PDB Short entry for 1NVD HEADER LYASE 03-FEB-03 1NVD TITLE CRYSTAL STRUCTURE OF 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX WITH TITLE 2 ZN2+ AND CARBAPHOSPHONATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3-DEHYDROQUINATE SYNTHASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DHQS; COMPND 5 EC: 4.2.3.4; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: EMERICELLA NIDULANS; SOURCE 3 ORGANISM_TAXID: 162425; SOURCE 4 GENE: AROMA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: GLW38 (AROB-); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PTRC99A; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PTR51 KEYWDS SHIKIMATE PATHWAY, AROMATIC AMINO ACID BIOSYNTHESIS, DHQS, OPEN FORM, KEYWDS 2 FORM B, DOMAIN MOVEMENT, CYCLASE, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR C.E.NICHOLS,J.REN,H.K.LAMB,A.R.HAWKINS,D.K.STAMMERS REVDAT 3 25-OCT-23 1NVD 1 REMARK LINK REVDAT 2 24-FEB-09 1NVD 1 VERSN REVDAT 1 18-MAR-03 1NVD 0 JRNL AUTH C.E.NICHOLS,J.REN,H.K.LAMB,A.R.HAWKINS,D.K.STAMMERS JRNL TITL LIGAND-INDUCED CONFORMATIONAL CHANGES AND A MECHANISM FOR JRNL TITL 2 DOMAIN CLOSURE IN ASPERGILLUS NIDULANS DEHYDROQUINATE JRNL TITL 3 SYNTHASE JRNL REF J.MOL.BIOL. V. 327 129 2003 JRNL REFN ISSN 0022-2836 JRNL PMID 12614613 JRNL DOI 10.1016/S0022-2836(03)00086-X REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.E.NICHOLS,J.REN,H.LAMB,F.HALDANE,A.R.HAWKINS,D.K.STAMMERS REMARK 1 TITL IDENTIFICATION OF MANY CRYSTAL FORMS OF ASPERGILLUS NIDULANS REMARK 1 TITL 2 DEHYDROQUINATE SYNTHASE REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 57 306 2001 REMARK 1 REFN ISSN 0907-4449 REMARK 1 DOI 10.1107/S0907444900019429 REMARK 2 REMARK 2 RESOLUTION. 2.51 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) : 2.51 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1893027.810 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.4 REMARK 3 NUMBER OF REFLECTIONS : 29338 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) : 0.196 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 2929 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 : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.51 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.60 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2736 REMARK 3 BIN R VALUE (WORKING SET) : 0.3050 REMARK 3 BIN FREE R VALUE : 0.4070 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 260 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.025 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5871 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 37 REMARK 3 SOLVENT ATOMS : 694 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 48.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.09000 REMARK 3 B22 (A**2) : -3.39000 REMARK 3 B33 (A**2) : 3.30000 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) : 0.27 REMARK 3 ESD FROM SIGMAA (A) : 0.26 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) : 0.40 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.40 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) : 21.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.800 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) : 3.850 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 5.740 ; 6.