HEADER TRANSFERASE 08-JUN-09 2WKA TITLE STRUCTURE OF PLP_THR_DECANOYL-COA ALDIMINE FORM OF VIBRIO CHOLERAE TITLE 2 CQSA COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAI-1 AUTOINDUCER SYNTHASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: CHOLERAE QUORUM-SENSING AUTOINDUCER, CQSA; COMPND 5 EC: 2.3.-.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO CHOLERAE O1 BIOVAR EL TOR; SOURCE 3 ORGANISM_TAXID: 243277; SOURCE 4 STRAIN: N16961; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: ROSETTA KEYWDS OXOAMINE-SYNTHASES, PYRIDOXAL PHOSPHATE, CQSA, CAI-1, TRANSFERASE, KEYWDS 2 AUTOINDUCER, QUORUM-SENSING, ACYLTRANSFERASE, AMINOTRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR N.JAHAN,J.A.POTTER,M.A.SHEIKH,C.H.BOTTING,S.L.SHIRRAN,N.J.WESTWOOD, AUTHOR 2 G.L.TAYLOR REVDAT 6 08-MAY-24 2WKA 1 REMARK REVDAT 5 03-OCT-18 2WKA 1 COMPND HETNAM FORMUL REVDAT 4 07-MAR-18 2WKA 1 SOURCE REVDAT 3 15-SEP-09 2WKA 1 JRNL REVDAT 2 04-AUG-09 2WKA 1 JRNL REMARK REVDAT 1 21-JUL-09 2WKA 0 JRNL AUTH N.JAHAN,J.A.POTTER,M.A.SHEIKH,C.H.BOTTING,S.L.SHIRRAN, JRNL AUTH 2 N.J.WESTWOOD,G.L.TAYLOR JRNL TITL INSIGHTS INTO THE BIOSYNTHESIS OF THE VIBRIO CHOLERAE MAJOR JRNL TITL 2 AUTOINDUCER CAI-1 FROM THE CRYSTAL STRUCTURE OF THE JRNL TITL 3 PLP-DEPENDENT ENZYME CQSA. JRNL REF J.MOL.BIOL. V. 392 763 2009 JRNL REFN ISSN 0022-2836 JRNL PMID 19631226 JRNL DOI 10.1016/J.JMB.2009.07.042 REMARK 2 REMARK 2 RESOLUTION. 1.91 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0066 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) : 1.91 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.81 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 90.7 REMARK 3 NUMBER OF REFLECTIONS : 60048 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) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3197 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.91 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.96 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3562 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 74.06 REMARK 3 BIN R VALUE (WORKING SET) : 0.2690 REMARK 3 BIN FREE R VALUE SET COUNT : 180 REMARK 3 BIN FREE R VALUE : 0.3240 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6023 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 67 REMARK 3 SOLVENT ATOMS : 822 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.16 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01000 REMARK 3 B22 (A**2) : 0.22000 REMARK 3 B33 (A**2) : -0.21000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.186 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.173 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.109 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.675 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.942 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.913 