HEADER TRANSCRIPTION 20-MAR-07 2P7J TITLE CRYSTAL STRUCTURE OF THE DOMAIN OF PUTATIVE SENSORY BOX/GGDEF FAMILY TITLE 2 PROTEIN FROM VIBRIO PARAHAEMOLYTICUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE SENSORY BOX/GGDEF FAMILY PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 27-312; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO PARAHAEMOLYTICUS RIMD 2210633; SOURCE 3 ORGANISM_TAXID: 223926; SOURCE 4 STRAIN: 223926; SOURCE 5 GENE: VP0354; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PDM68 KEYWDS SENSORY BOX/GGDEF FAMILY PROTEIN, STRUCTURAL GENOMICS, MCSG, PSI-2, KEYWDS 2 PROTEIN STRUCTURE INITIATIVE, MIDWEST CENTER FOR STRUCTURAL KEYWDS 3 GENOMICS, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR R.WU,A.JAMES,A.JOACHIMIAK,MIDWEST CENTER FOR STRUCTURAL GENOMICS AUTHOR 2 (MCSG) REVDAT 4 06-NOV-24 2P7J 1 REMARK SEQADV LINK REVDAT 3 13-JUL-11 2P7J 1 VERSN REVDAT 2 24-FEB-09 2P7J 1 VERSN REVDAT 1 01-MAY-07 2P7J 0 JRNL AUTH R.WU,A.JAMES,A.JOACHIMIAK JRNL TITL THE CRYSTAL STRUCTURE OF THE DOMAIN OF PUTATIVE SENSORY JRNL TITL 2 BOX/GGDEF FAMILY PROTEIN FROM VIBRIO PARAHAEMOLYTICUS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD WITH PHASES REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.69 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 33090 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) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1746 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) : 2.25 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.31 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2173 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.32 REMARK 3 BIN R VALUE (WORKING SET) : 0.2090 REMARK 3 BIN FREE R VALUE SET COUNT : 110 REMARK 3 BIN FREE R VALUE : 0.2570 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4391 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 321 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 43.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.19 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.64000 REMARK 3 B22 (A**2) : 0.81000 REMARK 3 B33 (A**2) : -2.45000 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): 0.264 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.210 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.149 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.175 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.929 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4619 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6275 ; 1.544 ; 1.963 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 562 ;11.550 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 240 ;37.487 ;24.500 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 813 ;14.415 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 31 ;19.239 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 674 ; 0.115 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3581 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2048 ; 0.213 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3179 ; 0.306 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 353 ; 0.189 ; 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): 55 ; 0.248 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 