HEADER LYASE 25-AUG-04 1XAI TITLE CRYSTAL STRUCTURE OF STAPHLYOCOCCUS AUREUS 3-DEHYDROQUINATE TITLE 2 SYNTHASE (DHQS) IN COMPLEX WITH ZN2+, NAD+ AND TITLE 3 CARBAPHOSPHONATE 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, KEYWDS 2 SADHQS, 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 3 24-FEB-09 1XAI 1 VERSN REVDAT 2 22-MAR-05 1XAI 1 JRNL REVDAT 1 01-MAR-05 1XAI 0 JRNL AUTH C.E.NICHOLS,J.REN,K.LESLIE,B.DHALIWAL,M.LOCKYER, JRNL AUTH 2 I.CHARLES,A.R.HAWKINS,D.K.STAMMERS JRNL TITL COMPARISON OF LIGAND INDUCED CONFORMATIONAL JRNL TITL 2 CHANGES AND DOMAIN CLOSURE MECHANISMS, BETWEEN JRNL TITL 3 PROKARYOTIC AND EUKARYOTIC DEHYDROQUINATE JRNL TITL 4 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 1 REMARK 2 REMARK 2 RESOLUTION. 2.30 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.01 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 3263238.120 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 29303 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) : 0.211 REMARK 3 FREE R VALUE : 0.312 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2942 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 : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.34 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1291 REMARK 3 BIN R VALUE (WORKING SET) : 0.3680 REMARK 3 BIN FREE R VALUE : 0.4280 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 134 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.037 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5662 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 36 REMARK 3 SOLVENT ATOMS : 245 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 40.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 61.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 9.91000 REMARK 3 B22 (A**2) : 9.91000 REMARK 3 B33 (A**2) : -19.82000 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) : 0.53 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) : 0.47 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.56 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.30 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.80 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 : 0.34 REMARK 3 BSOL : 89.61 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 1XAI COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-NOV-04. REMARK 100 THE RCSB ID CODE IS RCSB030140. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-AUG-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9333 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29301 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 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 (%) : 97.9 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : 0.04400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.4600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.24700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.690 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: PDB ENTRY 1XAG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG3350, K2SO4, PH 7.5, VAPOR REMARK 280 DIFFUSION, 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 114.55550 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 171.83325 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 57.27775 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 PHE A 353 REMARK 465 LYS A 354 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 THR A 6 47.29 -94.78 REMARK 500 SER A 9 -168.90 -101.08 REMARK 