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6228 ; 0.007 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8434 ; 1.176 ; 1.962 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 767 ; 7.856 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 300 ;35.739 ;24.333 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1050 ;16.570 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 39 ;17.793 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 933 ; 0.080 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4737 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL 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): 3818 ; 0.516 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6137 ; 0.993 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2410 ; 1.632 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2295 ; 2.738 ; 4.500 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): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL 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 REFINED INDIVIDUALLY. REMARK 4 REMARK 4 2WKA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-JUN-09. REMARK 100 THE DEPOSITION ID IS D_1290040082. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.934 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 63292 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.0 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.01 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.47000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 89.01500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.28500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 89.01500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.28500 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 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: 8380 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -92.0 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 ASN A 2 REMARK 465 LYS A 3 REMARK 465 MET B 1 REMARK 465 ASN B 2 REMARK 465 LYS B 3 REMARK 465 GLU B 69 REMARK 465 GLN B 70 REMARK 465 GLN B 71 REMARK 465 SER B 72 REMARK 465 LEU B 73 REMARK 465 PHE B 74 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 GLN A 5 CG CD OE1 NE2 REMARK 470 GLN B 5 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 O HOH B 2189 O HOH B 2391 1.76 REMARK 500 N PRO B 4 O HOH B 2002 1.79 REMARK 500 O HOH A 2358 O HOH A 2359 1.82 REMARK 500 NH2 ARG A 92 O HOH A 2126 1.88 REMARK 500 NH2 ARG B 301 O HOH B 2327 1.89 REMARK 500 O HOH B 2223 O HOH B 2228 1.90 REMARK 500 OD2 ASP B 15 O HOH B 2030 1.90 REMARK 500 O HOH B 2427 O HOH B 2428 1.92 REMARK 500 O HOH A 2043 O HOH A 2292 1.92 REMARK 500 OH TYR B 142 O HOH B 2208 1.93 REMARK 500 NH2 ARG A 301 O HOH A 2323 1.95 REMARK 500 O HOH B 2169 O HOH B 2341 1.95 REMARK 