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 8.650 ; 6.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 10.770; 12.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.33 REMARK 3 BSOL : 68.84 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.PARAM 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 1NVD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-FEB-03. REMARK 100 THE DEPOSITION ID IS D_1000018244. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAR-00 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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 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 : 29338 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.510 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 (%) : 94.0 REMARK 200 DATA REDUNDANCY : 2.980 REMARK 200 R MERGE (I) : 0.04400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 29.7900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.51 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.79 REMARK 200 R MERGE FOR SHELL (I) : 0.09800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 13.30 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: 1NR5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG3350, HEPES, ETHYLENE GLYCOL, PH REMARK 280 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K 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 32.01500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 98.81500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.01500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 98.81500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.01500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.01500 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 300 REMARK: THE CRYSTALLOGRAPHIC DIMER IS EQUIVALENMT TO THE BIOLOGICAL REMARK 300 DIMER 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 REMARK 350 TOTAL BURIED SURFACE AREA: 4890 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -93.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 MET A 1 REMARK 465 SER A 2 REMARK 465 ASN A 3 REMARK 465 THR A 226 REMARK 465 PRO A 227 REMARK 465 GLY A 228 REMARK 465 GLU A 229 REMARK 465 HIS A 230 REMARK 465 MET B 1 REMARK 465 SER B 2 REMARK 465 ASN B 3 REMARK 465 ARG B 223 REMARK 465 GLU B 224 REMARK 465 VAL B 225 REMARK 465 THR B 226 REMARK 465 PRO B 227 REMARK 465 GLY B 228 REMARK 465 GLU B 229 REMARK 465 HIS B 230 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 ARG A 77 CG CD NE CZ NH1 NH2 REMARK 470 VAL A 225 O REMARK 470 ARG B 77 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 222 O 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 25 -43.29 -144.55 REMARK 500 ASP A 146 -75.44 -151.70 REMARK 500 ALA A 154 168.95 176.82 REMARK 500 SER A 202 -54.30 -120.98 REMARK 500 GLU A 233 -105.63 -19.76 REMARK 500 ASP A 257 60.31 -156.87 REMARK 500 LYS A 341 124.12 -32.81 REMARK 500 THR A 377 37.85 -98.56 REMARK 500 TYR B 25 -43.66 -142.86 REMARK 500 ASP B 146 -74.02 -150.05 REMARK 500 ALA B 154 167.52 175.69 REMARK 500 SER B 202 -53.69 -121.22 REMARK 500 GLU B 233 -99.48 -25.84 REMARK 500 ASP B 331 115.65 -15.54 REMARK 500 ALA B 339 -49.49 -26.94 REMARK 500 THR B 377 39.10 -97.90 