500 ASN A 10 95.95 2.52 REMARK 500 TYR A 23 1.36 -59.60 REMARK 500 TYR A 27 -55.15 -120.30 REMARK 500 LEU A 28 -44.47 -28.18 REMARK 500 GLN A 30 8.82 -179.12 REMARK 500 PHE A 50 51.59 -114.51 REMARK 500 SER A 55 33.68 -70.44 REMARK 500 GLU A 68 -5.15 -50.53 REMARK 500 SER A 85 7.72 -57.55 REMARK 500 VAL A 88 -168.75 -68.50 REMARK 500 ASN A 91 54.63 -109.08 REMARK 500 VAL A 117 -163.98 -124.14 REMARK 500 ASP A 130 -67.30 -90.60 REMARK 500 LEU A 161 3.76 -68.16 REMARK 500 ASP A 228 62.67 -155.59 REMARK 500 GLN A 232 62.12 -100.91 REMARK 500 ARG A 235 -9.52 -57.01 REMARK 500 PRO A 255 151.15 -48.16 REMARK 500 LEU A 274 -82.08 -98.01 REMARK 500 LYS A 278 78.04 49.89 REMARK 500 PRO A 294 -80.18 -51.26 REMARK 500 LEU A 295 24.78 80.44 REMARK 500 LEU A 301 178.06 -59.32 REMARK 500 ASP A 302 100.80 -165.34 REMARK 500 ASP A 313 137.41 -37.61 REMARK 500 GLN A 328 140.29 -176.20 REMARK 500 PHE A 329 105.50 -46.12 REMARK 500 VAL A 337 63.79 -150.84 REMARK 500 ASP A 338 155.69 -36.74 REMARK 500 LEU A 340 -79.02 -48.42 REMARK 500 THR B 6 39.59 -91.63 REMARK 500 SER B 9 -165.46 -128.79 REMARK 500 ASN B 10 81.19 2.16 REMARK 500 TYR B 23 1.65 -58.85 REMARK 500 LEU B 28 -39.23 -30.71 REMARK 500 ASN B 29 77.99 -108.04 REMARK 500 GLN B 30 -22.44 -160.35 REMARK 500 LYS B 49 -36.88 -32.93 REMARK 500 PHE B 50 50.35 -116.58 REMARK 500 SER B 55 37.04 -67.33 REMARK 500 GLU B 68 -6.02 -50.86 REMARK 500 SER B 85 6.53 -57.31 REMARK 500 HIS B 87 59.77 39.43 REMARK 500 VAL B 88 -169.24 -68.51 REMARK 500 ASN B 91 55.08 -109.37 REMARK 500 VAL B 117 -164.68 -124.80 REMARK 500 ASP B 130 -67.14 -90.19 REMARK 500 LEU B 161 3.77 -67.61 REMARK 500 ASP B 228 63.16 -155.94 REMARK 500 PRO B 255 150.54 -40.18 REMARK 500 LEU B 274 -85.75 -96.01 REMARK 500 LYS B 278 73.68 52.05 REMARK 500 PRO B 294 -80.53 -50.79 REMARK 500 LEU B 295 23.60 80.86 REMARK 500 LEU B 301 177.19 -57.44 REMARK 500 ASP B 302 101.03 -164.20 REMARK 500 GLN B 328 140.73 -175.79 REMARK 500 PHE B 329 106.02 -46.48 REMARK 500 VAL B 337 64.90 -152.45 REMARK 500 ASP B 338 158.19 -40.48 REMARK 500 GLN B 339 -19.05 -43.34 REMARK 500 LEU B 340 -77.17 -51.72 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 634 DISTANCE = 6.07 ANGSTROMS REMARK 525 HOH A 677 DISTANCE = 5.66 ANGSTROMS REMARK 525 HOH A 678 DISTANCE = 5.77 ANGSTROMS REMARK 525 HOH B 679 DISTANCE = 5.10 ANGSTROMS REMARK 525 HOH A 679 DISTANCE = 5.65 ANGSTROMS REMARK 525 HOH A 680 DISTANCE = 5.29 ANGSTROMS REMARK 525 HOH B 713 DISTANCE = 6.40 ANGSTROMS REMARK 525 HOH A 713 DISTANCE = 5.31 ANGSTROMS 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 HIS A 256 NE2 REMARK 620 2 CRB A 500 O5 89.0 REMARK 620 3 GLU A 178 OE1 95.5 159.2 REMARK 620 4 HIS A 242 NE2 113.7 87.6 108.8 REMARK 620 5 CRB A 500 O4 151.5 74.5 92.6 89.1 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 HIS B 256 NE2 REMARK 620 2 HIS B 242 NE2 109.8 REMARK 620 3 CRB B 501 O4 148.0 93.0 REMARK 620 4 CRB B 501 O5 85.3 88.5 72.7 REMARK 620 5 GLU B 178 OE1 90.6 113.6 100.8 157.5 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 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 601 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CRB A 500 REMARK 800 SITE_IDENTIFIER: AC4 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 REMARK 900 COMPLEX WITH ZN2+, NAD+ AND CARBAPHOSPHONATE, CRYSTAL FORM REMARK 900 C, CLOSED FORM WITH COFACTOR AND SUBSTRATE ANALOGUE REMARK 900 RELATED ID: 1NRX RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF 3-DEHYDROQUINATE