HEADER LYASE 26-AUG-04 1XAL TITLE CRYSTAL STRUCTURE OF STAPHLYOCOCCUS AUREUS 3-DEHYDROQUINATE SYNTHASE TITLE 2 (DHQS) IN COMPLEX WITH ZN2+, NAD+ AND CARBAPHOSPHONATE (SOAK) COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3-DEHYDROQUINATE SYNTHASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: SADHQS; COMPND 5 EC: 4.2.3.4; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 GENE: AROB; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3 PLYSS); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PMUT27 KEYWDS SHIKIMATE PATHWAY, AROMATIC AMINO ACID BIOSYNTHESIS, DHQS, SADHQS, KEYWDS 2 CLOSED FORM, FORM B, DOMAIN MOVEMENT, CYCLASE, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR C.E.NICHOLS,J.REN,K.LESLIE,B.DHALIWAL,M.LOCKYER,I.CHARLES, AUTHOR 2 A.R.HAWKINS,D.K.STAMMERS REVDAT 4 14-FEB-24 1XAL 1 REMARK LINK REVDAT 3 24-FEB-09 1XAL 1 VERSN REVDAT 2 22-MAR-05 1XAL 1 JRNL REVDAT 1 01-MAR-05 1XAL 0 JRNL AUTH C.E.NICHOLS,J.REN,K.LESLIE,B.DHALIWAL,M.LOCKYER,I.CHARLES, JRNL AUTH 2 A.R.HAWKINS,D.K.STAMMERS JRNL TITL COMPARISON OF LIGAND INDUCED CONFORMATIONAL CHANGES AND JRNL TITL 2 DOMAIN CLOSURE MECHANISMS, BETWEEN PROKARYOTIC AND JRNL TITL 3 EUKARYOTIC DEHYDROQUINATE SYNTHASES. JRNL REF J.MOL.BIOL. V. 343 533 2004 JRNL REFN ISSN 0022-2836 JRNL PMID 15465043 JRNL DOI 10.1016/J.JMB.2004.08.039 REMARK 2 REMARK 2 RESOLUTION. 2.80 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.86 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1931777.930 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 16571 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) : 0.203 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1663 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.90 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1411 REMARK 3 BIN R VALUE (WORKING SET) : 0.3310 REMARK 3 BIN FREE R VALUE : 0.3730 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 11.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 181 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.028 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5378 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 124 REMARK 3 SOLVENT ATOMS : 138 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 74.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 63.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 7.18000 REMARK 3 B22 (A**2) : 7.18000 REMARK 3 B33 (A**2) : -14.37000 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) : 0.34 REMARK 3 ESD FROM SIGMAA (A) : 0.56 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) : 0.45 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.66 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.700 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) : 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.28 REMARK 3 BSOL : 50.16 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 : LIG.PAR REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : LIG.