17 ; 0.280 ; 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): 2771 ; 0.709 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4502 ; 1.378 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1911 ; 2.154 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1773 ; 3.484 ; 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 10 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 9 A 60 REMARK 3 RESIDUE RANGE : A 61 A 120 REMARK 3 RESIDUE RANGE : A 121 A 180 REMARK 3 RESIDUE RANGE : A 181 A 240 REMARK 3 RESIDUE RANGE : A 241 A 273 REMARK 3 RESIDUE RANGE : B 8 B 60 REMARK 3 RESIDUE RANGE : B 61 B 120 REMARK 3 RESIDUE RANGE : B 121 B 180 REMARK 3 RESIDUE RANGE : B 181 B 240 REMARK 3 RESIDUE RANGE : B 241 B 281 REMARK 3 ORIGIN FOR THE GROUP (A): 43.3463 28.0199 9.8719 REMARK 3 T TENSOR REMARK 3 T11: -0.0815 T22: -0.0562 REMARK 3 T33: -0.0792 T12: -0.0376 REMARK 3 T13: 0.0194 T23: -0.0190 REMARK 3 L TENSOR REMARK 3 L11: 0.3320 L22: 0.5334 REMARK 3 L33: 0.6171 L12: -0.0627 REMARK 3 L13: 0.1315 L23: -0.1556 REMARK 3 S TENSOR REMARK 3 S11: -0.0217 S12: 0.0485 S13: -0.0119 REMARK 3 S21: -0.0377 S22: 0.0122 S23: -0.0057 REMARK 3 S31: 0.0506 S32: -0.0055 S33: 0.0094 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 2P7J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-MAR-07. REMARK 100 THE DEPOSITION ID IS D_1000042064. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-FEB-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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) : 0.97930 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL 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 : 33442 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 9.000 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 32.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.80 REMARK 200 R MERGE FOR SHELL (I) : 0.58300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.960 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: HKL-3000 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M LISO4, 25% PEG 4000, PH 7.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 36.49000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 60.92550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.79800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 60.92550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 36.49000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.79800 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 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 2 CHAIN(S). AUTHORS STATE THAT THE REMARK 300 BIOLOGICAL UNIT OF THIS PROTEIN IS A DIMER. SEE REMARK 350 REMARK 300 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). 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 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 ASN A 0 REMARK 465 GLN A 1 REMARK 465 LYS A 2 REMARK 465 TYR A 3 REMARK 465 GLN A 4 REMARK 465 ALA A 5 REMARK 465 LEU A 6 REMARK 465 LEU A 7 REMARK 465 ALA A 8 REMARK 465 ARG A 274 REMARK 465 ALA A 275 REMARK 465 THR A 276 REMARK 465 ARG A 277 REMARK 465 ASP A 278 REMARK 465 ILE A 279 REMARK 465 ASN A 280 REMARK 465 ASP A 281 REMARK 465 LEU A 282 REMARK 465 ILE A 283 REMARK 465 GLN A 284 REMARK 465 GLU A 285 REMARK 465 SER A 286 