500 CA P89 B 605 O HOH B 2427 1.96 REMARK 500 O HOH B 2221 O HOH B 2224 1.97 REMARK 500 ND2 ASN A 144 O HOH A 2192 1.98 REMARK 500 OE2 GLU A 250 O HOH A 2276 1.98 REMARK 500 O HOH A 2164 O HOH A 2166 1.99 REMARK 500 CG GLN A 70 CB ASN B 54 1.99 REMARK 500 C TYR A 240 O HOH A 2270 2.00 REMARK 500 CG GLU B 101 NH2 ARG B 253 2.00 REMARK 500 CB GLN B 146 O HOH B 2212 2.00 REMARK 500 CD GLU B 101 NH2 ARG B 253 2.00 REMARK 500 OH TYR B 84 O HOH B 2130 2.01 REMARK 500 OE1 GLN B 291 O HOH B 2319 2.01 REMARK 500 OD1 ASP A 156 O HOH A 2212 2.02 REMARK 500 O HOH B 2178 O HOH B 2363 2.03 REMARK 500 ND1 HIS A 292 O3 SO4 A 1390 2.04 REMARK 500 O HOH A 2299 O HOH A 2303 2.05 REMARK 500 O HOH A 2104 O HOH B 2091 2.05 REMARK 500 O HOH A 2280 O HOH B 2026 2.07 REMARK 500 OG1 THR A 178 O HOH A 2222 2.09 REMARK 500 OE2 GLU A 329 O HOH A 2349 2.09 REMARK 500 OD1 ASP A 15 O HOH A 2023 2.09 REMARK 500 O HOH A 2065 O HOH A 2173 2.10 REMARK 500 O HOH B 2118 O HOH B 2119 2.11 REMARK 500 O HOH A 2059 O HOH A 2166 2.11 REMARK 500 O HOH A 2014 O HOH A 2025 2.11 REMARK 500 O LEU A 335 O ASN A 338 2.11 REMARK 500 OD1 ASN A 54 NZ LYS A 59 2.12 REMARK 500 O HOH B 2223 O HOH B 2226 2.14 REMARK 500 O ARG A 389 O HOH A 2388 2.15 REMARK 500 OE1 GLU B 220 O HOH B 2269 2.17 REMARK 500 OD1 ASP B 156 O HOH B 2229 2.18 REMARK 500 CE LYS B 13 O HOH B 2023 2.19 REMARK 500 O HOH B 2159 O HOH B 2323 2.19 REMARK 500 OE1 GLU B 194 O HOH B 2254 2.19 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 2101 O HOH B 2101 2675 2.00 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 B 141 NE - CZ - NH2 ANGL. DEV. = -3.3 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 GLU A 69 -161.15 116.12 REMARK 500 LEU A 73 51.30 -103.01 REMARK 500 ASN A 153 18.97 56.07 REMARK 500 ASN A 213 17.11 58.89 REMARK 500 LYS A 236 -105.42 -109.01 REMARK 500 ASN A 248 43.59 -98.38 REMARK 500 ASN A 249 -167.04 -170.52 REMARK 500 ALA A 286 44.30 -88.26 REMARK 500 LEU B 67 153.25 -41.62 REMARK 500 LYS B 236 -109.23 -110.01 REMARK 500 ASN B 248 53.86 -98.10 REMARK 500 ASN B 249 -170.40 178.59 REMARK 500 ALA B 286 46.82 -91.24 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLN A 70 GLN A 71 139.90 REMARK 500 ARG A 347 PRO A 348 73.79 REMARK 500 ARG B 347 PRO B 348 65.44 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 A2019 DISTANCE = 5.90 ANGSTROMS REMARK 525 HOH A2038 DISTANCE = 6.39 ANGSTROMS REMARK 525 HOH A2040 DISTANCE = 6.23 ANGSTROMS REMARK 525 HOH A2067 DISTANCE = 5.88 ANGSTROMS REMARK 525 HOH B2027 DISTANCE = 6.03 ANGSTROMS REMARK 525 HOH B2054 DISTANCE = 5.96 ANGSTROMS REMARK 525 HOH B2055 DISTANCE = 6.60 ANGSTROMS REMARK 525 HOH B2190 DISTANCE = 5.84 ANGSTROMS REMARK 525 HOH B2204 DISTANCE = 7.03 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE P89 A 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE P89 