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 194 OE2 REMARK 620 2 HIS A 271 NE2 99.3 REMARK 620 3 HIS A 287 NE2 98.4 102.7 REMARK 620 4 CRB A 500 O4 102.5 84.0 156.8 REMARK 620 5 CRB A 500 O5 170.9 81.8 90.2 68.5 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 194 OE2 REMARK 620 2 HIS B 271 NE2 96.8 REMARK 620 3 HIS B 287 NE2 94.3 107.5 REMARK 620 4 CRB B 501 O4 96.4 80.3 165.9 REMARK 620 5 CRB B 501 O5 163.1 93.1 95.7 71.7 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 B 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 600 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CRB A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 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 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 COFACTOR 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 AND REDUCED CO-FACTOR 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 CARBAPHOSPHONATE, CRYSTAL FORM H, CLOSED FORM REMARK 900 WITH CO-FACTOR ANALOGUE AND SUBSTRATE ANALOGUE DBREF 1NVD A 1 393 UNP P07547 ARO1_EMENI 1 393 DBREF 1NVD B 1 393 UNP P07547 ARO1_EMENI 1 393 SEQRES 1 A 393 MET SER ASN PRO THR LYS ILE SER ILE LEU GLY ARG GLU SEQRES 2 A 393 SER ILE ILE ALA ASP PHE GLY LEU TRP ARG ASN TYR VAL SEQRES 3 A 393 ALA LYS ASP LEU ILE SER ASP CYS SER SER THR THR TYR SEQRES 4 A 393 VAL LEU VAL THR ASP THR ASN ILE GLY SER ILE TYR THR SEQRES 5 A 393 PRO SER PHE GLU GLU ALA PHE ARG LYS ARG ALA ALA GLU SEQRES 6 A 393 ILE THR PRO SER PRO ARG LEU LEU ILE TYR ASN ARG PRO SEQRES 7 A 393 PRO GLY GLU VAL SER LYS SER ARG GLN THR LYS ALA ASP SEQRES 8 A 393 ILE GLU ASP TRP MET LEU SER GLN ASN PRO PRO CYS GLY SEQRES 9 A 393 ARG ASP THR VAL VAL ILE ALA LEU GLY GLY GLY VAL ILE SEQRES 10 A 393 GLY ASP LEU THR GLY PHE VAL ALA SER THR TYR MET ARG SEQRES 11 A 393 GLY VAL ARG TYR VAL GLN VAL PRO THR THR LEU LEU ALA SEQRES 12 A 393 MET VAL ASP SER SER ILE GLY GLY LYS THR ALA ILE ASP SEQRES 13 A 393 THR PRO LEU GLY LYS ASN LEU ILE GLY ALA ILE TRP GLN SEQRES 14 A 393 PRO THR LYS ILE TYR ILE ASP LEU GLU PHE LEU GLU THR SEQRES 15 A 393 LEU PRO VAL ARG GLU PHE ILE ASN GLY MET ALA GLU VAL SEQRES 16 A 393 ILE LYS THR ALA ALA ILE SER SER GLU GLU GLU PHE THR SEQRES 17 A 393 ALA LEU GLU GLU ASN ALA GLU THR ILE LEU LYS ALA VAL SEQRES 18 A 393 ARG ARG GLU VAL THR PRO GLY GLU HIS ARG PHE GLU GLY SEQRES 19 A 393 THR GLU GLU ILE LEU LYS ALA ARG ILE LEU ALA SER ALA SEQRES 20 A 393 ARG HIS LYS ALA TYR VAL VAL SER ALA ASP GLU ARG GLU SEQRES 21 A 393 GLY GLY LEU ARG ASN LEU LEU ASN TRP GLY HIS SER ILE SEQRES 22 A 393 GLY HIS ALA ILE GLU ALA ILE LEU THR PRO GLN ILE LEU SEQRES 23 A 393 HIS GLY GLU CYS VAL ALA ILE GLY MET VAL LYS GLU ALA SEQRES 24 A 393 GLU LEU ALA ARG HIS LEU GLY ILE LEU LYS GLY VAL ALA SEQRES 25 A 393 VAL SER ARG ILE VAL LYS CYS LEU ALA ALA TYR GLY LEU SEQRES 26 A 393 PRO THR SER LEU LYS ASP ALA ARG ILE ARG LYS LEU THR SEQRES 27 A 393 ALA GLY LYS HIS CYS SER VAL ASP GLN LEU MET PHE ASN SEQRES 28 A 393 MET ALA LEU ASP LYS LYS ASN ASP GLY PRO LYS LYS LYS SEQRES 29 A 393 ILE VAL LEU LEU SER ALA ILE GLY THR PRO TYR GLU THR SEQRES 30 A 393 ARG ALA SER VAL VAL ALA ASN GLU ASP ILE ARG VAL VAL SEQRES 31 A 393 LEU ALA PRO SEQRES 1 B 393 MET SER ASN PRO THR LYS ILE SER ILE LEU GLY ARG GLU SEQRES 2 B 393 SER