REMARK 465 ASN B 0 REMARK 465 GLN B 1 REMARK 465 LYS B 2 REMARK 465 TYR B 3 REMARK 465 GLN B 4 REMARK 465 ALA B 5 REMARK 465 LEU B 6 REMARK 465 LEU B 7 REMARK 465 LEU B 282 REMARK 465 ILE B 283 REMARK 465 GLN B 284 REMARK 465 GLU B 285 REMARK 465 SER B 286 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 SER A 101 CB OG REMARK 470 SER B 101 CB OG 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 OD1 ASP A 139 O HOH A 646 1.90 REMARK 500 OE1 GLN B 35 O HOH B 730 1.91 REMARK 500 O HOH B 658 O HOH B 728 1.92 REMARK 500 NH2 ARG A 110 O HOH A 646 2.01 REMARK 500 NE ARG A 110 O HOH A 646 2.16 REMARK 500 O HOH B 658 O HOH B 697 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 NH2 ARG A 186 OD2 ASP B 34 4455 2.08 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 ASP A 172 N - CA - C ANGL. DEV. = -22.8 DEGREES REMARK 500 ARG A 186 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ASP B 172 N - CA - C ANGL. DEV. = -23.2 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 PRO A 56 47.59 -70.60 REMARK 500 LYS A 76 -26.57 68.43 REMARK 500 SER A 202 146.91 -176.98 REMARK 500 TYR A 209 37.96 70.21 REMARK 500 VAL A 255 -63.90 68.27 REMARK 500 LYS B 76 -30.25 69.55 REMARK 500 GLU B 127 -0.08 65.32 REMARK 500 ASP B 161 15.60 58.71 REMARK 500 ASP B 161 15.60 59.21 REMARK 500 SER B 202 145.82 -171.64 REMARK 500 ALA B 237 141.66 -171.93 REMARK 500 VAL B 255 -61.24 66.98 REMARK 500 ARG B 274 5.29 -64.99 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 VAL A 171 ASP A 172 -128.51 REMARK 500 LEU A 271 SER A 272 32.66 REMARK 500 VAL B 171 ASP B 172 -126.22 REMARK 500 TYR B 225 PRO B 226 -130.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY B 601 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: APC90919.1 RELATED DB: TARGETDB DBREF 2P7J A 1 286 UNP Q87SR8 Q87SR8_VIBPA 27 312 DBREF 2P7J B 1 286 UNP Q87SR8 Q87SR8_VIBPA 27 312 SEQADV 2P7J ASN A 0 UNP Q87SR8 CLONING ARTIFACT SEQADV 2P7J MSE A 67 UNP Q87SR8 MET 93 MODIFIED RESIDUE SEQADV 2P7J MSE A 155 UNP Q87SR8 MET 181 MODIFIED RESIDUE SEQADV 2P7J MSE A 224 UNP Q87SR8 MET 250 MODIFIED RESIDUE SEQADV 2P7J ASN B 0 UNP Q87SR8 CLONING ARTIFACT SEQADV 2P7J MSE B 67 UNP Q87SR8 MET 93 MODIFIED RESIDUE SEQADV 2P7J MSE B 155 UNP Q87SR8 MET 181 MODIFIED RESIDUE SEQADV 2P7J MSE B 224 UNP Q87SR8 MET 250 MODIFIED RESIDUE SEQRES 1 A 287 ASN GLN LYS TYR GLN ALA LEU LEU ALA ASN ASN VAL GLU SEQRES 2 A 287 ASN THR ALA LYS GLU ALA LEU HIS GLN LEU ALA TYR THR SEQRES 3 A 287 GLY ARG GLU TYR ASN ASN ILE GLN ASP GLN ILE GLU THR SEQRES 4 A 287 ILE SER ASP LEU LEU GLY HIS SER GLN SER LEU TYR ASP SEQRES 5 A 287 TYR LEU ARG GLU PRO SER LYS ALA ASN LEU THR ILE LEU SEQRES 6 A 287 GLU ASN MSE TRP SER SER VAL ALA ARG ASN GLN LYS LEU SEQRES 7 A 287 TYR LYS GLN ILE ARG PHE LEU ASP THR SER GLY THR GLU SEQRES 8 A 287 LYS VAL ARG ILE LYS TYR ASP PHE LYS THR SER ILE ALA SEQRES 9 A 287 GLY PRO SER LEU ILE LEU ARG ASP LYS SER ALA ARG GLU SEQRES 10 A 287 TYR PHE LYS TYR ALA GLN SER LEU ASP ASN GLU GLN ILE SEQRES 11 A 287 SER ALA TRP GLY ILE GLU LEU GLU ARG ASP LYS GLY GLU SEQRES 12 A 287 LEU VAL TYR PRO LEU SER PRO SER LEU ARG ILE LEU MSE SEQRES 13 A 287 PRO ILE SER VAL ASN ASP VAL ARG GLN GLY TYR LEU VAL SEQRES 14 A 287 LEU ASN VAL ASP ILE GLU TYR LEU SER SER LEU LEU ASN SEQRES 