B 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 1390 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1390 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1391 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2WK7 RELATED DB: PDB REMARK 900 STRUCTURE OF APO FORM OF VIBRIO CHOLERAE CQSA REMARK 900 RELATED ID: 2WK8 RELATED DB: PDB REMARK 900 STRUCTURE OF HOLO FORM OF VIBRIO CHOLERAE CQSA REMARK 900 RELATED ID: 2WK9 RELATED DB: PDB REMARK 900 STRUCTURE OF PLP_THR ALDIMINE FORM OF VIBRIO CHOLERAE CQSA DBREF 2WKA A 1 389 UNP Q9KM65 CQSA_VIBCH 1 389 DBREF 2WKA B 1 389 UNP Q9KM65 CQSA_VIBCH 1 389 SEQRES 1 A 389 MET ASN LYS PRO GLN LEU PRO ASP PHE ILE GLN ASN LYS SEQRES 2 A 389 ILE ASP HIS TYR ILE GLU ASN TYR PHE ASP ILE ASN LYS SEQRES 3 A 389 ASN GLY LYS HIS LEU VAL LEU GLY LYS GLN ALA SER PRO SEQRES 4 A 389 ASP ASP ILE ILE LEU GLN SER ASN ASP TYR LEU ALA LEU SEQRES 5 A 389 ALA ASN HIS PRO LEU ILE LYS ALA ARG LEU ALA LYS SER SEQRES 6 A 389 LEU LEU GLU GLU GLN GLN SER LEU PHE MET SER ALA SER SEQRES 7 A 389 PHE LEU GLN ASN ASP TYR ASP LYS PRO MET ILE GLU LYS SEQRES 8 A 389 ARG LEU ALA LYS PHE THR GLY PHE ASP GLU CYS LEU LEU SEQRES 9 A 389 SER GLN SER GLY TRP ASN ALA ASN VAL GLY LEU LEU GLN SEQRES 10 A 389 THR ILE CYS GLN PRO ASN THR ASN VAL TYR ILE ASP PHE SEQRES 11 A 389 PHE ALA HIS MET SER LEU TRP GLU GLY ALA ARG TYR ALA SEQRES 12 A 389 ASN ALA GLN ALA HIS PRO PHE MET HIS ASN ASN CYS ASP SEQRES 13 A 389 HIS LEU ARG MET LEU ILE GLN ARG HIS GLY PRO GLY ILE SEQRES 14 A 389 ILE VAL VAL ASP SER ILE TYR SER THR LEU GLY THR ILE SEQRES 15 A 389 ALA PRO LEU ALA GLU LEU VAL ASN ILE SER LYS GLU PHE SEQRES 16 A 389 GLY CYS ALA LEU LEU VAL ASP GLU SER HIS SER LEU GLY SEQRES 17 A 389 THR HIS GLY PRO ASN GLY ALA GLY LEU LEU ALA GLU LEU SEQRES 18 A 389 GLY LEU THR ARG GLU VAL HIS PHE MET THR ALA SER LEU SEQRES 19 A 389 ALA LYS THR PHE ALA TYR ARG ALA GLY ALA ILE TRP CYS SEQRES 20 A 389 ASN ASN GLU VAL ASN ARG CYS VAL PRO PHE ILE SER TYR SEQRES 21 A 389 PRO ALA ILE PHE SER SER THR LEU LEU PRO TYR GLU ALA SEQRES 22 A 389 ALA GLY LEU GLU THR THR LEU GLU ILE ILE GLU SER ALA SEQRES 23 A 389 ASP ASN ARG ARG GLN HIS LEU ASP ARG MET ALA ARG LYS SEQRES 24 A 389 LEU ARG ILE GLY LEU SER GLN LEU GLY LEU THR ILE ARG SEQRES 25 A 389 SER GLU SER GLN ILE ILE GLY LEU GLU THR GLY ASP GLU SEQRES 26 A 389 ARG ASN THR GLU LYS VAL ARG ASP TYR LEU GLU SER ASN SEQRES 27 A 389 GLY VAL PHE GLY SER VAL PHE CYS ARG PRO ALA THR SER SEQRES 28 A 389 LYS ASN LYS ASN ILE ILE ARG LEU SER LEU ASN SER ASP SEQRES 29 A 389 VAL ASN ASP GLU GLN ILE ALA LYS ILE ILE GLU VAL CYS SEQRES 30 A 389 SER ASP ALA VAL ASN TYR GLY ASP PHE TYR PHE ARG SEQRES 1 B 389 MET ASN LYS PRO GLN LEU PRO ASP PHE ILE GLN ASN LYS SEQRES 2 B 389 ILE ASP HIS TYR ILE GLU ASN TYR PHE ASP ILE ASN LYS SEQRES 3 B 389 ASN GLY LYS HIS LEU