HEADER TRANSCRIPTION REGULATOR 23-MAY-08 3D8U TITLE THE CRYSTAL STRUCTURE OF A PURR FAMILY TRANSCRIPTIONAL REGULATOR FROM TITLE 2 VIBRIO PARAHAEMOLYTICUS RIMD 2210633 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PURR TRANSCRIPTIONAL REGULATOR; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO PARAHAEMOLYTICUS; SOURCE 3 ORGANISM_TAXID: 670; SOURCE 4 STRAIN: RIMD 2210633; SOURCE 5 GENE: VPA0232; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PMCSG8 KEYWDS APC91343.1, PURR, TRANSCRIPTIONAL REGULATOR, VIBRIO PARAHAEMOLYTICUS KEYWDS 2 RIMD 2210633, STRUCTURAL GENOMICS, PSI-2, PROTEIN STRUCTURE KEYWDS 3 INITIATIVE, MIDWEST CENTER FOR STRUCTURAL GENOMICS, MCSG, DNA- KEYWDS 4 BINDING, TRANSCRIPTION, TRANSCRIPTION REGULATION, TRANSCRIPTION KEYWDS 5 REGULATOR EXPDTA X-RAY DIFFRACTION AUTHOR K.TAN,C.HATZOS,S.MOY,A.JOACHIMIAK,MIDWEST CENTER FOR STRUCTURAL AUTHOR 2 GENOMICS (MCSG) REVDAT 3 13-JUL-11 3D8U 1 VERSN REVDAT 2 24-FEB-09 3D8U 1 VERSN REVDAT 1 22-JUL-08 3D8U 0 JRNL AUTH K.TAN,C.HATZOS,S.MOY,A.JOACHIMIAK JRNL TITL THE CRYSTAL STRUCTURE OF A PURR FAMILY TRANSCRIPTIONAL JRNL TITL 2 REGULATOR FROM VIBRIO PARAHAEMOLYTICUS RIMD 2210633 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.88 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.88 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.30 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 16601 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) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.283 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 891 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) : 2.88 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1054 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.48 REMARK 3 BIN R VALUE (WORKING SET) : 0.2600 REMARK 3 BIN FREE R VALUE SET COUNT : 53 REMARK 3 BIN FREE R VALUE : 0.3180 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3930 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 77.62 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.28000 REMARK 3 B22 (A**2) : -0.28000 REMARK 3 B33 (A**2) : 0.42000 REMARK 3 B12 (A**2) : -0.14000 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): 1.345 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.405 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.290 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 32.729 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.939 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.886 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4011 ; 0.015 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5437 ; 1.654 ; 1.953 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 531 ; 7.059 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 159 ;40.667 ;23.836 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 622 ;22.726 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;21.292 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 628 ; 0.117 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3018 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2029 ; 0.265 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2734 ; 0.321 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 147 ; 0.159 ; 0.200 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): 34 ; 0.312 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 6 ; 0.304 ; 0.200 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): 2685 ; 0.524 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4165 ; 0.952 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1446 ; 1.644 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1271 ; 2.616 ; 4.500 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 : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 71 A 169 REMARK 3 RESIDUE RANGE : A 302 A 321 REMARK 3 ORIGIN FOR THE GROUP (A): 65.1050 78.8530 26.3330 REMARK 3 T TENSOR REMARK 3 T11: 0.2094 T22: 0.3447 REMARK 3 T33: 0.4827 T12: -0.1352 REMARK 3 T13: 0.0957 T23: -0.3309 REMARK 3 L TENSOR REMARK 3 L11: 8.4026 L22: 1.0588 REMARK 3 L33: 4.3852 L12: -0.1407 REMARK 3 L13: 1.8062 L23: -2.0851 REMARK 3 S TENSOR REMARK 3 S11: -0.7859 S12: -0.1035 S13: 0.9516 REMARK 3 S21: -0.2386 S22: 1.0512 S23: -0.6778 REMARK 3 S31: -0.7658 S32: 0.1363 S33: -0.2653 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 170 A 301 REMARK 3 RESIDUE RANGE : A 328 A 340 REMARK 3 ORIGIN FOR THE GROUP (A): 70.0150 49.4070 28.6470 REMARK 3 T TENSOR REMARK 3 T11: -0.5697 T22: 0.2080 REMARK 3 T33: -0.3700 T12: 0.0525 REMARK 3 T13: 0.0261 T23: 0.0231 REMARK 3 L TENSOR REMARK 3 L11: 9.1962 L22: 3.6923 REMARK 3 L33: 3.4444 L12: 0.3190 REMARK 3 L13: 1.7538 L23: -1.3533 REMARK 3 S TENSOR REMARK 3 S11: -0.2336 S12: -1.7464 S13: -0.0339 REMARK 3 S21: -0.0117 S22: 0.3237 S23: -0.1207 REMARK 3 S31: -0.2219 S32: -0.4877 S33: -0.0901 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 71 B 169 REMARK 3 RESIDUE RANGE : B 302 B 324 REMARK 3 ORIGIN FOR THE GROUP (A): 43.1610 76.4340 18.7750 REMARK 3 T TENSOR REMARK 3 T11: 0.1722 T22: 0.3555 REMARK 3 T33: 0.3336 T12: -0.1525 REMARK 3 T13: -0.0329 T23: 0.3766 REMARK 3 L TENSOR REMARK 3 L11: 7.4207 L22: 6.5790 REMARK 3 L33: 4.9849 L12: 1.1214 REMARK 3 L13: 1.8882 L23: 3.4325 REMARK 3 S TENSOR REMARK 3 S11: -0.7233 S12: 0.6488 S13: 1.5124 REMARK 3 S21: -0.1817 S22: 0.4618 S23: 0.7536 REMARK 3 S31: -0.9865 S32: 0.0580 S33: 0.2615 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 170 B 301 REMARK 3 RESIDUE RANGE : B 326 B 342 REMARK 3 ORIGIN FOR THE GROUP (A): 39.4820 49.1370 29.0470 REMARK 3 T TENSOR REMARK 3 T11: -0.5916 T22: -0.0865 REMARK 3 T33: -0.4143 T12: -0.0245 REMARK 3 T13: 0.0503 T23: 0.0148 REMARK 3 L TENSOR REMARK 3 L11: 6.6177 L22: 4.9941 REMARK 3 L33: 3.6184 L12: -1.3494 REMARK 3 L13: 2.2913 L23: -0.8915 REMARK 3 S TENSOR REMARK 3 S11: -0.2010 S12: 0.7415 S13: 0.1318 REMARK 3 S21: 0.1287 S22: 0.1286 S23: 0.2988 REMARK 3 S31: -0.0385 S32: -0.0133 S33: 0.0723 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 REMARK 4 REMARK 4 3D8U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JUN-08. REMARK 100 THE RCSB ID CODE IS RCSB047737. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JUL-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97945, 0.97959 REMARK 200 MONOCHROMATOR : SI 111 CRYSTAL REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17527 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.880 REMARK 200 RESOLUTION RANGE LOW (A) : 41.