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : WATER_REP.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1XAL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-NOV-04. REMARK 100 THE DEPOSITION ID IS D_1000030143. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-NOV-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 2 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 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : OSMIC MULTILAYER OPTICS REMARK 200 OPTICS : OSMIC MULTILAYER 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 : 16571 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -1.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.8700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 3.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.48100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.570 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG3350, KCL, PH 8.0, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 116.15950 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 174.23925 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 58.07975 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 LEU A 54 REMARK 465 SER A 55 REMARK 465 TYR A 56 REMARK 465 GLU A 57 REMARK 465 ILE A 298 REMARK 465 THR A 299 REMARK 465 ASP A 300 REMARK 465 LEU A 301 REMARK 465 ASP A 302 REMARK 465 PHE A 303 REMARK 465 GLU A 304 REMARK 465 THR A 305 REMARK 465 LEU A 306 REMARK 465 TYR A 307 REMARK 465 GLN A 308 REMARK 465 TYR A 309 REMARK 465 PHE A 353 REMARK 465 LYS A 354 REMARK 465 LEU B 54 REMARK 465 SER B 55 REMARK 465 TYR B 56 REMARK 465 GLU B 57 REMARK 465 ILE B 298 REMARK 465 THR B 299 REMARK 465 ASP B 300 REMARK 465 LEU B 301 REMARK 465 ASP B 302 REMARK 465 PHE B 303 REMARK 465 GLU B 304 REMARK 465 THR B 305 REMARK 465 LEU B 306 REMARK 465 TYR B 307 REMARK 465 GLN B 308 REMARK 465 TYR B 309 REMARK 465 PHE B 353 REMARK 465 LYS B 354 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 TYR A 7 162.41 -44.52 REMARK 500 THR A 26 -15.51 -44.54 REMARK 500 LEU A 28 -54.11 -11.63 REMARK 500 ASN A 29 38.93 -88.92 REMARK 500 LYS A 49 -19.72 -46.66 REMARK 500 ASP A 52 2.23 -54.38 REMARK 500 GLU A 68 -18.94 -49.58 REMARK 500 SER A 85 11.91 -64.37 REMARK 500 HIS A 87 41.62 34.13 REMARK 500 VAL A 88 -175.30 -51.61 REMARK 500 ASN A 91 45.64 -92.81 REMARK 500 PHE A 105 -70.80 -72.77 REMARK 500 VAL A 117 -161.32 -108.18 REMARK 500 VAL A 122 72.29 -115.39 REMARK 500 ALA A 128 3.05 -67.19 REMARK 500 ASN A 146 80.37 45.73 REMARK 500 LEU A 161 -7.71 -58.12 REMARK 500 LYS A 165 -4.55 -53.78 REMARK 500 SER A 189 -54.26 -20.61 REMARK 500 HIS A 197 -65.07 -99.93 REMARK 500 GLU A 202 -70.52 -50.72 REMARK 500 LEU A 222 -37.07 -36.49 REMARK 500 ALA A 227 -90.90 -89.33 REMARK 500 ASN A 239 31.84 -86.66 REMARK 500 HIS A 246 -37.36 -32.43 REMARK 500 ALA A 247 -73.56 -70.53 REMARK 500 GLU A 249 -71.39 -72.31 REMARK 500 LYS A 253 44.61 39.23 REMARK 500 LEU A 274 -71.26 -103.82 REMARK 500 LYS A 278 58.83 -96.17 REMARK 500 PRO A 294 -81.91 -34.59 REMARK 500 LEU A 295 50.07 79.02 REMARK 500 SER A 312 0.42 172.12 REMARK 500 ASP A 313 -177.32 -46.02 REMARK 500 LYS A 318 95.23 -46.24 REMARK 500 GLN A 319 -30.49 173.29 REMARK 500 GLN A 328 148.92 177.46 REMARK 500 ASP A 331 67.65 -163.52 REMARK 500 GLN A 343 -71.78 -88.52 REMARK 500 HIS A 344 -38.66 -38.89 REMARK 500 GLU A 347 -36.36 -130.73 REMARK 500 THR A 351 31.02 -82.99 REMARK 500 TYR B 7 162.21 -44.57 REMARK 500 THR B 26 -15.40 -44.61 REMARK 500 LEU B 28 -54.25 -11.96 REMARK 500 ASN B 29 39.25 -89.12 REMARK 500 LYS B 49 -19.86 -46.64 REMARK 500 ASP B 52 2.43 -54.60 REMARK 500 GLU B 68 -17.00 -49.89 REMARK 500 SER B 85 11.80 -64.41 REMARK 500 REMARK 500 THIS ENTRY HAS 84 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 600 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 178 OE1 REMARK 620 2 HIS A 242 NE2 90.2 REMARK 620 3 HIS A 256 NE2 114.5 119.2 REMARK 620 4 CRB A 500 O5 156.7 87.9 86.4 REMARK 620 5 CRB A 500 O4 88.4 74.4 151.9 68.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 601 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 178 OE1 REMARK 620 2 HIS B 242 NE2 90.7 REMARK 620 3 HIS B 256 NE2 114.9 118.6 REMARK 620 4 CRB B 501 O4 88.8 74.9 151.1 REMARK 620 5 CRB B 501 O5 156.8 87.5 86.0 68.4 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 600 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD A 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CRB A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CRB B 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1NR5 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX REMARK 900 WITH ZN2+, NAD+ AND CARBAPHOSPHONATE, CRYSTAL FORM C, CLOSED FORM REMARK 900 WITH COFACTOR AND SUBSTRATE ANALOGUE REMARK 900 RELATED ID: 1NRX RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX REMARK 900 WITH ZN2+ AND NAD+, CRYSTAL FORM F, OPEN FORM WITH COFACTOR REMARK 900 RELATED ID: 1NVE RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX REMARK 900 WITH ZN2+ AND NAD+, CRYSTAL FORM E, OPEN FORM WITH CO-FACTOR REMARK 900 RELATED ID: 1NVD RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX REMARK 900 WITH ZN2+ AND CARBAPHOSPHONATE, CRYSTAL FORM B, CLOSED FORM WITH REMARK 900 SUBSTRATE ANALOGUE REMARK 900 RELATED ID: 1NVB RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX REMARK 900 WITH ZN2+ AND CARBAPHOSPHONATE, CRYSTAL FORM C, CLOSED FORM WITH REMARK 900 SUBSTRATE ANALOGUE REMARK 900 RELATED ID: 1NUA RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX REMARK 900 WITH ZN2+, APO, CRYSTAL FORM D, OPEN FORM