PDB Short entry for 1L9W HEADER LYASE 26-MAR-02 1L9W TITLE CRYSTAL STRUCTURE OF 3-DEHYDROQUINASE FROM SALMONELLA TYPHI COMPLEXED TITLE 2 WITH REACTION PRODUCT COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3-DEHYDROQUINATE DEHYDRATASE AROD; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: 3-DEHYDROQUINASE; COMPND 5 EC: 4.2.1.10; COMPND 6 OTHER_DETAILS: THE PRODUCT 3-DEHYDROSHIKIMATE IS COVALENTLY ATTACHED COMPND 7 TO THE ACTIVE SITE LYS 170 BY BOROHYDRIDE REDUCTION OF THE IMINE COMPND 8 (SCHIFF BASE) SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SALMONELLA TYPHI; SOURCE 3 ORGANISM_TAXID: 601 KEYWDS TIM-BARREL, COMPLEX WITH PRODUCT, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR W.H.LEE,L.A.PERLES,R.A.P.NAGEM,A.K.SHRIVE,A.HAWKINS,L.SAWYER, AUTHOR 2 I.POLIKARPOV REVDAT 5 16-AUG-23 1L9W 1 REMARK LINK REVDAT 4 08-FEB-12 1L9W 1 REMARK SITE REVDAT 3 13-JUL-11 1L9W 1 VERSN REVDAT 2 24-FEB-09 1L9W 1 VERSN REVDAT 1 26-MAR-03 1L9W 0 JRNL AUTH W.H.LEE,L.A.PERLES,R.A.NAGEM,A.K.SHRIVE,A.HAWKINS,L.SAWYER, JRNL AUTH 2 I.POLIKARPOV JRNL TITL COMPARISON OF DIFFERENT CRYSTAL FORMS OF 3-DEHYDROQUINASE JRNL TITL 2 FROM SALMONELLA TYPHI AND ITS IMPLICATION FOR THE ENZYME JRNL TITL 3 ACTIVITY. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 58 798 2002 JRNL REFN ISSN 0907-4449 JRNL PMID 11976491 JRNL DOI 10.1107/S0907444902003918 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 49700 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 + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2485 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7736 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 44 REMARK 3 SOLVENT ATOMS : 207 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.018 ; NULL REMARK 3 ANGLE DISTANCE (A) : 2.400 ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL 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 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1L9W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-MAR-02. REMARK 100 THE DEPOSITION ID IS D_1000015778. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 277 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 3 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X31 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.928 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49700 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 10.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 76.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL 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) : 2.15 REMARK 200 COMPLETENESS FOR SHELL (%) : 70.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1QFE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, CITRATE-PHOSPHATE, PH 5.