15 A 287 TYR SER PRO VAL ARG ASP PHE HIS ILE GLU LEU VAL LYS SEQRES 16 A 287 HIS LYS GLY PHE TYR ILE ALA SER PRO ASP GLU SER ARG SEQRES 17 A 287 LEU TYR GLY ASP ILE ILE PRO GLU ARG SER GLN PHE ASN SEQRES 18 A 287 PHE SER ASN MSE TYR PRO ASP ILE TRP PRO ARG VAL VAL SEQRES 19 A 287 SER GLU GLN ALA GLY TYR SER TYR SER GLY GLU HIS LEU SEQRES 20 A 287 ILE ALA PHE SER SER ILE LYS PHE VAL SER ASN GLU PRO SEQRES 21 A 287 LEU HIS LEU ILE ILE ASP LEU SER ASN GLU GLN LEU SER SEQRES 22 A 287 LYS ARG ALA THR ARG ASP ILE ASN ASP LEU ILE GLN GLU SEQRES 23 A 287 SER SEQRES 1 B 287 ASN GLN LYS TYR GLN ALA LEU LEU ALA ASN ASN VAL GLU SEQRES 2 B 287 ASN THR ALA LYS GLU ALA LEU HIS GLN LEU ALA TYR THR SEQRES 3 B 287 GLY ARG GLU TYR ASN ASN ILE GLN ASP GLN ILE GLU THR SEQRES 4 B 287 ILE SER ASP LEU LEU GLY HIS SER GLN SER LEU TYR ASP SEQRES 5 B 287 TYR LEU ARG GLU PRO SER LYS ALA ASN LEU THR ILE LEU SEQRES 6 B 287 GLU ASN MSE TRP SER SER VAL ALA ARG ASN GLN LYS LEU SEQRES 7 B 287 TYR LYS GLN ILE ARG PHE LEU ASP THR SER GLY THR GLU SEQRES 8 B 287 LYS VAL ARG ILE LYS TYR ASP PHE LYS THR SER ILE ALA SEQRES 9 B 287 GLY PRO SER LEU ILE LEU ARG ASP LYS SER ALA ARG GLU SEQRES 10 B 287 TYR PHE LYS TYR ALA GLN SER LEU ASP ASN GLU GLN ILE SEQRES 11 B 287 SER ALA TRP GLY ILE GLU LEU GLU ARG ASP LYS GLY GLU SEQRES 12 B 287 LEU VAL TYR PRO LEU SER PRO SER LEU ARG ILE LEU MSE SEQRES 13 B 287 PRO ILE SER VAL ASN ASP VAL ARG GLN GLY TYR LEU VAL SEQRES 14 B 287 LEU ASN VAL ASP ILE GLU TYR LEU SER SER LEU LEU ASN SEQRES 15 B 287 TYR SER PRO VAL ARG ASP PHE HIS ILE GLU LEU VAL LYS SEQRES 16 B 287 HIS LYS GLY PHE TYR ILE ALA SER PRO ASP GLU SER ARG SEQRES 17 B 287 LEU TYR GLY ASP ILE ILE PRO GLU ARG SER GLN PHE ASN SEQRES 18 B 287 PHE SER ASN MSE TYR PRO ASP ILE TRP PRO ARG VAL VAL SEQRES 19 B 287 SER GLU GLN ALA GLY TYR SER TYR SER GLY GLU HIS LEU SEQRES 20 B 287 ILE ALA PHE SER SER ILE LYS PHE VAL SER ASN GLU PRO SEQRES 21 B 287 LEU HIS LEU ILE ILE ASP LEU SER ASN GLU GLN LEU SER SEQRES 22 B 287 LYS ARG ALA THR ARG ASP ILE ASN ASP LEU ILE GLN GLU SEQRES 23 B 287 SER MODRES 2P7J MSE A 67 MET SELENOMETHIONINE MODRES 2P7J MSE A 155 MET SELENOMETHIONINE MODRES 2P7J MSE A 224 MET SELENOMETHIONINE MODRES 2P7J MSE B 67 MET SELENOMETHIONINE MODRES 2P7J MSE B 155 MET SELENOMETHIONINE MODRES 2P7J MSE B 224 MET SELENOMETHIONINE HET MSE A 67 8 HET MSE A 155 8 HET MSE A 224 8 HET MSE B 67 16 HET MSE B 155 8 HET MSE B 224 8 HET SO4 A 501 5 HET NA B 401 1 HET SO4 B 502 5 HET ACY B 601 4 HETNAM MSE SELENOMETHIONINE HETNAM SO4 SULFATE ION HETNAM NA SODIUM ION HETNAM ACY ACETIC ACID FORMUL 1 MSE 6(C5 H11 N O2 SE) FORMUL 3 SO4 2(O4 S 2-) FORMUL 4 NA NA 1+ FORMUL 6 ACY C2 H4 O2 FORMUL 7 HOH *321(H2 O) HELIX 1 1 ASN A 9 HIS A 45 1 37 HELIX 2 2 SER A 46 GLU A 55 1 10 HELIX 3 3 SER A 57 LYS A 76 1 20 HELIX 4 4 ARG A 115 SER A 123 1 9 HELIX 5 5 ILE A 173 ASN A 181 1 9 HELIX 6 6 ASP A 204 LEU A 208 5 5 HELIX 7 7 ASN A 220 TYR A 225 1 6 HELIX 8 8 ILE A 228 SER A 234 1 7 HELIX 9 9 ASN A 268 SER A 272 1 5 HELIX 10 10 ASN B 9 HIS B 45 1 37 HELIX 11 11 SER B 46 GLU B 55 1 10 HELIX 12 12 SER B 57 LYS B 76 1 20 HELIX 13 13 ARG B 115 SER B 123 1 9 HELIX 14 14 ILE B 173 ASN B 181 1 9 HELIX 15 15 ASP B 204 LEU B 208 5 5 HELIX 16 16 ILE B 213 SER B 217 5 5 HELIX 17 17 ASN