A 232 LEU MET ASN ARG TYR VAL ASN PHE GLN GLN ALA THR GLU SEQRES 6 A 232 ASP ALA LEU ARG PHE THR CYS ARG HIS LEU GLY LEU ASP SEQRES 7 A 232 LEU ASP ALA ARG THR ARG SER THR LEU CYS ASP ALA TYR SEQRES 8 A 232 LEU ARG LEU ALA PRO PHE SER GLU VAL PRO ASP SER LEU SEQRES 9 A 232 ARG GLU LEU LYS ARG ARG GLY LEU LYS LEU ALA ILE LEU SEQRES 10 A 232 SER ASN GLY SER PRO GLN SER ILE ASP ALA VAL VAL SER SEQRES 11 A 232 HIS ALA GLY LEU ARG ASP GLY PHE ASP HIS LEU LEU SER SEQRES 12 A 232 VAL ASP PRO VAL GLN VAL TYR LYS PRO ASP ASN ARG VAL SEQRES 13 A 232 TYR GLU LEU ALA GLU GLN ALA LEU GLY LEU ASP ARG SER SEQRES 14 A 232 ALA ILE LEU PHE VAL SER SER ASN ALA TRP ASP ALA THR SEQRES 15 A 232 GLY ALA ARG TYR PHE GLY PHE PRO THR CYS TRP ILE ASN SEQRES 16 A 232 ARG THR GLY ASN VAL PHE GLU GLU MET GLY GLN THR PRO SEQRES 17 A 232 ASP TRP GLU VAL THR SER LEU ARG ALA VAL VAL GLU LEU SEQRES 18 A 232 PHE GLU THR ALA ALA GLY LYS ALA GLU LYS GLY HET LAC A 300 6 HETNAM LAC LACTIC ACID FORMUL 2 LAC C3 H6 O3 FORMUL 3 HOH *16(H2 O) HELIX 1 1 VAL A 18 ASP A 26 5 9 HELIX 2 2 GLY A 33 LEU A 53 1 21 HELIX 3 3 PHE A 60 HIS A 74 1 15 HELIX 4 4 ALA A 81 CYS A 88 1 8 HELIX 5 5 TYR A 91 ARG A 93 5 3 HELIX 6 6 VAL A 100 ARG A 110 1 11 HELIX 7 7 PRO A 122 HIS A 131 1 10 HELIX 8 8 ARG A 135 GLY A 137 5 3 HELIX 9 9 ASP A 145 VAL A 147 5 3 HELIX 10 10 ASN A 154 ALA A 163 1 10 HELIX 11 11 ARG A 168 ALA A 170 5 3 HELIX 12 12 ASP A 180 PHE A 187 1 8 HELIX 13 13 LEU A 215 VAL A 219 1 5 SHEET 1 A 6 TRP A 210 VAL A 212 0 SHEET 2 A 6 PRO A 190 ILE A 194 1 N TRP A 193 O TRP A 210 SHEET 3 A 6 ILE A 171 SER A 175 1 N PHE A 173 O PRO A 190 SHEET 4 A 6 GLY A 6 PHE A 9 1 N GLY A 6 O LEU A 172 SHEET 5 A 6 LYS A 113 SER A 118 1 N LYS A 113 O ILE A 7 SHEET 6 A 6 HIS A 140 SER A 143 1 N HIS A 140 O ILE A 116 CISPEP 1 LYS A 151 PRO A 152 0 0.00 SITE 1 AC1 7 ASP A 10 LEU A 11 TYR A 12 ARG A 41 SITE 2 AC1 7 SER A 118 ASN A 119 LYS A 151 CRYST1 91.810 62.760 51.380 90.00 123.07 90.00 C 1 2 1 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 0.010892 0.000000 0.007092 0.00000 SCALE2 0.000000 0.015934 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023225 0.00000