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 79.28000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 2920 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 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 350 REMARK 350 BIOMOLECULE: 2 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: 2950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18840 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NE2 GLN D 95 O HOH D 305 1.98 REMARK 500 O HOH C 314 O HOH C 323 2.05 REMARK 500 OE1 GLN C 176 O HOH C 341 2.09 REMARK 500 OE2 GLU D 86 O HOH D 311 2.12 REMARK 500 NE ARG D 38 O HOH D 342 2.13 REMARK 500 O HOH A 310 O HOH A 313 2.17 REMARK 500 NH2 ARG D 66 O HOH D 347 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH B 352 O HOH C 324 1655 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 25 CD - NE - CZ ANGL. DEV. = 23.0 DEGREES REMARK 500 ARG A 25 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 ARG A 25 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ASP A 26 CB - CG - OD1 ANGL. DEV. = -7.4 DEGREES REMARK 500 ASP A 26 CB - CG - OD2 ANGL. DEV. = 8.0 DEGREES REMARK 500 ARG A 38 NE - CZ - NH1 ANGL. DEV. = 5.2 DEGREES REMARK 500 ASP A 54 CB - CG - OD1 ANGL. DEV. = 8.6 DEGREES REMARK 500 ASP A 54 CB - CG - OD2 ANGL. DEV. = -15.9 DEGREES REMARK 500 SER A 60 N - CA - CB ANGL. DEV. = 9.6 DEGREES REMARK 500 ARG A 69 NE - CZ - NH2 ANGL. DEV. = -6.4 DEGREES REMARK 500 ASP A 70 CB - CG - OD1 ANGL. DEV. = -7.5 DEGREES REMARK 500 ASP A 70 CB - CG - OD2 ANGL. DEV. = 6.2 DEGREES REMARK 500 ASP A 74 CB - CG - OD1 ANGL. DEV. = 6.5 DEGREES REMARK 500 ARG A 102 NE - CZ - NH1 ANGL. DEV. = 8.1 DEGREES REMARK 500 ASP A 106 CB - CG - OD2 ANGL. DEV. = 7.4 DEGREES REMARK 500 LEU A 117 CB - CG - CD2 ANGL. DEV. = 10.9 DEGREES REMARK 500 TYR A 137 CB - CG - CD2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ASP A 144 CB - CG - OD2 ANGL. DEV. = -7.1 DEGREES REMARK 500 HIS A 146 CA - CB - CG ANGL. DEV. = -10.9 DEGREES REMARK 500 ARG A 157 NE - CZ - NH1 ANGL. DEV. = 5.9 DEGREES REMARK 500 ARG A 157 NE - CZ - NH2 ANGL. DEV. = -4.9 DEGREES REMARK 500 ASP A 167 CB - CG - OD2 ANGL. DEV. = 7.2 DEGREES REMARK 500 HIS A 179 CA - CB - CG ANGL. DEV. = -10.6 DEGREES REMARK 500 LEU A 189 CB - CG - CD2 ANGL. DEV. = 11.5 DEGREES REMARK 500 ARG A 198 NE - CZ - NH1 ANGL. DEV. = 8.7 DEGREES REMARK 500 ARG A 198 NE - CZ - NH2 ANGL. DEV. = -8.9 DEGREES REMARK 500 ARG A 243 NE - CZ - NH1 ANGL. DEV. = 6.2 DEGREES REMARK 500 ARG A 243 NE - CZ - NH2 ANGL. DEV. = -5.1 DEGREES REMARK 500 LEU A 249 CA - CB - CG ANGL. DEV. = 14.6 DEGREES REMARK 500 MET B 1 CA - CB - CG ANGL. DEV. = 10.4 DEGREES REMARK 500 GLU B 13 CA - CB - CG ANGL. DEV. = 13.3 DEGREES REMARK 500 ARG B 