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 10.400 REMARK 200 R MERGE (I) : 0.10500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 30.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.88 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.8 REMARK 200 DATA REDUNDANCY IN SHELL : 7.50 REMARK 200 R MERGE FOR SHELL (I) : 0.82200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHELXD/MLPHARE/DM/RESOLVE/HKL3000 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.0M SODIUM CITRATE 0.1M IMIDAZOLE, REMARK 280 PH 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 27.92000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 55.84000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 55.84000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 27.92000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 REMARK: AUTHORS STATE THAT THE BIOLOGICAL ASSEMBLY IS REMARK 300 EXPERIMENTALLY UNKNOWN. THE CHAINS A AND B ARE PREDICTED TO FORM A REMARK 300 DIMER. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23240 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 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 SER A 68 REMARK 465 ASN A 69 REMARK 465 ALA A 70 REMARK 465 PRO A 322 REMARK 465 GLU A 323 REMARK 465 GLU A 324 REMARK 465 ARG A 325 REMARK 465 PRO A 326 REMARK 465 THR A 327 REMARK 465 ILE A 341 REMARK 465 ASN A 342 REMARK 465 SER B 68 REMARK 465 ASN B 69 REMARK 465 ALA B 70 REMARK 465 GLY B 320 REMARK 465 ARG B 325 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 TYR A 71 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 PHE A 81 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 98 CG CD CE NZ REMARK 470 TYR A 101 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLN A 102 CG CD OE1 NE2 REMARK 470 ARG A 126 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 139 CG CD OE1 NE2 REMARK 470 ARG A 140 CG CD NE CZ NH1 NH2 REMARK 470 THR A 141 OG1 CG2 REMARK 470 LEU A 144 CG CD1 CD2 REMARK 470 LEU A 145 CG CD1 CD2 REMARK 470 GLU A 146 CG CD OE1 OE2 REMARK 470 GLU A 154 CG CD OE1 OE2 REMARK 470 LYS A 161 CG CD CE NZ REMARK 470 ILE A 167 CG1 CG2 CD1 REMARK 470 LYS A 309 CG CD CE NZ REMARK 470 LYS A 319 CG CD CE NZ REMARK 470 GLU A 321 CG CD OE1 OE2 REMARK 470 LYS A 332 CG CD CE NZ REMARK 470 TYR B 71 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LEU B 80 CG CD1 CD2 REMARK 470 PHE B 81 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLN B 102 CG CD OE1 NE2 REMARK 470 LEU B 104 CG CD1 CD2 REMARK 470 GLU B 113 CG CD OE1 OE2 REMARK 470 GLN B 114 CG CD OE1 NE2 REMARK 470 LYS B 117 CG CD CE NZ REMARK 470 LEU B 118 CG CD1 CD2 REMARK 470 LEU B 119 CG CD1 CD2 REMARK 470 SER B 120 OG REMARK 470 LEU B 123 CG CD1 CD2 REMARK 470 GLU B 124 CG CD OE1 OE2 REMARK 470 ARG B 126 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 136 CG CD OE1 OE2 REMARK 470 GLN B 139 CG CD OE1 NE2 REMARK 470 ARG B 140 CG CD NE CZ NH1 NH2 REMARK 470 GLN B 143 CG CD OE1 NE2 REMARK 470 LEU B 144 CG CD1 CD2 REMARK 