REMARK 900 RELATED ID: 1NVA RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX REMARK 900 WITH ZN2+ AND ADP, CRYSTAL FORM D, OPEN FORM WITH CO-FACTOR ANALOGUE REMARK 900 RELATED ID: 1NVF RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX REMARK 900 WITH ZN2+, ADP AND CBP, CRYSTAL FORM H, CLOSED FORM WITH CO-FACTOR REMARK 900 ANALOGUE AND SUBSTRATE ANALOGUE REMARK 900 RELATED ID: 1XAG RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF STAPHLYOCOCCUS AUREUS 3-DEHYDROQUINATE REMARK 900 SYNTHASE (DHQS) IN COMPLEX WITH ZN2+ AND CAR REMARK 900 RELATED ID: 1XAH RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF STAPHLYOCOCCUS AUREUS 3-DEHYDROQUINATE REMARK 900 SYNTHASE (DHQS) IN COMPLEX WITH ZN2+ AND CARBAPHOSPHONATE REMARK 900 RELATED ID: 1XAI RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF STAPHLYOCOCCUS AUREUS 3-DEHYDROQUINATE REMARK 900 SYNTHASE (DHQS) IN COMPLEX WITH ZN2+, NAD+ AND CARBAPHOSPHONATE REMARK 900 RELATED ID: 1XAJ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF STAPHLYOCOCCUS AUREUS 3-DEHYDROQUINATE REMARK 900 SYNTHASE (DHQS) IN COMPLEX WITH ZN2+, NAD+ AND CARBAPHOSPHONATE REMARK 999 REMARK 999 SEQUENCE REMARK 999 THESE CONFLICTS REFLECT CLONAL VARIATION FROM DATABASE SEQUENCE. DBREF 1XAL A 1 354 UNP Q6GGU4 AROB_STAAR 1 354 DBREF 1XAL B 1 354 UNP Q6GGU4 AROB_STAAR 1 354 SEQADV 1XAL LYS A 22 UNP Q6GGU4 ASP 22 SEE REMARK 999 SEQADV 1XAL TYR A 23 UNP Q6GGU4 HIS 23 SEE REMARK 999 SEQADV 1XAL GLY A 25 UNP Q6GGU4 SER 25 SEE REMARK 999 SEQADV 1XAL LEU A 28 UNP Q6GGU4 ILE 28 SEE REMARK 999 SEQADV 1XAL ASN A 29 UNP Q6GGU4 ASP 29 SEE REMARK 999 SEQADV 1XAL LEU A 36 UNP Q6GGU4 ILE 36 SEE REMARK 999 SEQADV 1XAL TYR A 41 UNP Q6GGU4 HIS 41 SEE REMARK 999 SEQADV 1XAL ASN A 48 UNP Q6GGU4 ASP 48 SEE REMARK 999 SEQADV 1XAL VAL A 109 UNP Q6GGU4 ILE 109 SEE REMARK 999 SEQADV 1XAL LYS A 170 UNP Q6GGU4 GLU 170 SEE REMARK 999 SEQADV 1XAL VAL A 226 UNP Q6GGU4 ILE 226 SEE REMARK 999 SEQADV 1XAL SER A 282 UNP Q6GGU4 ASN 282 SEE REMARK 999 SEQADV 1XAL MET A 326 UNP Q6GGU4 ILE 326 SEE REMARK 999 SEQADV 1XAL LYS B 22 UNP Q6GGU4 ASP 22 SEE REMARK 999 SEQADV 1XAL TYR B 23 UNP Q6GGU4 HIS 23 SEE REMARK 999 SEQADV 1XAL GLY B 25 UNP Q6GGU4 SER 25 SEE REMARK 999 SEQADV 1XAL LEU B 28 UNP Q6GGU4 ILE 28 SEE REMARK 999 SEQADV 1XAL ASN B 29 UNP Q6GGU4 ASP 29 SEE REMARK 999 SEQADV 1XAL LEU B 36 UNP Q6GGU4 ILE 36 SEE REMARK 999 SEQADV 1XAL TYR B 41 UNP Q6GGU4 HIS 41 SEE REMARK 999 SEQADV 1XAL ASN B 48 UNP Q6GGU4 ASP 48 SEE REMARK 999 SEQADV 1XAL VAL B 109 UNP Q6GGU4 ILE 109 SEE REMARK 999 SEQADV 1XAL LYS B 170 UNP Q6GGU4 GLU 170 SEE REMARK 999 SEQADV 1XAL VAL B 226 UNP Q6GGU4 ILE 226 SEE REMARK 999 SEQADV 1XAL SER B 282 UNP Q6GGU4 ASN 282 SEE REMARK 999 SEQADV 1XAL MET B 326 UNP Q6GGU4 ILE 326 SEE REMARK 999 SEQRES 1 A 354 MET LYS LEU GLN THR THR TYR PRO SER ASN ASN TYR PRO SEQRES 2 A 354 