25 CD - NE - CZ ANGL. DEV. = 31.8 DEGREES REMARK 500 ARG B 25 NE - CZ - NH1 ANGL. DEV. = 6.1 DEGREES REMARK 500 ASP B 26 CB - CG - OD2 ANGL. DEV. = 14.4 DEGREES REMARK 500 ARG B 38 NE - CZ - NH1 ANGL. DEV. = -9.3 DEGREES REMARK 500 ARG B 38 NE - CZ - NH2 ANGL. DEV. = 6.1 DEGREES REMARK 500 ASP B 43 CB - CG - OD1 ANGL. DEV. = -6.4 DEGREES REMARK 500 LEU B 45 CD1 - CG - CD2 ANGL. DEV. = -19.1 DEGREES REMARK 500 MET B 53 CA - CB - CG ANGL. DEV. = 16.8 DEGREES REMARK 500 ASP B 54 CB - CG - OD1 ANGL. DEV. = 8.2 DEGREES REMARK 500 ARG B 66 NE - CZ - NH2 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG B 69 CD - NE - CZ ANGL. DEV. = 23.8 DEGREES REMARK 500 ARG B 69 NE - CZ - NH1 ANGL. DEV. = 8.2 DEGREES REMARK 500 ARG B 69 NE - CZ - NH2 ANGL. DEV. = -4.7 DEGREES REMARK 500 ASP B 74 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 PHE B 79 CB - CG - CD1 ANGL. DEV. = -5.4 DEGREES REMARK 500 LYS B 85 CB - CG - CD ANGL. DEV. = 16.8 DEGREES REMARK 500 ARG B 102 CD - NE - CZ ANGL. DEV. = 11.4 DEGREES REMARK 500 ASP B 106 CB - CG - OD1 ANGL. DEV. = -5.9 DEGREES REMARK 500 ASP B 111 CB - CG - OD1 ANGL. DEV. = -6.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 113 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL 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 LYS A 7 -138.34 58.22 REMARK 500 ASP A 54 52.13 -103.35 REMARK 500 ALA A 206 179.49 69.12 REMARK 500 LYS A 229 -50.81 -128.78 REMARK 500 LYS B 7 -135.34 56.61 REMARK 500 ASN B 8 35.70 -98.98 REMARK 500 ASP B 54 39.89 -92.41 REMARK 500 SER B 150 170.83 -59.79 REMARK 500 ALA B 206 -179.34 65.66 REMARK 500 LYS C 7 -126.32 55.13 REMARK 500 ASP C 54 47.15 -83.15 REMARK 500 ALA C 206 176.88 70.31 REMARK 500 LYS D 7 -118.48 55.64 REMARK 500 ASP D 54 49.26 -95.88 REMARK 500 ALA D 206 -171.82 62.39 REMARK 500 LYS D 229 -56.01 -122.67 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ASP B 43 12.01 REMARK 500 ALA C 84 -10.92 REMARK 500 SER C 107 12.07 REMARK 500 LEU C 115 -11.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN DHS: 3-AMINO-4,5-DIHYDROXY-CYCLOHEX-1-ENECARBOXYLATE REMARK 600 GROUP. FORMULA:4(C7 H8 N1 O4). THE PRODUCT IS COVALENTLY LINKED REMARK 600 TO LYS170 THROUGH FORMATION OF A SCHIFF BASE (IMINE) REMARK 600 INTERMEDIATE THAT IS THEN REDUCED WITH BOROHYDRIDE. THE REMARK 600 EMPIRICAL FORMULA GIVEN CONTAINS THE CARBOXYLATE PROTON BUT NOT REMARK 600 THE 3-KETO OXYGEN (WHICH IS REPLACED BY THE NZ OF LYS170 IN REMARK 600 FORMING THE SCHIFF BASE). LYS 170 FORMS THE IMINE INTERMEDIATE REMARK 600 WITH THE AID OF HIS 143. ARG 213 INTERACTS WITH THE CARBOXYL REMARK 600 GROUP OF THE 3-DEHYDROQUINATE SUBSTRATE. REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 HOH B 314 REMARK 615 HOH C 343 REMARK 615 HOH