470 LEU B 145 CG CD1 CD2 REMARK 470 GLU B 146 CG CD OE1 OE2 REMARK 470 ASN B 149 CG OD1 REMARK 470 LYS B 161 CG CD CE NZ REMARK 470 LEU B 165 CG CD1 CD2 REMARK 470 GLU B 304 CG CD OE1 OE2 REMARK 470 LYS B 313 CG CD CE NZ REMARK 470 LEU B 315 CG CD1 CD2 REMARK 470 HIS B 316 CG ND1 CD2 CE1 NE2 REMARK 470 ILE B 318 CG1 CG2 CD1 REMARK 470 LYS B 319 CG CD CE NZ REMARK 470 GLU B 321 CG CD OE1 OE2 REMARK 470 PRO B 322 CG CD REMARK 470 GLU B 323 CG CD OE1 OE2 REMARK 470 GLU B 324 CG CD OE1 OE2 REMARK 470 PRO B 326 CG CD 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 PRO A 78 C - N - CA ANGL. DEV. = 9.1 DEGREES REMARK 500 PRO B 220 C - N - CA ANGL. DEV. = 14.2 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 SER A 91 -38.70 -35.73 REMARK 500 ALA A 99 58.98 -112.50 REMARK 500 TYR A 110 -2.55 77.21 REMARK 500 ARG A 126 99.80 -49.30 REMARK 500 ALA A 128 77.15 40.89 REMARK 500 ARG A 140 27.05 -68.73 REMARK 500 THR A 141 -24.62 -159.52 REMARK 500 GLU A 146 30.47 -73.19 REMARK 500 ALA A 147 -69.82 -131.83 REMARK 500 SER A 148 2.18 -57.36 REMARK 500 ASN A 149 56.19 33.20 REMARK 500 ALA A 156 169.32 169.08 REMARK 500 ALA A 162 -0.72 61.65 REMARK 500 ARG A 196 6.14 80.87 REMARK 500 ASN A 198 -4.05 73.99 REMARK 500 GLU A 215 -39.16 -35.26 REMARK 500 GLU A 284 83.15 -156.65 REMARK 500 SER A 287 -17.91 -32.88 REMARK 500 SER A 295 -179.05 -46.01 REMARK 500 LYS A 334 101.20 -57.39 REMARK 500 SER A 338 14.43 -58.03 REMARK 500 LYS B 83 -53.64 -28.90 REMARK 500 ASP B 109 81.69 -45.44 REMARK 500 TYR B 110 52.47 28.26 REMARK 500 GLU B 116 -71.22 -58.82 REMARK 500 GLU B 124 2.10 -66.81 REMARK 500 SER B 125 -67.22 -106.75 REMARK 500 PRO B 127 -103.22 -62.87 REMARK 500 ALA B 128 -140.76 47.48 REMARK 500 HIS B 137 -157.75 -144.81 REMARK 500 GLN B 143 -79.89 -68.64 REMARK 500 ASN B 149 -2.93 54.24 REMARK 500 LYS B 161 95.89 31.88 REMARK 500 ALA B 162 -50.26 -26.08 REMARK 500 SER B 163 44.68 -85.03 REMARK 500 ARG B 196 54.14 37.49 REMARK 500 PRO B 220 44.87 -98.67 REMARK 500 ASP B 246 112.86 -166.29 REMARK 500 LEU B 249 137.18 -34.84 REMARK 500 GLU B 284 69.62 -161.68 REMARK 500 ASP B 302 79.94 -115.92 REMARK 500 THR B 327 66.69 -155.44 REMARK 500 LYS B 334 101.57 -59.93 REMARK 500 ARG B 336 -157.34 -128.02 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 TYR A 164 24.7 L L OUTSIDE RANGE REMARK 500 THR B 179 22.5 L L OUTSIDE RANGE REMARK 500 ASN B 189 20.6 L L OUTSIDE RANGE REMARK 500 LEU B 296 24.8 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: APC91343.1 RELATED DB: TARGETDB DBREF 3D8U A 71 342 UNP Q87JL7 Q87JL7_VIBPA 71 342 DBREF 3D8U B 71 342 UNP Q87JL7 Q87JL7_VIBPA 71 342 SEQADV 3D8U SER A 68 UNP Q87JL7 EXPRESSION TAG SEQADV 3D8U ASN A 69 UNP Q87JL7 EXPRESSION TAG SEQADV 3D8U ALA A 70 UNP Q87JL7 EXPRESSION TAG SEQADV 3D8U SER B 68 UNP Q87JL7 EXPRESSION TAG SEQADV 3D8U ASN B 69 UNP Q87JL7 EXPRESSION TAG SEQADV 3D8U ALA B 70 UNP Q87JL7 EXPRESSION TAG SEQRES 1 A 275 SER ASN ALA TYR SER ILE ALA LEU ILE ILE PRO SER LEU SEQRES 2 A 275 PHE GLU LYS ALA CYS ALA HIS PHE LEU PRO SER PHE GLN SEQRES 3 A 275 GLN ALA LEU ASN LYS ALA GLY TYR GLN LEU LEU LEU GLY SEQRES 4 A 275 TYR SER ASP TYR