ILE TYR VAL GLU HIS GLY ALA ILE LYS TYR ILE GLY THR SEQRES 3 A 354 TYR LEU ASN GLN PHE ASP GLN SER PHE LEU LEU ILE ASP SEQRES 4 A 354 GLU TYR VAL ASN GLN TYR PHE ALA ASN LYS PHE ASP ASP SEQRES 5 A 354 ILE LEU SER TYR GLU ASN VAL HIS LYS VAL ILE ILE PRO SEQRES 6 A 354 ALA GLY GLU LYS THR LYS THR PHE GLU GLN TYR GLN GLU SEQRES 7 A 354 THR LEU GLU TYR ILE LEU SER HIS HIS VAL THR ARG ASN SEQRES 8 A 354 THR ALA ILE ILE ALA VAL GLY GLY GLY ALA THR GLY ASP SEQRES 9 A 354 PHE ALA GLY PHE VAL ALA ALA THR LEU LEU ARG GLY VAL SEQRES 10 A 354 HIS PHE ILE GLN VAL PRO THR THR ILE LEU ALA HIS ASP SEQRES 11 A 354 SER SER VAL GLY GLY LYS VAL GLY ILE ASN SER LYS GLN SEQRES 12 A 354 GLY LYS ASN LEU ILE GLY ALA PHE TYR ARG PRO THR ALA SEQRES 13 A 354 VAL ILE TYR ASP LEU ASP PHE LEU LYS THR LEU PRO PHE SEQRES 14 A 354 LYS GLN ILE LEU SER GLY TYR ALA GLU VAL TYR LYS HIS SEQRES 15 A 354 ALA LEU LEU ASN GLY GLU SER ALA THR GLN ASP ILE GLU SEQRES 16 A 354 GLN HIS PHE LYS ASP ARG GLU ILE LEU GLN SER LEU ASN SEQRES 17 A 354 GLY MET ASP LYS TYR ILE ALA LYS GLY ILE GLU THR LYS SEQRES 18 A 354 LEU ASP ILE VAL VAL ALA ASP GLU LYS GLU GLN GLY VAL SEQRES 19 A 354 ARG LYS PHE LEU ASN LEU GLY HIS THR PHE GLY HIS ALA SEQRES 20 A 354 VAL GLU TYR TYR HIS LYS ILE PRO HIS GLY HIS ALA VAL SEQRES 21 A 354 MET VAL GLY ILE ILE TYR GLN PHE ILE VAL ALA ASN ALA SEQRES 22 A 354 LEU PHE ASP SER LYS HIS ASP ILE SER HIS TYR ILE GLN SEQRES 23 A 354 TYR LEU ILE GLN LEU GLY TYR PRO LEU ASP MET ILE THR SEQRES 24 A 354 ASP LEU ASP PHE GLU THR LEU TYR GLN TYR MET LEU SER SEQRES 25 A 354 ASP LYS LYS ASN ASP LYS GLN GLY VAL GLN MET VAL LEU SEQRES 26 A 354 MET ARG GLN PHE GLY ASP ILE VAL VAL GLN HIS VAL ASP SEQRES 27 A 354 GLN LEU THR LEU GLN HIS ALA CYS GLU GLN LEU LYS THR SEQRES 28 A 354 TYR PHE LYS SEQRES 1 B 354 MET LYS LEU GLN THR THR TYR PRO SER ASN ASN TYR PRO SEQRES 2 B 354 ILE TYR VAL GLU HIS GLY ALA ILE LYS TYR ILE GLY THR SEQRES 3 B 354 TYR LEU ASN GLN PHE ASP GLN SER PHE LEU LEU ILE ASP SEQRES 4 B 354 GLU TYR VAL ASN GLN TYR PHE ALA ASN LYS PHE ASP ASP SEQRES 5 B 354 ILE LEU SER TYR GLU ASN VAL HIS LYS VAL ILE ILE PRO SEQRES 6 B 354 ALA GLY GLU LYS THR LYS THR PHE GLU GLN TYR GLN GLU SEQRES 7 B 354 THR LEU GLU TYR ILE LEU SER HIS HIS VAL THR ARG ASN SEQRES 8 B 354 THR ALA ILE ILE ALA VAL GLY GLY GLY ALA THR GLY ASP SEQRES 9 B 354 PHE ALA GLY PHE VAL ALA ALA THR LEU LEU ARG GLY VAL SEQRES 10 B 354 HIS PHE ILE GLN VAL PRO THR THR ILE LEU ALA HIS ASP SEQRES 11 B 354 SER SER VAL GLY GLY LYS VAL GLY ILE ASN SER LYS GLN SEQRES 12 B 354 GLY LYS ASN LEU ILE GLY ALA PHE TYR ARG PRO THR ALA SEQRES 13 B 354 VAL ILE TYR ASP LEU ASP PHE LEU LYS THR LEU PRO PHE SEQRES 14 B 354 LYS GLN ILE LEU SER GLY TYR ALA GLU VAL TYR LYS HIS SEQRES 15 B 354 ALA LEU LEU ASN GLY GLU SER ALA THR GLN ASP ILE GLU SEQRES 16 B 354 GLN HIS PHE LYS ASP ARG GLU ILE LEU GLN