C 347 REMARK 615 HOH D 331 REMARK 615 HOH D 350 REMARK 615 HOH D 355 REMARK 615 HOH D 358 REMARK 615 HOH D 364 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DHS A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DHS B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DHS C 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DHS D 304 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1QFE RELATED DB: PDB REMARK 900 THE STRUCTURE OF TYPE I 3-DEHYDROQUINATE DEHYDRATASE FROM REMARK 900 SALMONELLA TYPHI REMARK 900 RELATED ID: 1GQN RELATED DB: PDB REMARK 900 NATIVE 3-DEHYDROQUINASE FROM SALMONELLA TYPHI DBREF 1L9W A 1 252 UNP P24670 AROD_SALTI 1 252 DBREF 1L9W B 1 252 UNP P24670 AROD_SALTI 1 252 DBREF 1L9W C 1 252 UNP P24670 AROD_SALTI 1 252 DBREF 1L9W D 1 252 UNP P24670 AROD_SALTI 1 252 SEQRES 1 A 252 MET LYS THR VAL THR VAL LYS ASN LEU ILE ILE GLY GLU SEQRES 2 A 252 GLY MET PRO LYS ILE ILE VAL SER LEU MET GLY ARG ASP SEQRES 3 A 252 ILE ASN SER VAL LYS ALA GLU ALA LEU ALA TYR ARG GLU SEQRES 4 A 252 ALA THR PHE ASP ILE LEU GLU TRP ARG VAL ASP HIS PHE SEQRES 5 A 252 MET ASP ILE ALA SER THR GLN SER VAL LEU THR ALA ALA SEQRES 6 A 252 ARG VAL ILE ARG ASP ALA MET PRO ASP ILE PRO LEU LEU SEQRES 7 A 252 PHE THR PHE ARG SER ALA LYS GLU GLY GLY GLU GLN THR SEQRES 8 A 252 ILE THR THR GLN HIS TYR LEU THR LEU ASN ARG ALA ALA SEQRES 9 A 252 ILE ASP SER GLY LEU VAL ASP MET ILE ASP LEU GLU LEU SEQRES 10 A 252 PHE THR GLY ASP ALA ASP VAL LYS ALA THR VAL ASP TYR SEQRES 11 A 252 ALA HIS ALA HIS ASN VAL TYR VAL VAL MET SER ASN HIS SEQRES 12 A 252 ASP PHE HIS GLN THR PRO SER ALA GLU GLU MET VAL SER SEQRES 13 A 252 ARG LEU ARG LYS MET GLN ALA LEU GLY ALA ASP ILE PRO SEQRES 14 A 252 LYS ILE ALA VAL MET PRO GLN SER LYS HIS ASP VAL LEU SEQRES 15 A 252 THR LEU LEU THR ALA THR LEU GLU MET GLN GLN HIS TYR SEQRES 16 A 252 ALA ASP ARG PRO VAL ILE THR MET SER MET ALA LYS GLU SEQRES 17 A 252 GLY VAL ILE SER ARG LEU ALA GLY GLU VAL PHE GLY SER SEQRES 18 A 252 ALA ALA THR PHE GLY ALA VAL LYS GLN ALA SER ALA PRO SEQRES 19 A 252 GLY GLN ILE ALA VAL ASN ASP LEU ARG SER VAL LEU MET SEQRES 20 A 252 ILE LEU HIS ASN ALA SEQRES 1 B 252 MET LYS THR VAL THR VAL LYS ASN LEU ILE ILE GLY GLU SEQRES 2 B 252 GLY MET PRO LYS ILE ILE VAL SER LEU MET GLY ARG ASP SEQRES 3 B 252 ILE ASN SER VAL LYS ALA GLU ALA LEU ALA TYR ARG GLU SEQRES 4 B 252 ALA THR PHE ASP ILE LEU GLU TRP ARG VAL ASP HIS PHE SEQRES 5 B 252 MET ASP ILE ALA SER THR GLN SER VAL LEU THR ALA ALA SEQRES 6 B 252 ARG VAL ILE ARG ASP ALA MET PRO ASP ILE PRO LEU LEU SEQRES 7 B 252 PHE THR PHE ARG SER ALA LYS GLU GLY GLY GLU GLN THR SEQRES 8 B 252 ILE THR THR GLN HIS TYR LEU THR LEU ASN ARG ALA ALA SEQRES 9 B 252 ILE ASP SER GLY LEU VAL ASP MET ILE ASP LEU GLU