HEADER ISOMERASE 10-JAN-07 2OHV TITLE STRUCTURAL BASIS FOR GLUTAMATE RACEMASE INHIBITION COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTAMATE RACEMASE; COMPND 3 CHAIN: A; COMPND 4 EC: 5.1.1.3; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PYOGENES M1 GAS; SOURCE 3 ORGANISM_TAXID: 160490; SOURCE 4 STRAIN: ATCC 700294; SOURCE 5 GENE: MURI; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS ISOMERASE, RACEMASE EXPDTA X-RAY DIFFRACTION AUTHOR E.E.KIM REVDAT 3 25-OCT-23 2OHV 1 REMARK REVDAT 2 24-FEB-09 2OHV 1 VERSN REVDAT 1 25-SEP-07 2OHV 0 JRNL AUTH K.H.KIM,Y.J.BONG,J.K.PARK,K.J.SHIN,K.Y.HWANG,E.E.KIM JRNL TITL STRUCTURAL BASIS FOR GLUTAMATE RACEMASE INHIBITION JRNL REF J.MOL.BIOL. V. 372 434 2007 JRNL REFN ISSN 0022-2836 JRNL PMID 17658548 JRNL DOI 10.1016/J.JMB.2007.05.003 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.87 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 93090.010 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 12501 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) : 0.226 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.300 REMARK 3 FREE R VALUE TEST SET COUNT : 1288 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.66 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1858 REMARK 3 BIN R VALUE (WORKING SET) : 0.3400 REMARK 3 BIN FREE R VALUE : 0.3380 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 191 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.024 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1990 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 21 REMARK 3 SOLVENT ATOMS : 60 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 56.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.73000 REMARK 3 B22 (A**2) : -5.73000 REMARK 3 B33 (A**2) : 11.46000 REMARK 3 B12 (A**2) : 3.06000 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) : 0.33 REMARK 3 ESD FROM SIGMAA (A) : 0.44 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.35 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.45 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.840 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 6.020 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 9.470 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 9.160 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 13.320; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 66.26 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.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : INH.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : INH.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2OHV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-JAN-07. REMARK 100 THE DEPOSITION ID IS D_1000041155. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-APR-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : WIGGLER REMARK 200 OPTICS : WIGGLER REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12607 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.07400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 42.0000 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) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.28900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: 2OHG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 8% PEG6000, 7% GLYCEROL, 0.1M BICINE, REMARK 280 PH 8.