SER LEU ASN SEQRES 17 B 354 GLY MET ASP LYS TYR ILE ALA LYS GLY ILE GLU THR LYS SEQRES 18 B 354 LEU ASP ILE VAL VAL ALA ASP GLU LYS GLU GLN GLY VAL SEQRES 19 B 354 ARG LYS PHE LEU ASN LEU GLY HIS THR PHE GLY HIS ALA SEQRES 20 B 354 VAL GLU TYR TYR HIS LYS ILE PRO HIS GLY HIS ALA VAL SEQRES 21 B 354 MET VAL GLY ILE ILE TYR GLN PHE ILE VAL ALA ASN ALA SEQRES 22 B 354 LEU PHE ASP SER LYS HIS ASP ILE SER HIS TYR ILE GLN SEQRES 23 B 354 TYR LEU ILE GLN LEU GLY TYR PRO LEU ASP MET ILE THR SEQRES 24 B 354 ASP LEU ASP PHE GLU THR LEU TYR GLN TYR MET LEU SER SEQRES 25 B 354 ASP LYS LYS ASN ASP LYS GLN GLY VAL GLN MET VAL LEU SEQRES 26 B 354 MET ARG GLN PHE GLY ASP ILE VAL VAL GLN HIS VAL ASP SEQRES 27 B 354 GLN LEU THR LEU GLN HIS ALA CYS GLU GLN LEU LYS THR SEQRES 28 B 354 TYR PHE LYS HET ZN A 600 1 HET NAD A 400 44 HET CRB A 500 17 HET ZN B 601 1 HET NAD B 401 44 HET CRB B 501 17 HETNAM ZN ZINC ION HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM CRB [1R-(1ALPHA,3BETA,4ALPHA,5BETA)]-5-(PHOSPHONOMETHYL)-1, HETNAM 2 CRB 3,4-TRIHYDROXYCYCLOHEXANE-1-CARBOXYLIC ACID HETSYN CRB CARBAPHOSPHONATE FORMUL 3 ZN 2(ZN 2+) FORMUL 4 NAD 2(C21 H27 N7 O14 P2) FORMUL 5 CRB 2(C8 H15 O8 P) FORMUL 9 HOH *138(H2 O) HELIX 1 1 GLY A 19 TYR A 23 5 5 HELIX 2 2 ILE A 24 ASN A 29 1 6 HELIX 3 3 GLU A 40 ALA A 47 1 8 HELIX 4 4 ALA A 66 LYS A 71 5 6 HELIX 5 5 THR A 72 SER A 85 1 14 HELIX 6 6 GLY A 99 LEU A 113 1 15 HELIX 7 7 LEU A 114 GLY A 116 5 3 HELIX 8 8 LEU A 127 SER A 132 1 6 HELIX 9 9 ASP A 162 LEU A 167 5 6 HELIX 10 10 PRO A 168 LEU A 185 1 18 HELIX 11 11 ASN A 186 GLN A 196 1 11 HELIX 12 12 ASP A 200 SER A 206 1 7 HELIX 13 13 GLY A 209 ASP A 228 1 20 HELIX 14 14 GLY A 233 LEU A 240 5 8 HELIX 15 15 GLY A 241 TYR A 251 1 11 HELIX 16 16 PRO A 255 ASP A 276 1 22 HELIX 17 17 ASP A 280 GLY A 292 1 13 HELIX 18 18 LEU A 340 LEU A 349 1 10 HELIX 19 19 LYS A 350 TYR A 352 5 3 HELIX 20 20 GLY B 19 TYR B 23 5 5 HELIX 21 21 ILE B 24 ASN B 29 1 6 HELIX 22 22 GLU B 40 ALA B 47 1 8 HELIX 23 23 ALA B 66 LYS B 71 5 6 HELIX 24 24 THR B 72 SER B 85 1 14 HELIX 25 25 GLY B 99 LEU B 113 1 15 HELIX 26 26 LEU B 114 GLY B 116 5 3 HELIX 27 27 LEU B 127 SER B 132 1 6 HELIX 28 28 ASP B 162 LEU B 167 5 6 HELIX 29 29 PRO B 168 LEU B 185 1 18 HELIX 30 30 ASN B 186 GLN B 196 1 11 HELIX 31 31 ASP B 200 SER B 206 1 7 HELIX 32 32 GLY B 209 ASP B 228 1 20 HELIX 33 33 GLY B 233 LEU B 240 5 8 HELIX 34 34 GLY B 241 TYR B 251 1 11 HELIX 35 35 PRO B 255 ASP B 276 1 22 HELIX 36 36 ASP B 280 GLY B 292 1 13 HELIX 37 37 LEU B 340 LEU B 349 1 10 HELIX 38 38 LYS B 350 TYR B 352 5 3 SHEET 1 A 7 LYS A 2 GLN A 4 0 SHEET 2 A 7 PRO A 13 GLU A 17 -1 O ILE A 14 N LEU A 3 SHEET 3 A 7 ALA A 156 ASP A 160 1 O TYR A 159 N TYR A 15 SHEET 4 A 7 HIS A 118 PRO A 123 1 N GLN A 121 O ILE A 158 SHEET 5 A 7 ALA A 93 GLY A 98 1 N ILE A 94 O ILE A 120 SHEET 6 A 7 SER A 34 ASP A 