HEADER LYASE 23-JAN-03 1NR5 TITLE CRYSTAL STRUCTURE OF 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX WITH TITLE 2 ZN2+, NAD 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, KEYWDS 2 CARBAPHOSPHONATE, CLOSED FORM, 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 13-JUL-11 1NR5 1 VERSN REVDAT 2 24-FEB-09 1NR5 1 VERSN REVDAT 1 18-MAR-03 1NR5 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. 2.10 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.22 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 2963347.690 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.8 REMARK 3 NUMBER OF REFLECTIONS : 48900 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) : 0.185 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2451 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.23 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 7467 REMARK 3 BIN R VALUE (WORKING SET) : 0.2980 REMARK 3 BIN FREE R VALUE : 0.3230 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 379 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.017 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5985 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 127 REMARK 3 SOLVENT ATOMS : 383 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.36000 REMARK 3 B22 (A**2) : 7.53000 REMARK 3 B33 (A**2) : -4.17000 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) : 0.24 REMARK 3 ESD FROM SIGMAA (A) : 0.33 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) : 0.30 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.33 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.30 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.93 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 : 0.33 REMARK 3 BSOL : 71.95 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 1NR5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-JAN-03. REMARK 100 THE RCSB ID CODE IS RCSB018135. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-OCT-99 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 8 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 : NULL 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 : 48900 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 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 (%) : 94.9 REMARK 200 DATA REDUNDANCY : 2.910 REMARK 200 R MERGE (I) : 0.10100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.9600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.61 REMARK 200 R MERGE FOR SHELL (I) : 0.41200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 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: PDB ENTRY 1DQS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULPHATE, PH 8, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 66.99500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.28000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 66.99500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.28000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 BIOLOGICAL ASSEMBLY IS A DIMER, EACH MONOMER IN THE REMARK 300 ASYMETRIC UNIT GENERATING ONE DIMER BY SYMETRY ACROSS A TWO FOLD REMARK 300 AXIS. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 7270 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -105.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 -133.99000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 86.56000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 CL CL B 604 LIES ON A SPECIAL POSITION. REMARK 375 CL CL A 603 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1686 LIES ON A SPECIAL POSITION. 