ILE ILE ALA ASP PHE GLY LEU TRP ARG ASN TYR VAL SEQRES 3 B 393 ALA LYS ASP LEU ILE SER ASP CYS SER SER THR THR TYR SEQRES 4 B 393 VAL LEU VAL THR ASP THR ASN ILE GLY SER ILE TYR THR SEQRES 5 B 393 PRO SER PHE GLU GLU ALA PHE ARG LYS ARG ALA ALA GLU SEQRES 6 B 393 ILE THR PRO SER PRO ARG LEU LEU ILE TYR ASN ARG PRO SEQRES 7 B 393 PRO GLY GLU VAL SER LYS SER ARG GLN THR LYS ALA ASP SEQRES 8 B 393 ILE GLU ASP TRP MET LEU SER GLN ASN PRO PRO CYS GLY SEQRES 9 B 393 ARG ASP THR VAL VAL ILE ALA LEU GLY GLY GLY VAL ILE SEQRES 10 B 393 GLY ASP LEU THR GLY PHE VAL ALA SER THR TYR MET ARG SEQRES 11 B 393 GLY VAL ARG TYR VAL GLN VAL PRO THR THR LEU LEU ALA SEQRES 12 B 393 MET VAL ASP SER SER ILE GLY GLY LYS THR ALA ILE ASP SEQRES 13 B 393 THR PRO LEU GLY LYS ASN LEU ILE GLY ALA ILE TRP GLN SEQRES 14 B 393 PRO THR LYS ILE TYR ILE ASP LEU GLU PHE LEU GLU THR SEQRES 15 B 393 LEU PRO VAL ARG GLU PHE ILE ASN GLY MET ALA GLU VAL SEQRES 16 B 393 ILE LYS THR ALA ALA ILE SER SER GLU GLU GLU PHE THR SEQRES 17 B 393 ALA LEU GLU GLU ASN ALA GLU THR ILE LEU LYS ALA VAL SEQRES 18 B 393 ARG ARG GLU VAL THR PRO GLY GLU HIS ARG PHE GLU GLY SEQRES 19 B 393 THR GLU GLU ILE LEU LYS ALA ARG ILE LEU ALA SER ALA SEQRES 20 B 393 ARG HIS LYS ALA TYR VAL VAL SER ALA ASP GLU ARG GLU SEQRES 21 B 393 GLY GLY LEU ARG ASN LEU LEU ASN TRP GLY HIS SER ILE SEQRES 22 B 393 GLY HIS ALA ILE GLU ALA ILE LEU THR PRO GLN ILE LEU SEQRES 23 B 393 HIS GLY GLU CYS VAL ALA ILE GLY MET VAL LYS GLU ALA SEQRES 24 B 393 GLU LEU ALA ARG HIS LEU GLY ILE LEU LYS GLY VAL ALA SEQRES 25 B 393 VAL SER ARG ILE VAL LYS CYS LEU ALA ALA TYR GLY LEU SEQRES 26 B 393 PRO THR SER LEU LYS ASP ALA ARG ILE ARG LYS LEU THR SEQRES 27 B 393 ALA GLY LYS HIS CYS SER VAL ASP GLN LEU MET PHE ASN SEQRES 28 B 393 MET ALA LEU ASP LYS LYS ASN ASP GLY PRO LYS LYS LYS SEQRES 29 B 393 ILE VAL LEU LEU SER ALA ILE GLY THR PRO TYR GLU THR SEQRES 30 B 393 ARG ALA SER VAL VAL ALA ASN GLU ASP ILE ARG VAL VAL SEQRES 31 B 393 LEU ALA PRO HET ZN A 600 1 HET CL A 602 1 HET CRB A 500 17 HET ZN B 601 1 HET CRB B 501 17 HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION 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 CL CL 1- FORMUL 5 CRB 2(C8 H15 O8 P) FORMUL 8 HOH *694(H2 O) HELIX 1 1 GLY A 20 TYR A 25 1 6 HELIX 2 2 TYR A 25 CYS A 34 1 10 HELIX 3 3 THR A 45 ALA A 64 1 20 HELIX 4 4 GLY A 80 LYS A 84 5 5 HELIX 5 5 SER A 85 SER A 98 1 14 HELIX 6 6 GLY A 114 TYR A 128 1 15 HELIX 7 7 MET A 129 GLY A 131 5 3 HELIX 8 8 THR A 140 ASP A 146 1 7 HELIX 9 9 GLU A 178 LEU A 183 5 6 HELIX 10 10 PRO A 184 ILE A 201 1 18 HELIX 11 11 SER A 203 ARG A 223 1 21 HELIX 12 12 PHE A 232 GLY A 234 5 3 HELIX 13 13 THR A 235 ASP A 257 1 23 HELIX 14 14 GLY A 262 TRP A 269 5 8 HELIX 15 15 GLY A 270 THR A 282 1 13 HELIX 16 16 LEU A 286 LEU A 305 1 20 HELIX 17 17 LYS A 309 TYR A 323 1 15 HELIX 18 18 ASP A 331 ALA A 339 1 9 HELIX 19 19 SER A 344 ALA A 353 1 10 HELIX 20 20 ALA A 383 ALA A 392 1 10 HELIX 21 21 GLY B 20 TYR B 25 1 6 HELIX 22 22 TYR B 25 CYS B 34 1 10 HELIX 23 23 THR B 45 ALA B 64 1 20 HELIX 24 24 GLY B 80 LYS B 84 5 5 HELIX 25 25 SER B 85 GLN B 99 1 15 HELIX 26 26 GLY B 114 TYR B 128 1 15 HELIX 27 27 MET B 129 GLY B 131 5 3 HELIX 28 28 THR B 140 ASP B 146 1 7 HELIX 29 29 GLU B 178 LEU B 183 5 6 