SER ILE GLU GLN GLU GLU LYS LEU LEU SEQRES 5 A 275 SER THR PHE LEU GLU SER ARG PRO ALA GLY VAL VAL LEU SEQRES 6 A 275 PHE GLY SER GLU HIS SER GLN ARG THR HIS GLN LEU LEU SEQRES 7 A 275 GLU ALA SER ASN THR PRO VAL LEU GLU ILE ALA GLU LEU SEQRES 8 A 275 SER SER LYS ALA SER TYR LEU ASN ILE GLY VAL ASP HIS SEQRES 9 A 275 PHE GLU VAL GLY LYS ALA CYS THR ARG HIS LEU ILE GLU SEQRES 10 A 275 GLN GLY PHE LYS ASN VAL GLY PHE ILE GLY ALA ARG GLY SEQRES 11 A 275 ASN HIS SER THR LEU GLN ARG GLN LEU HIS GLY TRP GLN SEQRES 12 A 275 SER ALA MSE ILE GLU ASN TYR LEU THR PRO ASP HIS PHE SEQRES 13 A 275 LEU THR THR HIS GLU ALA PRO SER SER GLN LEU GLY ALA SEQRES 14 A 275 GLU GLY LEU ALA LYS LEU LEU LEU ARG ASP SER SER LEU SEQRES 15 A 275 ASN ALA LEU VAL CYS SER HIS GLU GLU ILE ALA ILE GLY SEQRES 16 A 275 ALA LEU PHE GLU CYS HIS ARG ARG VAL LEU LYS VAL PRO SEQRES 17 A 275 THR ASP ILE ALA ILE ILE CYS LEU GLU GLY SER SER MSE SEQRES 18 A 275 GLY GLU HIS ALA TYR PRO SER LEU THR SER ALA GLU PHE SEQRES 19 A 275 ASP TYR GLU ARG MSE GLY THR LYS ALA ALA GLU LYS LEU SEQRES 20 A 275 LEU HIS ALA ILE LYS GLY GLU PRO GLU GLU ARG PRO THR SEQRES 21 A 275 SER MSE GLY PHE LYS LEU LYS ARG ARG ALA SER THR ALA SEQRES 22 A 275 ILE ASN SEQRES 1 B 275 SER ASN ALA TYR SER ILE ALA LEU ILE ILE PRO SER LEU SEQRES 2 B 275 PHE GLU LYS ALA CYS ALA HIS PHE LEU PRO SER PHE GLN SEQRES 3 B 275 GLN ALA LEU ASN LYS ALA GLY TYR GLN LEU LEU LEU GLY SEQRES 4 B 275 TYR SER ASP TYR SER ILE GLU GLN GLU GLU LYS LEU LEU SEQRES 5 B 275 SER THR PHE LEU GLU SER ARG PRO ALA GLY VAL VAL LEU SEQRES 6 B 275 PHE GLY SER GLU HIS SER GLN ARG THR HIS GLN LEU LEU SEQRES 7 B 275 GLU ALA SER ASN THR PRO VAL LEU GLU ILE ALA GLU LEU SEQRES 8 B 275 SER SER LYS ALA SER TYR LEU ASN ILE GLY VAL ASP HIS SEQRES 9 B 275 PHE GLU VAL GLY LYS ALA CYS THR ARG HIS LEU ILE GLU SEQRES 10 B 275 GLN GLY PHE LYS ASN VAL GLY PHE ILE GLY ALA ARG GLY SEQRES 11 B 275 ASN HIS SER THR LEU GLN ARG GLN LEU HIS GLY TRP GLN SEQRES 12 B 275 SER ALA MSE ILE GLU ASN TYR LEU THR PRO ASP HIS PHE SEQRES 13 B 275 LEU THR THR HIS GLU ALA PRO SER SER GLN LEU GLY ALA SEQRES 14 B 275 GLU GLY LEU ALA LYS LEU LEU LEU ARG ASP SER SER LEU SEQRES 15 B 275 ASN ALA LEU VAL CYS SER HIS GLU GLU ILE ALA ILE GLY SEQRES 16 B 275 ALA LEU PHE GLU CYS HIS ARG ARG VAL LEU LYS VAL PRO SEQRES 17 B 275 THR ASP ILE ALA ILE ILE CYS LEU GLU GLY SER SER MSE SEQRES 18 B 275 GLY GLU HIS ALA TYR PRO SER LEU THR SER ALA GLU PHE SEQRES 19 B 275 ASP TYR GLU ARG MSE GLY THR LYS ALA ALA GLU LYS LEU SEQRES 20 B 275 LEU HIS ALA ILE LYS GLY GLU PRO GLU GLU ARG PRO THR SEQRES 21 B 275 SER MSE GLY PHE LYS LEU LYS ARG ARG ALA SER THR ALA SEQRES 22 B 275 ILE ASN MODRES 3D8U MSE A 213 MET SELENOMETHIONINE MODRES 3D8U MSE A 288 MET SELENOMETHIONINE MODRES 3D8U MSE A 306 MET SELENOMETHIONINE MODRES 3D8U MSE A 329 MET SELENOMETHIONINE MODRES 3D8U MSE B 213 MET SELENOMETHIONINE MODRES 3D8U MSE B 288 MET SELENOMETHIONINE MODRES 3D8U MSE B 306 MET SELENOMETHIONINE MODRES 3D8U MSE B 329 MET SELENOMETHIONINE HET MSE A 213 8 HET MSE A 288 8 HET MSE A 306 8 HET MSE A 329 8 HET MSE B 213 8 HET MSE B 288 8 HET MSE B 306 8 HET MSE B 329 13 