B 220 TYR B 225 1 6 HELIX 18 18 ILE B 228 GLU B 235 1 8 HELIX 19 19 ASN B 268 ARG B 274 1 7 SHEET 1 A 6 ILE A 102 PRO A 105 0 SHEET 2 A 6 GLU A 90 ASP A 97 -1 N LYS A 95 O GLY A 104 SHEET 3 A 6 TYR A 78 LEU A 84 -1 N PHE A 83 O LYS A 91 SHEET 4 A 6 VAL A 162 ASP A 172 -1 O TYR A 166 N LEU A 84 SHEET 5 A 6 PRO A 149 VAL A 159 -1 N ILE A 157 O GLN A 164 SHEET 6 A 6 SER A 130 LEU A 136 -1 N SER A 130 O LEU A 154 SHEET 1 B 2 ARG A 138 ASP A 139 0 SHEET 2 B 2 GLU A 142 LEU A 143 -1 O GLU A 142 N ASP A 139 SHEET 1 C 3 TYR A 182 SER A 183 0 SHEET 2 C 3 PHE A 188 VAL A 193 -1 O PHE A 188 N SER A 183 SHEET 3 C 3 TYR A 199 ALA A 201 -1 O ILE A 200 N LEU A 192 SHEET 1 D 5 TYR A 182 SER A 183 0 SHEET 2 D 5 PHE A 188 VAL A 193 -1 O PHE A 188 N SER A 183 SHEET 3 D 5 PRO A 259 SER A 267 -1 O ILE A 263 N GLU A 191 SHEET 4 D 5 HIS A 245 LYS A 253 -1 N LEU A 246 O LEU A 266 SHEET 5 D 5 GLY A 238 TYR A 241 -1 N SER A 240 O ILE A 247 SHEET 1 E 6 ILE B 102 PRO B 105 0 SHEET 2 E 6 GLU B 90 ASP B 97 -1 N ASP B 97 O ILE B 102 SHEET 3 E 6 TYR B 78 ASP B 85 -1 N PHE B 83 O LYS B 91 SHEET 4 E 6 VAL B 162 ASP B 172 -1 O VAL B 168 N ARG B 82 SHEET 5 E 6 PRO B 149 VAL B 159 -1 N ILE B 157 O GLN B 164 SHEET 6 E 6 SER B 130 LEU B 136 -1 N SER B 130 O LEU B 154 SHEET 1 F 2 ARG B 138 ASP B 139 0 SHEET 2 F 2 GLU B 142 LEU B 143 -1 O GLU B 142 N ASP B 139 SHEET 1 G 3 TYR B 182 SER B 183 0 SHEET 2 G 3 PHE B 188 VAL B 193 -1 O PHE B 188 N SER B 183 SHEET 3 G 3 TYR B 199 ALA B 201 -1 O ILE B 200 N LEU B 192 SHEET 1 H 5 TYR B 182 SER B 183 0 SHEET 2 H 5 PHE B 188 VAL B 193 -1 O PHE B 188 N SER B 183 SHEET 3 H 5 PRO B 259 SER B 267 -1 O ILE B 263 N GLU B 191 SHEET 4 H 5 HIS B 245 LYS B 253 -1 N SER B 250 O LEU B 262 SHEET 5 H 5 ALA B 237 TYR B 241 -1 N SER B 240 O ILE B 247 LINK C ASN A 66 N MSE A 67 1555 1555 1.33 LINK C MSE A 67 N TRP A 68 1555 1555 1.33 LINK C LEU A 154 N MSE A 155 1555 1555 1.32 LINK C MSE A 155 N PRO A 156 1555 1555 1.35 LINK C AASN A 223 N MSE A 224 1555 1555 1.33 LINK C BASN A 223 N MSE A 224 1555 1555 1.33 LINK C MSE A 224 N TYR A 225 1555 1555 1.34 LINK C ASN B 66 N BMSE B 67 1555 1555 1.33 LINK C ASN B 66 N CMSE B 67 1555 1555 1.33 LINK C CMSE B 67 N TRP B 68 1555 1555 1.33 LINK C BMSE B 67 N TRP B 68 1555 1555 1.33 LINK C LEU B 154 N MSE B 155 1555 1555 1.33 LINK C MSE B 155 N PRO B 156 1555 1555 1.35 LINK C ASN B 223 N MSE B 224 1555 1555 1.33 LINK C MSE B 224 N TYR B 225 1555 1555 1.33 CISPEP 1 TYR A 145 PRO A 146 0 -2.02 CISPEP 2 ALA B 8 ASN B 9 0 -2.57 CISPEP 3 TYR B 145 PRO B 146 0 -3.62 CISPEP 4 SER B 242 GLY B 243 0 -4.65 SITE 1 AC1 3 LYS B 112 ARG B 115 GLY B 141 SITE 1 AC2 10 GLN A 80 ARG A 82 LYS A 112 ARG A 115 SITE 2 AC2 10 TYR A 117 GLU A 137 ARG A 138 ARG A 152 SITE 3 AC2 10 ASN A 170 HOH A 530 SITE 1 AC3 10 GLN B 80 ARG B 82 LYS B 112 ARG B 115 SITE 2 AC3 10 TYR B 117 GLU B 137 ARG B 138 ARG B 152 SITE 3 AC3 10 ASN B 170 HOH B 703 SITE 1 AC4 9 GLN B 80 GLU B 90 ARG B 93 ILE B 108 SITE 2 AC4 9 ARG B 110 LYS B 112 ARG B 138 ASP B 139 SITE 3 AC4 9 HOH B 703 CRYST1 72.980 81.596 121.851 90.00 90.00 90.00 P 21 21 21 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 0.013702 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012256 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008207 0.00000