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 PRO A 393 REMARK 465 MET B 1 REMARK 465 SER B 2 REMARK 465 ASN B 3 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 ALA A 392 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 ASP A 18 175.31 179.60 REMARK 500 TYR A 25 -52.54 -159.73 REMARK 500 ASP A 146 -70.26 -145.17 REMARK 500 ALA A 154 165.52 176.73 REMARK 500 ASN A 162 55.05 37.38 REMARK 500 SER A 202 -39.47 -131.20 REMARK 500 PHE A 232 41.73 -103.18 REMARK 500 ASP A 257 71.05 -163.74 REMARK 500 ALA A 339 104.56 -49.98 REMARK 500 THR A 377 43.75 -87.63 REMARK 500 TYR B 25 -51.33 -160.88 REMARK 500 ASP B 146 -68.31 -149.13 REMARK 500 ALA B 154 173.72 179.13 REMARK 500 ASN B 162 57.88 34.05 REMARK 500 PHE B 232 40.24 -102.12 REMARK 500 ASP B 257 67.83 -160.45 REMARK 500 GLU B 260 72.15 48.52 REMARK 500 THR B 338 30.64 -95.29 REMARK 500 LYS B 341 116.26 -169.53 REMARK 500 THR B 377 41.73 -91.07 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 B1619 DISTANCE = 5.26 ANGSTROMS REMARK 525 HOH B1670 DISTANCE = 6.36 ANGSTROMS REMARK 525 HOH B1676 DISTANCE = 6.30 ANGSTROMS REMARK 525 HOH B1678 DISTANCE = 5.58 ANGSTROMS REMARK 525 HOH B1683 DISTANCE = 5.17 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 GLU A 194 OE2 REMARK 620 2 HIS A 271 NE2 116.9 REMARK 620 3 CRB A1500 O4 90.9 91.8 REMARK 620 4 HIS A 287 NE2 97.2 97.4 163.4 REMARK 620 5 CRB A1500 O5 158.7 81.8 77.8 89.8 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 194 OE2 REMARK 620 2 HIS B 271 NE2 126.1 REMARK 620 3 CRB B1501 O4 87.8 95.4 REMARK 620 4 CRB B1501 O5 147.6 83.8 75.8 REMARK 620 5 HIS B 287 NE2 97.7 100.1 155.8 87.5 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 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 CO B 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD A 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CRB A 1500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CRB B 1501 REMARK 900 REMARK 900 RELATED ENTRIES 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 COFACTOR 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 AND REDUCED COFACTOR 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 AND REDUCED CO-FACTOR 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 CARBAPHOSPHONATE, CRYSTAL FORM REMARK 900 H, CLOSED FORM WITH CO-FACTOR ANALOGUE AND SUBSTRATE REMARK 900 ANALOGUE DBREF 1NR5 A 1 393 UNP P07547 ARO1_EMENI 1 393 DBREF 1NR5 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 ZN B 601 1 HET CO B 602 1 HET CL A 603 1 HET CL B 604 1 HET NAD A 400 44 HET NAD B 401 44 HET CRB A1500 17 HET CRB B1501 17 HETNAM ZN ZINC ION HETNAM CO COBALT (II) ION HETNAM CL CHLORIDE 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 5 CO CO 2+ FORMUL 6 CL 2(CL 1-) FORMUL 8 NAD 2(C21 H27 N7 O14 P2) FORMUL 10 CRB 2(C8 H15 O8 P) FORMUL 12 HOH *383(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 GLN A 99 1 15 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 THR A 235 ASP A 257 1 23 HELIX 13 13 GLY A 262 TRP A 269 5 8 HELIX 14 14 GLY A 270 THR A 282 1 13 HELIX 15 15 LEU A 286 LEU A 305 1 20 HELIX 16 16 LYS A 309 TYR A 323 1 15 HELIX 17 17 ASP A 331 THR A 338 1 8 HELIX 18 18 SER A 344 ALA A 353 1 10 HELIX 19 19 ALA A 383 ALA A 392 1 10 HELIX 20 20 GLY B 20 TYR B 25 1 6 HELIX 21 21 TYR B 25 CYS B 34 1 10 HELIX 22 22 THR B 45 ALA B 64 1 20 HELIX 23 23 GLY B 80 LYS B 84 5 5 HELIX 24 24 SER B 85 SER B 98 1 14 