HEADER LYASE 15-JAN-14 4CLM TITLE STRUCTURE OF SALMONELLA TYPHI TYPE I DEHYDROQUINASE IRREVERSIBLY TITLE 2 INHIBITED WITH A 1,3,4-TRIHYDROXYCICLOHEXANE-1-CARBOXYLIC ACID TITLE 3 DERIVATIVE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3-DEHYDROQUINATE DEHYDRATASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: 3-DEHYDROQUINASE, TYPE I DHQASE; COMPND 5 EC: 4.2.1.10; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR SOURCE 3 TYPHI; SOURCE 4 ORGANISM_TAXID: 90370; SOURCE 5 ATCC: 19430; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS TYPE I DEHYDROQUINASE, LYASE, INHIBITOR, SHIKIMIS ACID PATHWAY, KEYWDS 2 SUBSTRATE SPECIFICITY EXPDTA X-RAY DIFFRACTION AUTHOR J.M.OTERO,A.L.LLAMAS-SAIZ,L.TIZON,M.MANEIRO,E.LENCE,S.POZA,H.LAMB, AUTHOR 2 A.R.HAWKINS,B.BLANCO,A.SEDES,A.PEON,C.GONZALEZ-BELLO,M.J.VAN RAAIJ REVDAT 8 20-DEC-23 4CLM 1 REMARK REVDAT 7 28-AUG-19 4CLM 1 COMPND HETNAM LINK REVDAT 6 29-AUG-18 4CLM 1 COMPND HETNAM FORMUL REVDAT 5 01-AUG-18 4CLM 1 TITLE JRNL REVDAT 4 07-FEB-18 4CLM 1 AUTHOR JRNL REVDAT 3 14-JAN-15 4CLM 1 JRNL REVDAT 2 19-NOV-14 4CLM 1 JRNL REVDAT 1 05-NOV-14 4CLM 0 JRNL AUTH L.TIZON,M.MANEIRO,A.PEON,J.M.OTERO,E.LENCE,S.POZA, JRNL AUTH 2 M.J.VAN RAAIJ,P.THOMPSON,A.R.HAWKINS,C.GONZALEZ-BELLO JRNL TITL IRREVERSIBLE COVALENT MODIFICATION OF TYPE I DEHYDROQUINASE JRNL TITL 2 WITH A STABLE SCHIFF BASE. JRNL REF ORG. BIOMOL. CHEM. V. 13 706 2015 JRNL REFN ESSN 1477-0539 JRNL PMID 25370445 JRNL DOI 10.1039/C4OB01782J REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.21 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 81186 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) : 0.122 REMARK 3 R VALUE (WORKING SET) : 0.120 REMARK 3 FREE R VALUE : 0.155 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4293 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) : 1.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.48 REMARK 3 REFLECTION IN BIN (WORKING SET) : 9343 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 75.96 REMARK 3 BIN R VALUE (WORKING SET) : 0.1520 REMARK 3 BIN FREE R VALUE SET COUNT : 478 REMARK 3 BIN FREE R VALUE : 0.2140 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3790 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 17 REMARK 3 SOLVENT ATOMS : 665 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.23 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.16000 REMARK 3 B22 (A**2) : 0.69000 REMARK 3 B33 (A**2) : -0.80000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.47000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.060 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.054 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.031 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.702 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.978 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.970 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4090 ; 0.010 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4097 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5555 ; 1.533 ; 1.964 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9430 ; 0.947 ; 3.002 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 504 ; 5.678 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 178 ;39.369 ;24.382 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 774 ;13.353 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 27 ;15.135 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 687 ; 0.091 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4490 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 879 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1646 ; 0.284 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3819 ; 0.171 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1930 ; 0.172 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2350 ; 0.083 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 100 ; 0.163 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): 5 ; 0.119 ; 0.200 REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.151 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 1575 ; 0.287 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 83 ; 0.243 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 