LEU SEQRES 10 B 252 PHE THR GLY ASP ALA ASP VAL LYS ALA THR VAL ASP TYR SEQRES 11 B 252 ALA HIS ALA HIS ASN VAL TYR VAL VAL MET SER ASN HIS SEQRES 12 B 252 ASP PHE HIS GLN THR PRO SER ALA GLU GLU MET VAL SER SEQRES 13 B 252 ARG LEU ARG LYS MET GLN ALA LEU GLY ALA ASP ILE PRO SEQRES 14 B 252 LYS ILE ALA VAL MET PRO GLN SER LYS HIS ASP VAL LEU SEQRES 15 B 252 THR LEU LEU THR ALA THR LEU GLU MET GLN GLN HIS TYR SEQRES 16 B 252 ALA ASP ARG PRO VAL ILE THR MET SER MET ALA LYS GLU SEQRES 17 B 252 GLY VAL ILE SER ARG LEU ALA GLY GLU VAL PHE GLY SER SEQRES 18 B 252 ALA ALA THR PHE GLY ALA VAL LYS GLN ALA SER ALA PRO SEQRES 19 B 252 GLY GLN ILE ALA VAL ASN ASP LEU ARG SER VAL LEU MET SEQRES 20 B 252 ILE LEU HIS ASN ALA SEQRES 1 C 252 MET LYS THR VAL THR VAL LYS ASN LEU ILE ILE GLY GLU SEQRES 2 C 252 GLY MET PRO LYS ILE ILE VAL SER LEU MET GLY ARG ASP SEQRES 3 C 252 ILE ASN SER VAL LYS ALA GLU ALA LEU ALA TYR ARG GLU SEQRES 4 C 252 ALA THR PHE ASP ILE LEU GLU TRP ARG VAL ASP HIS PHE SEQRES 5 C 252 MET ASP ILE ALA SER THR GLN SER VAL LEU THR ALA ALA SEQRES 6 C 252 ARG VAL ILE ARG ASP ALA MET PRO ASP ILE PRO LEU LEU SEQRES 7 C 252 PHE THR PHE ARG SER ALA LYS GLU GLY GLY GLU GLN THR SEQRES 8 C 252 ILE THR THR GLN HIS TYR LEU THR LEU ASN ARG ALA ALA SEQRES 9 C 252 ILE ASP SER GLY LEU VAL ASP MET ILE ASP LEU GLU LEU SEQRES 10 C 252 PHE THR GLY ASP ALA ASP VAL LYS ALA THR VAL ASP TYR SEQRES 11 C 252 ALA HIS ALA HIS ASN VAL TYR VAL VAL MET SER ASN HIS SEQRES 12 C 252 ASP PHE HIS GLN THR PRO SER ALA GLU GLU MET VAL SER SEQRES 13 C 252 ARG LEU ARG LYS MET GLN ALA LEU GLY ALA ASP ILE PRO SEQRES 14 C 252 LYS ILE ALA VAL MET PRO GLN SER LYS HIS ASP VAL LEU SEQRES 15 C 252 THR LEU LEU THR ALA THR LEU GLU MET GLN GLN HIS TYR SEQRES 16 C 252 ALA ASP ARG PRO VAL ILE THR MET SER MET ALA LYS GLU SEQRES 17 C 252 GLY VAL ILE SER ARG LEU ALA GLY GLU VAL PHE GLY SER SEQRES 18 C 252 ALA ALA THR PHE GLY ALA VAL LYS GLN ALA SER ALA PRO SEQRES 19 C 252 GLY GLN ILE ALA VAL ASN ASP LEU ARG SER VAL LEU MET SEQRES 20 C 252 ILE LEU HIS ASN ALA SEQRES 1 D 252 MET LYS THR VAL THR VAL LYS ASN LEU ILE ILE GLY GLU SEQRES 2 D 252 GLY MET PRO LYS ILE ILE VAL SER LEU MET GLY ARG ASP SEQRES 3 D 252 ILE ASN SER VAL LYS ALA GLU ALA LEU ALA TYR ARG GLU SEQRES 4 D 252 ALA THR PHE ASP ILE LEU GLU TRP ARG VAL ASP HIS PHE SEQRES 5 D 252 MET ASP ILE ALA SER THR GLN SER VAL LEU THR ALA ALA SEQRES 6 D 252 ARG VAL ILE ARG ASP ALA MET PRO ASP ILE PRO LEU LEU SEQRES 7 D 252 PHE THR PHE ARG SER ALA LYS GLU GLY GLY GLU GLN THR SEQRES 8 D 252 ILE THR THR GLN HIS TYR LEU THR LEU ASN ARG ALA ALA SEQRES 9 D 252 ILE ASP SER GLY LEU VAL ASP MET ILE ASP LEU GLU LEU SEQRES 10 D 252 PHE THR GLY ASP ALA ASP VAL LYS ALA THR VAL ASP TYR SEQRES 11 D 252 ALA