HELIX 25 25 GLY B 114 TYR B 128 1 15 HELIX 26 26 MET B 129 GLY B 131 5 3 HELIX 27 27 THR B 140 ASP B 146 1 7 HELIX 28 28 GLU B 178 LEU B 183 5 6 HELIX 29 29 PRO B 184 ILE B 201 1 18 HELIX 30 30 SER B 203 ARG B 223 1 21 HELIX 31 31 THR B 235 ASP B 257 1 23 HELIX 32 32 GLY B 262 TRP B 269 5 8 HELIX 33 33 GLY B 270 THR B 282 1 13 HELIX 34 34 LEU B 286 LEU B 305 1 20 HELIX 35 35 LYS B 309 TYR B 323 1 15 HELIX 36 36 ASP B 331 THR B 338 1 8 HELIX 37 37 SER B 344 ALA B 353 1 10 HELIX 38 38 ALA B 383 ALA B 392 1 10 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 175 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 LEU A 41 SHEET 1 B 2 LYS A 152 THR A 157 0 SHEET 2 B 2 GLY A 160 ILE A 167 -1 O ILE A 164 N ILE A 155 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 137 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 LEU B 41 SHEET 1 F 2 LYS B 152 THR B 157 0 SHEET 2 F 2 GLY B 160 ILE B 167 -1 O ILE B 164 N ILE B 155 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 ZN ZN A 600 OE2 GLU A 194 1555 1555 2.01 LINK ZN ZN A 600 NE2 HIS A 271 1555 1555 2.19 LINK ZN ZN A 600 O4 CRB A1500 1555 1555 2.14 LINK ZN ZN B 601 OE2 GLU B 194 1555 1555 2.01 LINK ZN ZN B 601 NE2 HIS B 271 1555 1555 2.08 LINK ZN ZN A 600 NE2 HIS A 287 1555 1555 2.25 LINK ZN ZN A 600 O5 CRB A1500 1555 1555 2.28 LINK ZN ZN B 601 O4 CRB B1501 1555 1555 2.38 LINK ZN ZN B 601 O5 CRB B1501 1555 1555 2.33 LINK ZN ZN B 601 NE2 HIS B 287 1555 1555 2.30 CISPEP 1 THR A 67 PRO A 68 0 -0.21 CISPEP 2 ASN A 100 PRO A 101 0 0.14 CISPEP 3 THR A 282 PRO A 283 0 -0.39 CISPEP 4 THR B 67 PRO B 68 0 0.00 CISPEP 5 ASN B 100 PRO B 101 0 0.41 CISPEP 6 THR B 282 PRO B 283 0 0.93 SITE 1 AC1 5 GLU A 194 HIS A 271 HIS A 287 NAD A 400 SITE 2 AC1 5 CRB A1500 SITE 1 AC2 5 GLU B 194 HIS B 271 HIS B 287 NAD B 401 SITE 2 AC2 5 CRB B1501 SITE 1 AC3 1 ARG B 303 SITE 1 AC4 2 LYS A 89 HOH A1622 SITE 1 AC5 2 LYS B 89 HOH B1608 SITE 1 AC6 31 ASP A 44 ASN A 46 ILE A 47 GLU A 81 SITE 2 AC6 31 LYS A 84 GLY A 114 GLY A 115 VAL A 116 SITE 3 AC6 31 ASP A 119 THR A 139 THR A 140 ASP A 146 SITE 4 AC6 31 SER A 147 LYS A 152 LYS A 161 PHE A 179 SITE 5 AC6 31 THR A 182 LEU A 183 GLU A 187 ASN A 190 SITE 6 AC6 31 LYS A 250 HIS A 287 ZN A 600 CRB A1500 SITE 7 AC6 31 HOH A1506 HOH A1514 HOH A1525 HOH A1532 SITE 8 AC6 31 HOH A1539 HOH A1545 HOH A1570 SITE 1 AC7 30 ASP B 44 ASN B 46 GLU B 81 LYS B 84 SITE 2 AC7 30 GLY B 114 GLY B 115 VAL B 116 ASP B 119 SITE 3 AC7 30 THR B 139 THR B 140 ASP B 146 SER B 147 SITE 4 AC7 30 LYS B 152 LYS B 161 PHE B 179 THR B 182 SITE 5 AC7 30 LEU B 183 GLU B 187 ASN B 190 GLU B 194 SITE 6 AC7 30 LYS B 250 HIS B 287 ZN B 601 CRB B1501 SITE 7 AC7 30 HOH B1503 HOH B1508 HOH B1552 HOH B1566 SITE 8 AC7 30 HOH B1573 HOH B1577 SITE 1 AC8 19 ARG A 130 ASP A 146 LYS A 152 ASN A 162 SITE 2 AC8 19 GLU A 194 LYS A 197 LYS A 250 ARG A 264 SITE 3 AC8 19 LEU A 267 ASN A 268 HIS A 271 HIS A 275 SITE 4 AC8 19 HIS A 287 LYS A 356 NAD A 400 ZN A 600 SITE 5 AC8 19 HOH A1522 HOH A1532 HOH A1534 SITE 1 AC9 19 ARG B 130 ASP B 146 LYS B 152 ASN B 162 SITE 2 AC9 19 GLU B 194 LYS B 197 LYS B 250 ARG B 264 SITE 3 AC9 19 LEU B 267 ASN B 268 HIS B 271 HIS B 275 SITE 4 AC9 19 HIS B 287 LYS B 356 NAD B 401 ZN B 601 SITE 5 AC9 19 HOH B1503 HOH B1505 HOH B1532 CRYST1 133.990 86.560 74.820 90.00 90.00 90.00 P 21 21 2 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 0.007463 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011553 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013365 0.00000