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 8(C5 H11 N O2 SE) HELIX 1 1 GLU A 82 ALA A 99 1 18 HELIX 2 2 SER A 111 GLU A 124 1 14 HELIX 3 3 SER A 138 ASN A 149 1 12 HELIX 4 4 ASP A 170 GLU A 184 1 15 HELIX 5 5 HIS A 199 ASN A 216 1 18 HELIX 6 6 SER A 231 LEU A 244 1 14 HELIX 7 7 HIS A 256 ARG A 270 1 15 HELIX 8 8 SER A 286 HIS A 291 1 6 HELIX 9 9 ASP A 302 LYS A 319 1 18 HELIX 10 10 GLU B 82 GLY B 100 1 19 HELIX 11 11 SER B 111 GLU B 124 1 14 HELIX 12 12 SER B 138 SER B 148 1 11 HELIX 13 13 ASP B 170 GLN B 185 1 16 HELIX 14 14 HIS B 199 ASN B 216 1 18 HELIX 15 15 SER B 231 ASP B 246 1 16 HELIX 16 16 HIS B 256 VAL B 271 1 16 HELIX 17 17 SER B 286 HIS B 291 1 6 HELIX 18 18 ASP B 302 LYS B 319 1 18 HELIX 19 19 ARG B 336 ALA B 340 5 5 SHEET 1 A 3 GLN A 102 LEU A 103 0 SHEET 2 A 3 SER A 72 ILE A 77 1 N ILE A 73 O GLN A 102 SHEET 3 A 3 GLY A 106 TYR A 107 1 O GLY A 106 N ILE A 77 SHEET 1 B 5 GLN A 102 LEU A 103 0 SHEET 2 B 5 SER A 72 ILE A 77 1 N ILE A 73 O GLN A 102 SHEET 3 B 5 VAL A 130 PHE A 133 1 O VAL A 131 N ALA A 74 SHEET 4 B 5 VAL A 152 ILE A 155 1 O ILE A 155 N LEU A 132 SHEET 5 B 5 LEU A 165 ILE A 167 1 O ILE A 167 N GLU A 154 SHEET 1 C 6 PHE A 223 THR A 225 0 SHEET 2 C 6 VAL A 190 GLY A 194 1 N PHE A 192 O LEU A 224 SHEET 3 C 6 ALA A 251 CYS A 254 1 O VAL A 253 N ILE A 193 SHEET 4 C 6 ALA A 279 CYS A 282 1 O ILE A 281 N LEU A 252 SHEET 5 C 6 THR A 297 GLU A 300 1 O THR A 297 N CYS A 282 SHEET 6 C 6 LYS A 332 LYS A 334 -1 O LYS A 332 N GLU A 300 SHEET 1 D 5 LEU B 103 TYR B 107 0 SHEET 2 D 5 ILE B 73 ILE B 77 1 N ILE B 77 O GLY B 106 SHEET 3 D 5 VAL B 130 PHE B 133 1 O VAL B 131 N ALA B 74 SHEET 4 D 5 VAL B 152 ILE B 155 1 O ILE B 155 N LEU B 132 SHEET 5 D 5 LEU B 165 ILE B 167 1 O LEU B 165 N GLU B 154 SHEET 1 E 4 PHE B 223 THR B 226 0 SHEET 2 E 4 VAL B 190 ALA B 195 1 N GLY B 194 O LEU B 224 SHEET 3 E 4 ALA B 251 CYS B 254 1 O ALA B 251 N GLY B 191 SHEET 4 E 4 ALA B 279 CYS B 282 1 O ILE B 281 N CYS B 254 SHEET 1 F 2 SER B 298 GLU B 300 0 SHEET 2 F 2 LYS B 332 LYS B 334 -1 O LYS B 332 N GLU B 300 LINK C ALA A 212 N MSE A 213 1555 1555 1.33 LINK C MSE A 213 N ILE A 214 1555 1555 1.32 LINK C SER A 287 N MSE A 288 1555 1555 1.32 LINK C MSE A 288 N GLY A 289 1555 1555 1.33 LINK C ARG A 305 N MSE A 306 1555 1555 1.33 LINK C MSE A 306 N GLY A 307 1555 1555 1.34 LINK C SER A 328 N MSE A 329 1555 1555 1.33 LINK C MSE A 329 N GLY A 330 1555 1555 1.33 LINK C ALA B 212 N MSE B 213 1555 1555 1.35 LINK C MSE B 213 N ILE B 214 1555 1555 1.33 LINK C SER B 287 N MSE B 288 1555 1555 1.33 LINK C MSE B 288 N GLY B 289 1555 1555 1.33 LINK C ARG B 305 N MSE B 306 1555 1555 1.33 LINK C MSE B 306 N GLY B 307 1555 1555 1.33 LINK C SER B 328 N MSE B 329 1555 1555 1.33 LINK C MSE B 329 N GLY B 330 1555 1555 1.33 CISPEP 1 VAL A 274 PRO A 275 0 21.86 CISPEP 2 TYR A 293 PRO A 294 0 -7.50 CISPEP 3 VAL B 274 PRO B 275 0 8.37 CISPEP 4 TYR B 293 PRO B 294 0 -9.69 CRYST1 126.264 126.264 83.760 90.00 90.00 120.00 P 31 2 1 12 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 0.007920 0.004573 0.000000 0.00000 SCALE2 0.000000 0.009145 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011939 0.00000