HELIX 30 30 PRO B 184 ILE B 201 1 18 HELIX 31 31 SER B 203 ARG B 222 1 20 HELIX 32 32 PHE B 232 GLY B 234 5 3 HELIX 33 33 THR B 235 ASP B 257 1 23 HELIX 34 34 GLY B 262 TRP B 269 5 8 HELIX 35 35 GLY B 270 THR B 282 1 13 HELIX 36 36 LEU B 286 LEU B 305 1 20 HELIX 37 37 LYS B 309 TYR B 323 1 15 HELIX 38 38 ASP B 331 THR B 338 1 8 HELIX 39 39 SER B 344 ALA B 353 1 10 HELIX 40 40 ALA B 383 LEU B 391 1 9 SHEET 1 A 7 THR A 5 ILE A 9 0 SHEET 2 A 7 ARG A 12 ASP A 18 -1 O ARG A 12 N ILE A 9 SHEET 3 A 7 LYS A 172 ASP A 176 1 O ILE A 173 N ILE A 16 SHEET 4 A 7 ARG A 133 PRO A 138 1 N GLN A 136 O TYR A 174 SHEET 5 A 7 VAL A 108 GLY A 113 1 N ALA A 111 O VAL A 135 SHEET 6 A 7 THR A 38 ASP A 44 1 N VAL A 40 O ILE A 110 SHEET 7 A 7 ARG A 71 ARG A 77 1 O LEU A 73 N TYR A 39 SHEET 1 B 2 LYS A 152 THR A 157 0 SHEET 2 B 2 GLY A 160 ILE A 167 -1 O GLY A 160 N THR A 157 SHEET 1 C 2 LYS A 364 ILE A 365 0 SHEET 2 C 2 SER A 380 VAL A 381 -1 O SER A 380 N ILE A 365 SHEET 1 D 2 LEU A 368 ALA A 370 0 SHEET 2 D 2 THR A 373 PRO A 374 -1 O THR A 373 N ALA A 370 SHEET 1 E 7 THR B 5 ILE B 9 0 SHEET 2 E 7 ARG B 12 ASP B 18 -1 O ALA B 17 N THR B 5 SHEET 3 E 7 LYS B 172 ASP B 176 1 O ILE B 175 N ILE B 16 SHEET 4 E 7 ARG B 133 PRO B 138 1 N GLN B 136 O TYR B 174 SHEET 5 E 7 VAL B 108 GLY B 113 1 N ALA B 111 O VAL B 135 SHEET 6 E 7 THR B 38 ASP B 44 1 N VAL B 40 O ILE B 110 SHEET 7 E 7 ARG B 71 ARG B 77 1 O LEU B 73 N TYR B 39 SHEET 1 F 2 LYS B 152 THR B 157 0 SHEET 2 F 2 GLY B 160 ILE B 167 -1 O GLY B 160 N THR B 157 SHEET 1 G 2 LYS B 364 ILE B 365 0 SHEET 2 G 2 SER B 380 VAL B 381 -1 O SER B 380 N ILE B 365 SHEET 1 H 2 LEU B 368 ALA B 370 0 SHEET 2 H 2 THR B 373 PRO B 374 -1 O THR B 373 N ALA B 370 LINK OE2 GLU A 194 ZN ZN A 600 1555 1555 2.25 LINK NE2 HIS A 271 ZN ZN A 600 1555 1555 2.30 LINK NE2 HIS A 287 ZN ZN A 600 1555 1555 2.25 LINK O4 CRB A 500 ZN ZN A 600 1555 1555 2.50 LINK O5 CRB A 500 ZN ZN A 600 1555 1555 2.46 LINK OE2 GLU B 194 ZN ZN B 601 1555 1555 2.41 LINK NE2 HIS B 271 ZN ZN B 601 1555 1555 2.23 LINK NE2 HIS B 287 ZN ZN B 601 1555 1555 2.18 LINK O4 CRB B 501 ZN ZN B 601 1555 1555 2.46 LINK O5 CRB B 501 ZN ZN B 601 1555 1555 2.26 CISPEP 1 THR A 67 PRO A 68 0 0.31 CISPEP 2 ASN A 100 PRO A 101 0 0.10 CISPEP 3 THR A 282 PRO A 283 0 0.06 CISPEP 4 THR B 67 PRO B 68 0 0.14 CISPEP 5 ASN B 100 PRO B 101 0 0.15 CISPEP 6 THR B 282 PRO B 283 0 0.23 SITE 1 AC1 4 GLU B 194 HIS B 271 HIS B 287 CRB B 501 SITE 1 AC2 4 GLU A 194 HIS A 271 HIS A 287 CRB A 500 SITE 1 AC3 3 LYS A 89 HOH A 616 LYS B 89 SITE 1 AC4 17 ASP A 146 LYS A 152 ASN A 162 GLU A 194 SITE 2 AC4 17 LYS A 197 LYS A 250 ARG A 264 LEU A 267 SITE 3 AC4 17 ASN A 268 HIS A 271 HIS A 275 HIS A 287 SITE 4 AC4 17 LYS A 356 ZN A 600 HOH A 612 HOH A 621 SITE 5 AC4 17 ARG B 130 SITE 1 AC5 18 ARG A 130 ASP B 146 LYS B 152 ASN B 162 SITE 2 AC5 18 GLU B 194 LYS B 197 LYS B 250 ARG B 264 SITE 3 AC5 18 LEU B 267 ASN B 268 HIS B 271 HIS B 275 SITE 4 AC5 18 HIS B 287 LYS B 356 ZN B 601 HOH B 614 SITE 5 AC5 18 HOH B 617 HOH B 864 CRYST1 64.030 70.030 197.630 90.00 90.00 90.00 P 21 21 21 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 0.015618 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014280 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005060 0.00000