HIS ALA HIS ASN VAL TYR VAL VAL MET SER ASN HIS SEQRES 12 D 252 ASP PHE HIS GLN THR PRO SER ALA GLU GLU MET VAL SER SEQRES 13 D 252 ARG LEU ARG LYS MET GLN ALA LEU GLY ALA ASP ILE PRO SEQRES 14 D 252 LYS ILE ALA VAL MET PRO GLN SER LYS HIS ASP VAL LEU SEQRES 15 D 252 THR LEU LEU THR ALA THR LEU GLU MET GLN GLN HIS TYR SEQRES 16 D 252 ALA ASP ARG PRO VAL ILE THR MET SER MET ALA LYS GLU SEQRES 17 D 252 GLY VAL ILE SER ARG LEU ALA GLY GLU VAL PHE GLY SER SEQRES 18 D 252 ALA ALA THR PHE GLY ALA VAL LYS GLN ALA SER ALA PRO SEQRES 19 D 252 GLY GLN ILE ALA VAL ASN ASP LEU ARG SER VAL LEU MET SEQRES 20 D 252 ILE LEU HIS ASN ALA HET DHS A 301 11 HET DHS B 302 11 HET DHS C 303 11 HET DHS D 304 11 HETNAM DHS 3-AMINO-4,5-DIHYDROXY-CYCLOHEX-1-ENECARBOXYLATE FORMUL 5 DHS 4(C7 H10 N O4 1-) FORMUL 9 HOH *207(H2 O) HELIX 1 1 ASP A 26 ARG A 38 1 13 HELIX 2 2 ASP A 50 PHE A 52 5 3 HELIX 3 3 SER A 57 MET A 72 1 16 HELIX 4 4 SER A 83 GLY A 87 5 5 HELIX 5 5 THR A 93 SER A 107 1 15 HELIX 6 6 GLY A 120 ALA A 133 1 14 HELIX 7 7 SER A 150 LEU A 164 1 15 HELIX 8 8 SER A 177 TYR A 195 1 19 HELIX 9 9 MET A 205 ALA A 215 1 11 HELIX 10 10 ALA A 215 GLY A 220 1 6 HELIX 11 11 ALA A 238 ALA A 252 1 15 HELIX 12 12 ASP B 26 ARG B 38 1 13 HELIX 13 13 ASP B 50 PHE B 52 5 3 HELIX 14 14 SER B 57 MET B 72 1 16 HELIX 15 15 SER B 83 GLY B 87 5 5 HELIX 16 16 THR B 93 SER B 107 1 15 HELIX 17 17 GLY B 120 HIS B 134 1 15 HELIX 18 18 SER B 150 LEU B 164 1 15 HELIX 19 19 SER B 177 TYR B 195 1 19 HELIX 20 20 GLY B 209 ALA B 215 1 7 HELIX 21 21 ALA B 215 GLY B 220 1 6 HELIX 22 22 ALA B 238 ASN B 251 1 14 HELIX 23 23 ASP C 26 GLU C 39 1 14 HELIX 24 24 ASP C 50 PHE C 52 5 3 HELIX 25 25 SER C 57 MET C 72 1 16 HELIX 26 26 SER C 83 GLY C 87 5 5 HELIX 27 27 THR C 93 GLY C 108 1 16 HELIX 28 28 GLY C 120 HIS C 134 1 15 HELIX 29 29 SER C 150 LEU C 164 1 15 HELIX 30 30 SER C 177 TYR C 195 1 19 HELIX 31 31 MET C 205 ALA C 215 1 11 HELIX 32 32 ALA C 215 GLY C 220 1 6 HELIX 33 33 ALA C 238 ALA C 252 1 15 HELIX 34 34 ASP D 26 ARG D 38 1 13 HELIX 35 35 ASP D 50 PHE D 52 5 3 HELIX 36 36 SER D 57 MET D 72 1 16 HELIX 37 37 SER D 83 GLY D 87 5 5 HELIX 38 38 THR D 93 GLY D 108 1 16 HELIX 39 39 GLY D 120 HIS D 134 1 15 HELIX 40 40 SER D 150 LEU D 164 1 15 HELIX 41 41 SER D 177 TYR D 195 1 19 HELIX 42 42 MET D 205 ALA D 215 1 11 HELIX 43 43 ALA D 215 GLY D 220 1 6 HELIX 44 44 ALA D 238 ALA D 252 1 15 SHEET 1 A 2 VAL A 4 VAL A 6 0 SHEET 2 A 2 LEU A 9 ILE A 11 -1 O ILE A 11 N VAL A 4 SHEET 1 B 8 ILE A 201 SER A 204 0 SHEET 2 B 8 ILE A 168 VAL A 173 1 N ILE A 171 O ILE A 201 SHEET 3 B 8 TYR A 137 ASP A 144 1 N ASP A 144 O ALA A 172 SHEET 4 B 8 MET A 112 GLU A 116 1 N ILE A 113 O VAL A 139 SHEET 5 B 8 LEU A 77 THR A 80 1 N PHE A 79 O MET A 112 SHEET 6 B 8 ILE