SYNTHASE (DHQS) IN REMARK 900 COMPLEX WITH ZN2+ AND NAD+, CRYSTAL FORM F, OPEN FORM WITH REMARK 900 COFACTOR REMARK 900 RELATED ID: 1NVE RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF 3-DEHYDROQUINATE SYNTHASE (DHQS) IN REMARK 900 COMPLEX WITH ZN2+ AND NAD+, CRYSTAL FORM E, OPEN FORM WITH REMARK 900 CO-FACTOR REMARK 900 RELATED ID: 1NVD RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF 3-DEHYDROQUINATE SYNTHASE (DHQS) IN REMARK 900 COMPLEX WITH ZN2+ AND CARBAPHOSPHONATE, CRYSTAL FORM B, REMARK 900 CLOSED FORM WITH SUBSTRATE ANALOGUE REMARK 900 RELATED ID: 1NVB RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF 3-DEHYDROQUINATE SYNTHASE (DHQS) IN REMARK 900 COMPLEX WITH ZN2+ AND CARBAPHOSPHONATE, CRYSTAL FORM C, REMARK 900 CLOSED FORM WITH SUBSTRATE ANALOGUE REMARK 900 RELATED ID: 1NUA RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF 3-DEHYDROQUINATE SYNTHASE (DHQS) IN REMARK 900 COMPLEX 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 REMARK 900 COMPLEX WITH ZN2+ AND ADP, CRYSTAL FORM D, OPEN FORM WITH REMARK 900 CO-FACTOR ANALOGUE REMARK 900 RELATED ID: 1NVF RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF 3-DEHYDROQUINATE SYNTHASE (DHQS) IN REMARK 900 COMPLEX WITH ZN2+, ADP AND CBP, CRYSTAL FORM H, CLOSED FORM REMARK 900 WITH CO-FACTOR 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: 1XAJ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF STAPHLYOCOCCUS AUREUS 3-DEHYDROQUINATE REMARK 900 SYNTHASE (DHQS) IN COMPLEX WITH ZN2+, NAD+ AND REMARK 900 CARBAPHOSPHONATE REMARK 900 RELATED ID: 1XAL RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF STAPHLYOCOCCUS AUREUS 3-DEHYDROQUINATE REMARK 900 SYNTHASE (DHQS) IN COMPLEX WITH ZN2+, NAD+ AND REMARK 900 CARBAPHOSPHONATE (SOAK) REMARK 999 REMARK 999 SEQUENCE REMARK 999 THESE CONFLICTS REFLECT CLONAL VARIATION FROM DATABASE SEQUENCE. DBREF 1XAI A 1 354 UNP Q6GGU4 AROB_STAAR 1 354 DBREF 1XAI B 1 354 UNP Q6GGU4 AROB_STAAR 1 354 SEQADV 1XAI LYS A 22 UNP Q6GGU4 ASP 22 SEE REMARK 999 SEQADV 1XAI TYR A 23 UNP Q6GGU4 HIS 23 SEE REMARK 999 SEQADV 1XAI GLY A 25 UNP Q6GGU4 SER 25 SEE REMARK 999 SEQADV 1XAI LEU A 28 UNP Q6GGU4 ILE 28 SEE REMARK 999 SEQADV 1XAI ASN A 29 UNP Q6GGU4 ASP 29 SEE REMARK 999 SEQADV 1XAI LEU A 36 UNP Q6GGU4 ILE 36 SEE REMARK 999 SEQADV 1XAI TYR A 41 UNP Q6GGU4 HIS 41 SEE REMARK 999 SEQADV 1XAI ASN A 48 UNP Q6GGU4 ASP 48 SEE REMARK 999 SEQADV 1XAI VAL A 109 UNP Q6GGU4 ILE 109 SEE REMARK 999 SEQADV 1XAI LYS A 170 UNP Q6GGU4 GLU 170 SEE REMARK 999 SEQADV 1XAI VAL A 226 UNP Q6GGU4 ILE 226 SEE REMARK 999 SEQADV 1XAI SER A 282 UNP Q6GGU4 ASN 282 SEE REMARK 999 SEQADV 1XAI MET A 326 UNP Q6GGU4 ILE 326 SEE REMARK 999 SEQADV 1XAI LYS B 22 UNP Q6GGU4 ASP 22 SEE REMARK 999 SEQADV 1XAI TYR B 23 UNP Q6GGU4 HIS 23 SEE REMARK 999 SEQADV 1XAI GLY B 25 UNP Q6GGU4 SER 25 SEE REMARK 999 SEQADV 1XAI LEU B 28 UNP Q6GGU4 ILE 28 SEE REMARK 999 SEQADV 1XAI ASN B 29 UNP Q6GGU4 ASP 29 SEE REMARK 999 SEQADV 1XAI LEU B 36 UNP Q6GGU4 ILE 36 SEE REMARK 999 SEQADV 1XAI TYR B 41 UNP Q6GGU4 HIS 41 SEE REMARK 999 SEQADV 1XAI ASN B 48 UNP Q6GGU4 ASP 48 SEE REMARK 999 SEQADV 1XAI VAL B 109 UNP Q6GGU4 ILE 109 SEE REMARK 999 SEQADV 1XAI LYS B 170 UNP Q6GGU4 GLU 170 SEE REMARK 999 SEQADV 1XAI VAL B 226 UNP Q6GGU4 ILE 226 SEE REMARK 999 SEQADV 1XAI SER B 282 UNP Q6GGU4 ASN 282 SEE REMARK 999 SEQADV 1XAI 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 ZN B 601 1 HET CRB A 500 17 HET CRB B 501 17 HETNAM ZN ZINC ION HETNAM CRB [1R-(1ALPHA,3BETA,4ALPHA,5BETA)]-5-(PHOSPHONOMETHYL)- HETNAM 2 CRB 1,3,4-TRIHYDROXYCYCLOHEXANE-1-CARBOXYLIC ACID HETSYN CRB CARBAPHOSPHONATE FORMUL 3 ZN 2(ZN 2+) FORMUL 5 CRB 2(C8 H15 O8 P) FORMUL 7 HOH *245(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 TYR A 41 PHE A 46 1 6 HELIX 4 4 ALA A 66 THR A 70 5 5 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 GLY A 187 1 20 HELIX 11 11 GLY A 187 PHE A 198 1 12 HELIX 12 12 ASP A 200 LEU A 207 1 8 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 LYS A 253 1 13 HELIX 16 16 PRO A 255 LEU A 274 1 20 HELIX 17 17 ASP A 280 GLY A 292 1 13 HELIX 18 18 ASP A 296 LEU A 301 5 6 HELIX 19 19 ASP A 302 MET A 310 1 9 HELIX 20 20 ASP A 338 LEU A 349 1 12 HELIX 21 21 GLY B 19 TYR B 23 5 5 HELIX 22 22 ILE B 24 ASN B 29 1 6 HELIX 23 23 TYR B 41 PHE B 46 1 6 HELIX 24 24 ALA B 66 THR B 70 5 5 HELIX 25 25 THR B 72 SER B 85 1 14 HELIX 26 26 GLY B 99 LEU B 113 1 15 HELIX 27 27 LEU B 114 GLY B 116 5 3 HELIX 28 28 LEU B 127 SER B 132 1 6 HELIX 29 29 ASP B 162 LEU B 167 5 6 HELIX 30 30 PRO B 168 GLY B 187 1 20 HELIX 31 31 GLY B 187 PHE B 198 1 12 HELIX 32 32 ASP B 200 LEU B 207 1 8 HELIX 33 33 GLY B 209 ASP B 228 1 20 HELIX 34 34 GLY B 233 LEU B 240 5 8 HELIX 35 35 GLY B 241 LYS B 253 1 13 HELIX 36 36 PRO B 255 LEU B 274 1 20 HELIX 37 37 ASP B 280 GLY B 292 1 13 HELIX 38 38 ASP B 296 LEU B 301 5 6 HELIX 39 39 ASP B 302 MET B 310 1 9 HELIX 40 40 ASP B 338 LEU B 349 1 12 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 VAL A 157 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 THR A 92 GLY A 98 1 N ILE A 94 O HIS A 118 SHEET 6 A 7 GLN A 33 ASP A 39 1 N PHE A 35 O ALA A 93 SHEET 7 A 7 VAL A 59 ILE A 64 1 O VAL A 62 N LEU A 36 SHEET 1 B 2 LYS A 136 ILE A 139 0 SHEET 2 B 2 ILE A 148 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 ASP A 331 N GLN A 328 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 VAL B 157 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 THR B 92 GLY B 98 1 N ILE B 94 O HIS B 118 SHEET 6 D 7 GLN B 33 ASP B 39 1 N PHE B 35 O ALA B 93 SHEET 7 D 7 VAL B 59 ILE B 64 1 O VAL B 62 N LEU B 36 SHEET 1 E 2 LYS B 136 ILE B 139 0 SHEET 2 E 2 ILE B 148 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 ASP B 331 N GLN B 328 LINK ZN ZN A 600 NE2 HIS A 256 1555 1555 2.23 LINK ZN ZN A 600 O5 CRB A 500 1555 1555 2.42 LINK ZN ZN A 600 OE1 GLU A 178 1555 1555 2.20 LINK ZN ZN A 600 NE2 HIS A 242 1555 1555 2.23 LINK ZN ZN A 600 O4 CRB A 500 1555 1555 2.28 LINK ZN ZN B 601 NE2 HIS B 256 1555 1555 2.25 LINK ZN ZN B 601 NE2 HIS B 242 1555 1555 2.15 LINK ZN ZN B 601 O4 CRB B 501 1555 1555 2.23 LINK ZN ZN B 601 O5 CRB B 501 1555 1555 2.49 LINK ZN ZN B 601 OE1 GLU B 178 1555 1555 2.30 SITE 1 AC1 4 GLU A 178 HIS A 242 HIS A 256 CRB A 500 SITE 1 AC2 5 ASP B 130 GLU B 178 HIS B 242 HIS B 256 SITE 2 AC2 5 CRB B 501 SITE 1 AC3 15 ASP A 130 LYS A 136 ASN A 146 GLU A 178 SITE 2 AC3 15 LYS A 181 LYS A 221 ARG A 235 LEU A 238 SITE 3 AC3 15 ASN A 239 HIS A 242 HIS A 246 HIS A 256 SITE 4 AC3 15 LYS A 314 ZN A 600 ARG B 115 SITE 1 AC4 15 ARG A 115 ASP B 130 LYS B 136 ASN B 146 SITE 2 AC4 15 GLU B 178 LYS B 181 LYS B 221 ARG B 235 SITE 3 AC4 15 LEU B 238 ASN B 239 HIS B 242 HIS B 246 SITE 4 AC4 15 HIS B 256 LYS B 314 ZN B 601 CRYST1 54.898 54.898 229.111 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 0.018216 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018216 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004365 0.00000 MASTER 424 0 4 40 22 0 11 6 0 0 0 56 END