13 ; 0.265 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): 1 ; 0.071 ; 0.200 REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 4090 ; 5.777 ; 1.101 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 4097 ; 2.290 ; 1.151 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5551 ; 7.551 ; 1.623 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 7053 ; 8.568 ;11.130 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 9430 ; 4.247 ; 1.691 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 8187 ; 1.847 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 120 ;28.717 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 8673 ; 7.921 ; 5.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. U VALUES ARE REFINED INDIVIDUALLY. GAP BY DISORDERED REMARK 3 REGION BETWEEN VAL-228 AND ILE-237 IN CHAIN A. REMARK 4 REMARK 4 4CLM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1290059376. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-MAR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALBA REMARK 200 BEAMLINE : XALOC REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.87290 REMARK 200 MONOCHROMATOR : CHANNEL-CUT DOUBLE CRYSTAL REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : PLANE-ELLIPSOIDAL MIRRORS (SI, REMARK 200 RH, IR) REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 85495 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 47.170 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 76.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.22000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1QFE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 34% PEG 4000, 0.1 M CITRATE-PHOSPHATE REMARK 280 PH 5.6 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 22.23500 REMARK 290 SMTRY3 2 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 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: 2630 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19540 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -50.6 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 LYS A 229 REMARK 465 GLN A 230 REMARK 465 ALA A 231 REMARK 465 SER A 232 REMARK 465 ALA A 233 REMARK 465 PRO A 234 REMARK 465 GLY A 235 REMARK 465 GLN A 236 REMARK 465 MET B 1 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 LYS A 2 CG CD CE NZ REMARK 470 LYS B 229 CG CD CE NZ REMARK 470 GLN B 230 CG CD OE1 NE2 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 SD MET A 53 O HOH A 2170 2.01 REMARK 500 NH1 ARG A 243 O HOH A 2141 2.07 REMARK 500 O HOH A 2033 O HOH A 2034 2.08 REMARK 500 O MET A 23 O HOH A 2083 2.09 REMARK 500 O HOH A 2186 O HOH A 2187 2.09 REMARK 500 O HOH A 2280 O HOH A 2281 2.13 REMARK 500 O MET A 23 OE2 GLU A 33 2.14 REMARK 500 O HOH B 2070 O HOH B 2084 2.15 REMARK 500 OE1 GLU A 190 O HOH A 2335 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 A 2187 O HOH B 2111 1554 1.97 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 LYS B 170 C ILE B 171 N 0.143 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 MET A 53 CG - SD - CE ANGL. DEV. = -26.3 DEGREES REMARK 500 ARG B 69 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG B 69 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES 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 ALA A 206 177.62 72.44 REMARK 500 ASN B 8 -0.33 72.95 REMARK 500 ALA B 206 178.18 69.34 REMARK 500 LYS B 229 -37.34 -130.57 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 A2015 DISTANCE = 6.50 ANGSTROMS REMARK 525 HOH A2046 DISTANCE = 6.48 ANGSTROMS REMARK 525 HOH A2047 DISTANCE = 5.93 ANGSTROMS REMARK 525 HOH A2048 DISTANCE = 6.13 ANGSTROMS REMARK 525 HOH A2069 DISTANCE = 6.13 ANGSTROMS REMARK 525 HOH A2130 DISTANCE = 5.93 ANGSTROMS REMARK 525 HOH A2179 DISTANCE = 6.38 ANGSTROMS REMARK 525 HOH B2071 DISTANCE = 7.27 ANGSTROMS REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 WPL: THE PROTEIN IS MODIFIED USING AN IRREVERSIBLE INHIBITOR. A REMARK 600 THE INHIBITION TAKE PLACE VIA A NUCLEOPHILIC RING OPENING REMARK 600 OF THE EPOXIDE GROUP OF THE INHIBITOR BY THE NZ-ATOM OF LYS-170 REMARK 600 WHICH IS FOLLOWED BY ELIMINATION OF A WATER MOLECULE. 