A 44 ARG A 48 1 N LEU A 45 O LEU A 78 SHEET 7 B 8 LYS A 17 LEU A 22 1 N VAL A 20 O GLU A 46 SHEET 8 B 8 ALA A 223 PHE A 225 1 O THR A 224 N ILE A 19 SHEET 1 C 2 VAL B 4 VAL B 6 0 SHEET 2 C 2 LEU B 9 ILE B 11 -1 O ILE B 11 N VAL B 4 SHEET 1 D 8 ILE B 201 SER B 204 0 SHEET 2 D 8 ILE B 168 VAL B 173 1 N VAL B 173 O MET B 203 SHEET 3 D 8 TYR B 137 ASP B 144 1 N ASP B 144 O ALA B 172 SHEET 4 D 8 MET B 112 GLU B 116 1 N LEU B 115 O VAL B 139 SHEET 5 D 8 LEU B 77 THR B 80 1 N PHE B 79 O MET B 112 SHEET 6 D 8 ILE B 44 ARG B 48 1 N TRP B 47 O LEU B 78 SHEET 7 D 8 LYS B 17 LEU B 22 1 N LEU B 22 O GLU B 46 SHEET 8 D 8 ALA B 223 PHE B 225 1 O THR B 224 N ILE B 19 SHEET 1 E 2 VAL C 4 VAL C 6 0 SHEET 2 E 2 LEU C 9 ILE C 11 -1 O LEU C 9 N VAL C 6 SHEET 1 F 8 ILE C 201 SER C 204 0 SHEET 2 F 8 ILE C 168 VAL C 173 1 N VAL C 173 O MET C 203 SHEET 3 F 8 TYR C 137 ASP C 144 1 N MET C 140 O LYS C 170 SHEET 4 F 8 MET C 112 GLU C 116 1 N ILE C 113 O VAL C 139 SHEET 5 F 8 LEU C 77 THR C 80 1 N PHE C 79 O MET C 112 SHEET 6 F 8 ILE C 44 ARG C 48 1 N LEU C 45 O LEU C 78 SHEET 7 F 8 LYS C 17 LEU C 22 1 N LEU C 22 O GLU C 46 SHEET 8 F 8 ALA C 223 PHE C 225 1 O THR C 224 N LYS C 17 SHEET 1 G 2 VAL D 4 VAL D 6 0 SHEET 2 G 2 LEU D 9 ILE D 11 -1 O ILE D 11 N VAL D 4 SHEET 1 H 8 ILE D 201 SER D 204 0 SHEET 2 H 8 ILE D 168 VAL D 173 1 N ILE D 171 O ILE D 201 SHEET 3 H 8 TYR D 137 ASP D 144 1 N ASN D 142 O ALA D 172 SHEET 4 H 8 MET D 112 GLU D 116 1 N ILE D 113 O VAL D 139 SHEET 5 H 8 LEU D 77 THR D 80 1 N PHE D 79 O MET D 112 SHEET 6 H 8 ILE D 44 ARG D 48 1 N LEU D 45 O LEU D 78 SHEET 7 H 8 LYS D 17 LEU D 22 1 N VAL D 20 O GLU D 46 SHEET 8 H 8 ALA D 223 PHE D 225 1 O THR D 224 N LYS D 17 LINK NZ LYS A 170 C3 DHS A 301 1555 1555 2.97 LINK NZ LYS B 170 C3 DHS B 302 1555 1555 2.79 LINK NZ LYS C 170 C3 DHS C 303 1555 1555 2.97 LINK NZ LYS D 170 C3 DHS D 304 1555 1555 3.35 SITE 1 AC1 11 SER A 21 GLU A 46 ARG A 48 ARG A 82 SITE 2 AC1 11 HIS A 143 LYS A 170 ARG A 213 PHE A 225 SITE 3 AC1 11 SER A 232 ALA A 233 GLN A 236 SITE 1 AC2 11 SER B 21 GLU B 46 ARG B 48 ARG B 82 SITE 2 AC2 11 HIS B 143 LYS B 170 ARG B 213 PHE B 225 SITE 3 AC2 11 SER B 232 ALA B 233 GLN B 236 SITE 1 AC3 13 SER C 21 GLU C 46 ARG C 48 ARG C 82 SITE 2 AC3 13 HIS C 143 LYS C 170 MET C 203 MET C 205 SITE 3 AC3 13 ARG C 213 PHE C 225 SER C 232 ALA C 233 SITE 4 AC3 13 GLN C 236 SITE 1 AC4 11 SER D 21 GLU D 46 ARG D 48 ARG D 82 SITE 2 AC4 11 HIS D 143 LYS D 170 ARG D 213 PHE D 225 SITE 3 AC4 11 SER D 232 ALA D 233 GLN D 236 CRYST1 42.610 158.560 85.890 90.00 93.61 90.00 P 1 21 1 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 0.023469 -0.000001 0.001480 0.00000 SCALE2 0.000000 0.006307 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011666 0.00000