VAL LEU GLY LYS GLN ALA SER PRO SEQRES 4 B 389 ASP ASP ILE ILE LEU GLN SER ASN ASP TYR LEU ALA LEU SEQRES 5 B 389 ALA ASN HIS PRO LEU ILE LYS ALA ARG LEU ALA LYS SER SEQRES 6 B 389 LEU LEU GLU GLU GLN GLN SER LEU PHE MET SER ALA SER SEQRES 7 B 389 PHE LEU GLN ASN ASP TYR ASP LYS PRO MET ILE GLU LYS SEQRES 8 B 389 ARG LEU ALA LYS PHE THR GLY PHE ASP GLU CYS LEU LEU SEQRES 9 B 389 SER GLN SER GLY TRP ASN ALA ASN VAL GLY LEU LEU GLN SEQRES 10 B 389 THR ILE CYS GLN PRO ASN THR ASN VAL TYR ILE ASP PHE SEQRES 11 B 389 PHE ALA HIS MET SER LEU TRP GLU GLY ALA ARG TYR ALA SEQRES 12 B 389 ASN ALA GLN ALA HIS PRO PHE MET HIS ASN ASN CYS ASP SEQRES 13 B 389 HIS LEU ARG MET LEU ILE GLN ARG HIS GLY PRO GLY ILE SEQRES 14 B 389 ILE VAL VAL ASP SER ILE TYR SER THR LEU GLY THR ILE SEQRES 15 B 389 ALA PRO LEU ALA GLU LEU VAL ASN ILE SER LYS GLU PHE SEQRES 16 B 389 GLY CYS ALA LEU LEU VAL ASP GLU SER HIS SER LEU GLY SEQRES 17 B 389 THR HIS GLY PRO ASN GLY ALA GLY LEU LEU ALA GLU LEU SEQRES 18 B 389 GLY LEU THR ARG GLU VAL HIS PHE MET THR ALA SER LEU SEQRES 19 B 389 ALA LYS THR PHE ALA TYR ARG ALA GLY ALA ILE TRP CYS SEQRES 20 B 389 ASN ASN GLU VAL ASN ARG CYS VAL PRO PHE ILE SER TYR SEQRES 21 B 389 PRO ALA ILE PHE SER SER THR LEU LEU PRO TYR GLU ALA SEQRES 22 B 389 ALA GLY LEU GLU THR THR LEU GLU ILE ILE GLU SER ALA SEQRES 23 B 389 ASP ASN ARG ARG GLN HIS LEU ASP ARG MET ALA ARG LYS SEQRES 24 B 389 LEU ARG ILE GLY LEU SER GLN LEU GLY LEU THR ILE ARG SEQRES 25 B 389 SER GLU SER GLN ILE ILE GLY LEU GLU THR GLY ASP GLU SEQRES 26 B 389 ARG ASN THR GLU LYS VAL ARG ASP TYR LEU GLU SER ASN SEQRES 27 B 389 GLY VAL PHE GLY SER VAL PHE CYS ARG PRO ALA THR SER SEQRES 28 B 389 LYS ASN LYS ASN ILE ILE ARG LEU SER LEU ASN SER ASP SEQRES 29 B 389 VAL ASN ASP GLU GLN ILE ALA LYS ILE ILE GLU VAL CYS SEQRES 30 B 389 SER ASP ALA VAL ASN TYR GLY ASP PHE TYR PHE ARG HET P89 A 605 28 HET SO4 A1390 5 HET P89 B 605 28 HET CL B1390 1 HET SO4 B1391 5 HETNAM P89 [6-METHYL-5-OXIDANYL-4-[(~{E})-2- HETNAM 2 P89 OXIDANYLIDENEUNDECYLIMINOMETHYL]PYRIDIN-3-YL]METHYL HETNAM 3 P89 DIHYDROGEN PHOSPHATE HETNAM SO4 SULFATE ION HETNAM CL CHLORIDE ION FORMUL 3 P89 2(C19 H31 N2 O6 P) FORMUL 4 SO4 2(O4 S 2-) FORMUL 6 CL CL 1- FORMUL 8 HOH *822(H2 O) HELIX 1 1 PRO A 7 PHE A 22 1 16 HELIX 2 2 HIS A 55 GLU A 68 1 14 HELIX 3 3 SER A 76 GLN A 81 5 6 HELIX 4 4 ASN A 82 LYS A 86 5 5 HELIX 5 5 PRO A 87 THR A 97 1 11 HELIX 6 6 LEU A 115 CYS A 120 1 6 HELIX 7 7 HIS A 133 GLU A 138 1 6 HELIX 8 8 ASN A 154 HIS A 165 1 12 HELIX 9 9 PRO A 184 PHE A 195 1 12 HELIX 10 10 LEU A 223 VAL A 227 5 5 HELIX 11 11 GLU A 250 ARG A 253 5 4 HELIX 12 12 CYS A 254 SER A 259 1 6 HELIX 13 13 SER A 259 SER A 265 1 7 HELIX 14 14 LEU A 269 ALA A 274 1 6 HELIX 15 15 LEU A 276 SER A 285 1 10 HELIX 16 16 ALA A 286 ILE A 302 1 17 HELIX 17 17 ASP A 324 ASN A 338 1 