39 1 N LEU A 37 O VAL A 97 SHEET 7 A 7 HIS A 60 ILE A 64 1 O VAL A 62 N LEU A 36 SHEET 1 B 2 LYS A 136 SER A 141 0 SHEET 2 B 2 GLY A 144 PHE A 151 -1 O ILE A 148 N ILE A 139 SHEET 1 C 2 GLN A 322 GLN A 328 0 SHEET 2 C 2 ASP A 331 HIS A 336 -1 O VAL A 333 N LEU A 325 SHEET 1 D 7 LYS B 2 GLN B 4 0 SHEET 2 D 7 PRO B 13 GLU B 17 -1 O ILE B 14 N LEU B 3 SHEET 3 D 7 ALA B 156 ASP B 160 1 O TYR B 159 N TYR B 15 SHEET 4 D 7 HIS B 118 PRO B 123 1 N GLN B 121 O ILE B 158 SHEET 5 D 7 ALA B 93 GLY B 98 1 N ILE B 94 O ILE B 120 SHEET 6 D 7 SER B 34 ASP B 39 1 N LEU B 37 O VAL B 97 SHEET 7 D 7 HIS B 60 ILE B 64 1 O VAL B 62 N LEU B 36 SHEET 1 E 2 LYS B 136 SER B 141 0 SHEET 2 E 2 GLY B 144 PHE B 151 -1 O ILE B 148 N ILE B 139 SHEET 1 F 2 GLN B 322 GLN B 328 0 SHEET 2 F 2 ASP B 331 HIS B 336 -1 O VAL B 333 N LEU B 325 LINK OE1 GLU A 178 ZN ZN A 600 1555 1555 2.33 LINK NE2 HIS A 242 ZN ZN A 600 1555 1555 2.50 LINK NE2 HIS A 256 ZN ZN A 600 1555 1555 2.66 LINK O5 CRB A 500 ZN ZN A 600 1555 1555 2.59 LINK O4 CRB A 500 ZN ZN A 600 1555 1555 2.38 LINK OE1 GLU B 178 ZN ZN B 601 1555 1555 2.30 LINK NE2 HIS B 242 ZN ZN B 601 1555 1555 2.50 LINK NE2 HIS B 256 ZN ZN B 601 1555 1555 2.68 LINK O4 CRB B 501 ZN ZN B 601 1555 1555 2.38 LINK O5 CRB B 501 ZN ZN B 601 1555 1555 2.60 SITE 1 AC1 4 GLU A 178 HIS A 242 HIS A 256 CRB A 500 SITE 1 AC2 4 GLU B 178 HIS B 242 HIS B 256 CRB B 501 SITE 1 AC3 28 ASP A 39 TYR A 41 VAL A 42 TYR A 45 SITE 2 AC3 28 GLY A 67 GLU A 68 LYS A 71 GLY A 99 SITE 3 AC3 28 GLY A 100 ALA A 101 ASP A 104 THR A 124 SITE 4 AC3 28 THR A 125 LEU A 127 ASP A 130 SER A 131 SITE 5 AC3 28 LYS A 136 LYS A 145 ASN A 146 PHE A 163 SITE 6 AC3 28 THR A 166 LEU A 167 GLN A 171 CRB A 500 SITE 7 AC3 28 HOH A 628 HOH A 637 HOH A 659 GLN B 286 SITE 1 AC4 28 GLN A 286 ASP B 39 TYR B 41 VAL B 42 SITE 2 AC4 28 TYR B 45 GLY B 67 GLU B 68 LYS B 71 SITE 3 AC4 28 GLY B 99 GLY B 100 ALA B 101 ASP B 104 SITE 4 AC4 28 THR B 124 THR B 125 LEU B 127 ASP B 130 SITE 5 AC4 28 SER B 131 LYS B 136 LYS B 145 ASN B 146 SITE 6 AC4 28 PHE B 163 THR B 166 LEU B 167 GLN B 171 SITE 7 AC4 28 CRB B 501 HOH B 627 HOH B 636 HOH B 658 SITE 1 AC5 17 ASP A 130 LYS A 136 ASN A 146 GLU A 178 SITE 2 AC5 17 LYS A 181 LYS A 221 ARG A 235 LEU A 238 SITE 3 AC5 17 ASN A 239 HIS A 242 HIS A 246 HIS A 256 SITE 4 AC5 17 LYS A 314 NAD A 400 ZN A 600 HOH A 628 SITE 5 AC5 17 ARG B 115 SITE 1 AC6 17 ARG A 115 ASP B 130 LYS B 136 ASN B 146 SITE 2 AC6 17 GLU B 178 LYS B 181 LYS B 221 ARG B 235 SITE 3 AC6 17 LEU B 238 ASN B 239 HIS B 242 HIS B 246 SITE 4 AC6 17 HIS B 256 LYS B 314 NAD B 401 ZN B 601 SITE 5 AC6 17 HOH B 627 CRYST1 55.100 55.100 232.319 90.00 90.00 90.00 P 43 8 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 0.018149 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018149 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004304 0.00000