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 63.80000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 31.90000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 31.90000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 63.80000 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 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 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 95.70000 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 PRO A 41 REMARK 465 TYR A 42 REMARK 465 GLY A 43 REMARK 465 PRO A 44 REMARK 465 ARG A 45 REMARK 465 LYS A 230 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 ARG A 39 151.49 78.05 REMARK 500 THR A 63 7.69 -69.63 REMARK 500 GLU A 155 73.94 -108.68 REMARK 500 ASP A 222 62.14 32.81 REMARK 500 VAL A 232 -21.13 -149.67 REMARK 500 GLU A 247 -71.86 -57.21 REMARK 500 GLN A 255 140.51 175.93 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1B73 RELATED DB: PDB REMARK 900 GLUTAMATE RACEMASE FROM AQUIFEX PYROPHILUS REMARK 900 RELATED ID: 1ZUW RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF B.SUBTILIS GLUTAMATE RACEMASE WITH D-GLU REMARK 900 RELATED ID: 2OHG RELATED DB: PDB REMARK 900 RELATED ID: 2OHO RELATED DB: PDB DBREF 2OHV A 1 264 UNP Q9A1B7 MURI_STRP1 1 264 SEQRES 1 A 264 MET ASP THR ARG PRO ILE GLY PHE LEU ASP SER GLY VAL SEQRES 2 A 264 GLY GLY LEU THR VAL VAL CYS GLU LEU ILE ARG GLN LEU SEQRES 3 A 264 PRO HIS GLU LYS ILE VAL TYR ILE GLY ASP SER ALA ARG SEQRES 4 A 264 ALA PRO TYR GLY PRO ARG PRO LYS LYS GLN ILE LYS GLU SEQRES 5 A 264 TYR THR TRP GLU LEU VAL ASN PHE LEU LEU THR GLN ASN SEQRES 6 A 264 VAL LYS MET ILE VAL PHE ALA CYS ASN THR ALA THR ALA SEQRES 7 A 264 VAL ALA TRP GLU GLU VAL LYS ALA ALA LEU ASP ILE PRO SEQRES 8 A 264 VAL LEU GLY VAL VAL LEU PRO GLY ALA SER ALA ALA ILE SEQRES 9 A 264 LYS SER THR THR LYS GLY GLN VAL GLY VAL ILE GLY THR SEQRES 10 A 264 PRO MET THR VAL ALA SER ASP ILE TYR ARG LYS LYS ILE SEQRES 11 A 264 GLN LEU LEU ALA PRO SER ILE GLN VAL ARG SER LEU ALA SEQRES 12 A 264 CYS PRO LYS PHE VAL PRO ILE VAL GLU SER ASN GLU MET SEQRES 13 A 264 CYS SER SER ILE ALA LYS LYS ILE VAL TYR ASP SER LEU SEQRES 14 A 264 ALA PRO LEU VAL GLY LYS ILE ASP THR LEU VAL LEU GLY SEQRES 15 A 264 CYS THR HIS TYR PRO LEU LEU ARG PRO ILE ILE GLN ASN SEQRES 16 A 264 VAL MET GLY PRO SER VAL LYS LEU ILE ASP SER GLY ALA SEQRES 17 A 264 GLU CYS VAL ARG ASP ILE SER VAL LEU LEU ASN TYR PHE SEQRES 18 A 264 ASP ILE ASN GLY ASN TYR HIS GLN LYS ALA VAL GLU HIS SEQRES 19 A 264 ARG PHE PHE THR THR ALA ASN PRO GLU ILE PHE GLN GLU SEQRES 20 A 264 ILE ALA SER ILE TRP LEU LYS GLN LYS ILE ASN VAL GLU SEQRES 21 A 264 HIS VAL THR LEU HET NHL A 400 21 HETNAM NHL (4S)-4-(2-NAPHTHYLMETHYL)-D-GLUTAMIC ACID HETSYN NHL GAMMA-2-NAPHTHYLMETHYL-D-GLUTAMIC ACID FORMUL 2 NHL C16 H17 N O4 FORMUL 3 HOH *60(H2 O) HELIX 1 1 GLY A 15 LEU A 26 1 12 HELIX 2 2 PRO A 46 THR A 63 1 18 HELIX 3 3 CYS A 73 LEU A 88 1 16 HELIX 4 4 VAL A 95 THR A 107 1 13 HELIX 5 5 THR A 117 ASP A 124 1 8 HELIX 6 6 ASP A 124 ALA A 134 1 11 HELIX 7 7 LYS A 146 SER A 153 1 8 HELIX 8 8 SER A 158 ALA A 170 1 13 HELIX 9 9 PRO A 171 VAL A 173 5 3 HELIX 10 10 HIS A 185 LEU A 188 5 4 HELIX 11 11 LEU A 189 GLY A 198 1 10 HELIX 12 12 SER A 206 PHE A 221 1 16 HELIX 13 13 ASN A 241 LEU A 253 1 13 SHEET 1 A 6 VAL A 92 GLY A 94 0 SHEET 2 A 6 MET A 68 PHE A 71 1 N PHE A 71 O LEU A 93 SHEET 3 A 6 ILE A 6 ASP A 10 1 N GLY A 7 O MET A 68 SHEET 4 A 6 ILE A 31 GLY A 35 1 O ILE A 34 N ASP A 10 SHEET 5 A 6 ARG A 235 THR A 238 1 O PHE A 237 N TYR A 33 SHEET 6 A 6 VAL A 259 HIS A 261 1 O GLU A 260 N PHE A 236 SHEET 1 B 4 GLN A 138 ALA A 143 0 SHEET 2 B 4 GLN A 111 GLY A 116 1 N VAL A 112 O ARG A 140 SHEET 3 B 4 THR A 178 LEU A 181 1 O THR A 178 N GLY A 113 SHEET 4 B 4 LYS A 202 ASP A 205 1 O ILE A 204 N LEU A 181 CRYST1 79.745 79.745 95.700 90.00 90.00 120.00 P 32 2 1 6 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 0.012540 0.007240 0.000000 0.00000 SCALE2 0.000000 0.014480 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010449 0.00000