15 HELIX 18 18 ASN A 366 TYR A 383 1 18 HELIX 19 19 PRO B 7 PHE B 22 1 16 HELIX 20 20 HIS B 55 LEU B 67 1 13 HELIX 21 21 SER B 76 GLN B 81 5 6 HELIX 22 22 ASN B 82 LYS B 86 5 5 HELIX 23 23 PRO B 87 THR B 97 1 11 HELIX 24 24 LEU B 115 CYS B 120 1 6 HELIX 25 25 HIS B 133 GLU B 138 1 6 HELIX 26 26 ASN B 154 HIS B 165 1 12 HELIX 27 27 PRO B 184 PHE B 195 1 12 HELIX 28 28 LEU B 223 VAL B 227 5 5 HELIX 29 29 GLU B 250 VAL B 255 1 6 HELIX 30 30 PRO B 256 ILE B 258 5 3 HELIX 31 31 SER B 259 SER B 265 1 7 HELIX 32 32 LEU B 269 ALA B 274 1 6 HELIX 33 33 LEU B 276 SER B 285 1 10 HELIX 34 34 ALA B 286 ILE B 302 1 17 HELIX 35 35 ASP B 324 ASN B 338 1 15 HELIX 36 36 ASN B 366 TYR B 383 1 18 SHEET 1 AA 7 GLU A 101 LEU A 103 0 SHEET 2 AA 7 ILE A 245 CYS A 247 -1 O ILE A 245 N LEU A 103 SHEET 3 AA 7 PHE A 229 THR A 231 -1 O MET A 230 N TRP A 246 SHEET 4 AA 7 LEU A 199 ASP A 202 1 O LEU A 199 N PHE A 229 SHEET 5 AA 7 ILE A 170 ASP A 173 1 O ILE A 170 N LEU A 200 SHEET 6 AA 7 ASN A 125 ASP A 129 1 O TYR A 127 N VAL A 171 SHEET 7 AA 7 GLN A 146 PHE A 150 1 O GLN A 146 N VAL A 126 SHEET 1 AB 3 ILE A 317 GLU A 321 0 SHEET 2 AB 3 ILE A 356 SER A 360 -1 N ILE A 357 O LEU A 320 SHEET 3 AB 3 VAL A 344 PHE A 345 -1 O PHE A 345 N ILE A 356 SHEET 1 BA 7 GLU B 101 LEU B 103 0 SHEET 2 BA 7 ILE B 245 CYS B 247 -1 O ILE B 245 N LEU B 103 SHEET 3 BA 7 PHE B 229 THR B 231 -1 O MET B 230 N TRP B 246 SHEET 4 BA 7 LEU B 199 ASP B 202 1 O LEU B 199 N PHE B 229 SHEET 5 BA 7 ILE B 170 ASP B 173 1 O ILE B 170 N LEU B 200 SHEET 6 BA 7 ASN B 125 ASP B 129 1 O TYR B 127 N VAL B 171 SHEET 7 BA 7 GLN B 146 PHE B 150 1 O GLN B 146 N VAL B 126 SHEET 1 BB 3 ILE B 317 GLU B 321 0 SHEET 2 BB 3 ILE B 356 SER B 360 -1 N ILE B 357 O LEU B 320 SHEET 3 BB 3 VAL B 344 PHE B 345 -1 O PHE B 345 N ILE B 356 SITE 1 AC1 24 HIS A 30 SER A 107 GLY A 108 TRP A 109 SITE 2 AC1 24 HIS A 133 ASP A 173 SER A 177 ASP A 202 SITE 3 AC1 24 SER A 204 HIS A 205 SER A 233 LYS A 236 SITE 4 AC1 24 ALA A 242 PHE A 345 CYS A 346 PRO A 348 SITE 5 AC1 24 HOH A2264 HOH A2389 HOH A2390 ILE B 263 SITE 6 AC1 24 PHE B 264 SER B 265 SER B 266 CL B1390 SITE 1 AC2 22 PHE A 257 ILE A 263 PHE A 264 SER A 265 SITE 2 AC2 22 SER A 266 SER B 107 GLY B 108 TRP B 109 SITE 3 AC2 22 HIS B 133 ASP B 173 SER B 177 ASP B 202 SITE 4 AC2 22 SER B 204 HIS B 205 SER B 233 LYS B 236 SITE 5 AC2 22 PHE B 345 CYS B 346 PRO B 348 HOH B2427 SITE 6 AC2 22 HOH B2428 HOH B2429 SITE 1 AC3 5 P89 A 605 HOH A2060 MET B 75 SER B 76 SITE 2 AC3 5 PHE B 79 SITE 1 AC4 3 HIS A 292 ARG A 295 HOH A2392 SITE 1 AC5 5 GLN A 291 GLN B 291 HIS B 292 ARG B 295 SITE 2 AC5 5 HOH B2430 CRYST1 178.030 70.570 70.670 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 0.005617 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014170 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014150 0.00000