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 LI A1256 LI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2151 O REMARK 620 2 HOH A2210 O 169.2 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE WPL B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1253 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1254 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1255 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LI A 1256 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4CKW RELATED DB: PDB REMARK 900 STRUCTURE OF THE MYCOBACTERIUM TUBERCULOSIS TYPE II DEHYDROQUINASE REMARK 900 N12S MUTANT (CRYSTAL FORM 1) REMARK 900 RELATED ID: 4CKX RELATED DB: PDB REMARK 900 STRUCTURE OF THE MYCOBACTERIUM TUBERCULOSIS TYPE II DEHYDROQUINASE REMARK 900 N12S MUTANT (CRYSTAL FORM 2) REMARK 900 RELATED ID: 4CKY RELATED DB: PDB REMARK 900 STRUCTURE OF THE MYCOBACTERIUM TUBERCULOSIS TYPE II DEHYDROQUINASE REMARK 900 INHIBITED BY A 3-DEHYDROQUINIC ACID DERIVATIVE REMARK 900 RELATED ID: 4CKZ RELATED DB: PDB REMARK 900 STRUCTURE OF THE MYCOBACTERIUM TUBERCULOSIS TYPE II DEHYDROQUINASE REMARK 900 D88N MUTANT REMARK 900 RELATED ID: 4CL0 RELATED DB: PDB REMARK 900 STRUCTURE OF THE MYCOBACTERIUM TUBERCULOSIS TYPE II DEHYDROQUINASE REMARK 900 INHIBITED BY A 3-DEHYDROQUINIC ACID DERIVATIVE DBREF 4CLM A 1 252 UNP P24670 AROD_SALTI 1 252 DBREF 4CLM B 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 LEU 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 LEU 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 HET CL A1253 1 HET CL A1254 1 HET CL A1255 1 HET LI A1256 1 HET WPL B 301 14 HETNAM CL CHLORIDE ION HETNAM LI LITHIUM ION HETNAM WPL (1~{S},3~{S},4~{R},5~{R})-3-METHYL-1,4,5- HETNAM 2 WPL TRIS(HYDROXYL)CYCLOHEXANE-1-CARBOXYLIC ACID FORMUL 3 CL 3(CL 1-) FORMUL 6 LI LI 1+ FORMUL 7 WPL C8 H14 O5 FORMUL 8 HOH *665(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 HIS A 134 1 15 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 GLY A 220 1 16 HELIX 10 10 ALA A 238 ALA A 252 1 15 HELIX 11 11 ASP B 26 ARG B 38 1 13 HELIX 12 12 ASP B 50 PHE B 52 5 3 HELIX 13 13 SER B 57 MET B 72 1 16 HELIX 14 14 SER B 83 GLY B 87 5 5 HELIX 15 15 THR B 93 GLY B 108 1 16 HELIX 16 16 GLY B 120 HIS B 134 1 15 HELIX 17 17 SER B 150 LEU B 164 1 15 HELIX 18 18 SER B 177 TYR B 195 1 19 HELIX 19 19 GLY B 209 ALA B 215 1 7 HELIX 20 20 ALA B 215 GLY B 220 1 6 HELIX 21 21 ALA B 238 ALA B 252 1 15 SHEET 1 AA 2 VAL A 4 VAL A 6 0 SHEET 2 AA 2 LEU A 9 ILE A 11 -1 O LEU A 9 N VAL A 6 SHEET 1 AB 8 ILE A 201 SER A 204 0 SHEET 2 AB 8 ILE A 168 VAL A 173 1 O PRO A 169 N ILE A 201 SHEET 3 AB 8 TYR A 137 ASP A 144 1 O VAL A 138 N ILE A 168 SHEET 4 AB 8 MET A 112 GLU A 116 1 O ILE A 113 N VAL A 139 SHEET 5 AB 8 LEU A 77 THR A 80 1 O PHE A 79 N ASP A 114 SHEET 6 AB 8 ILE A 44 ARG A 48 1 O LEU A 45 N LEU A 78 SHEET 7 AB 8 LYS A 17 LEU A 22 1 O ILE A 18 N ILE A 44 SHEET 8 AB 8 ALA A 223 PHE A 225 1 O THR A 224 N ILE A 19 SHEET 1 BA 2 VAL B 4 VAL B 6 0 SHEET 2 BA 2 LEU B 9 ILE B 11 -1 O LEU B 9 N VAL B 6 SHEET 1 BB 8 ILE B 201 SER B 204 0 SHEET 2 BB 8 ILE B 168 VAL B 173 1 O PRO B 169 N ILE B 201 SHEET 3 BB 8 TYR B 137 ASP B 144 1 O VAL B 138 N ILE B 168 SHEET 4 BB 8 MET B 112 GLU B 116 1 O ILE B 113 N VAL B 139 SHEET 5 BB 8 LEU B 77 THR B 80 1 O LEU B 77 N MET B 112 SHEET 6 BB 8 ILE B 44 ARG B 48 1 O LEU B 45 N LEU B 78 SHEET 7 BB 8 LYS B 17 LEU B 22 1 O VAL B 20 N GLU B 46 SHEET 8 BB 8 ALA B 223 GLY B 226 1 O THR B 224 N ILE B 19 LINK NZ BLYS B 170 CAJBWPL B 301 1555 1555 1.32 LINK NZ ALYS B 170 CAJAWPL B 301 1555 1555 1.33 LINK LI LI A1256 O HOH A2151 1555 1555 1.80 LINK LI LI A1256 O HOH A2210 1555 1555 1.96 SITE 1 AC1 12 SER B 21 GLU B 46 ARG B 48 ARG B 82 SITE 2 AC1 12 LYS B 170 MET B 205 ARG B 213 PHE B 225 SITE 3 AC1 12 SER B 232 ALA B 233 GLN B 236 HOH B2129 SITE 1 AC2 3 HIS A 96 THR A 99 TYR B 130 SITE 1 AC3 5 ARG A 159 GLN A 162 HOH A2181 HOH A2310 SITE 2 AC3 5 HOH A2313 SITE 1 AC4 5 LYS A 170 LI A1256 HOH A2358 HOH A2360 SITE 2 AC4 5 HOH A2393 SITE 1 AC5 7 ARG A 48 ARG A 82 LYS A 170 CL A1255 SITE 2 AC5 7 HOH A2078 HOH A2151 HOH A2210 CRYST1 60.590 44.470 84.980 90.00 95.17 90.00 P 1 21 1 4 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 0.016504 0.000000 0.001493 0.00000 SCALE2 0.000000 0.022487 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011816 0.00000