HEADER SIGNALING PROTEIN 24-JAN-10 3LID TITLE CRYSTAL STRUCTURE OF THE EXTRACELLULAR DOMAIN OF THE PUTATIVE TITLE 2 HISTIDINE KINASE VPHK1S-Z8 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE SENSORY BOX/GGDEF FAMILY PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: EXTRACELLULAR DOMAIN (UNP RESIDUES 28-313); COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO PARAHAEMOLYTICUS; SOURCE 3 ORGANISM_TAXID: 670; SOURCE 4 GENE: VP0354; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET22B+ KEYWDS PDC FOLD, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Z.ZHANG,W.A.HENDRICKSON REVDAT 4 21-FEB-24 3LID 1 REMARK SEQADV REVDAT 3 01-NOV-17 3LID 1 REMARK REVDAT 2 11-AUG-10 3LID 1 JRNL REVDAT 1 05-MAY-10 3LID 0 JRNL AUTH Z.ZHANG,W.A.HENDRICKSON JRNL TITL STRUCTURAL CHARACTERIZATION OF THE PREDOMINANT FAMILY OF JRNL TITL 2 HISTIDINE KINASE SENSOR DOMAINS. JRNL REF J.MOL.BIOL. V. 400 335 2010 JRNL REFN ISSN 0022-2836 JRNL PMID 20435045 JRNL DOI 10.1016/J.JMB.2010.04.049 REMARK 2 REMARK 2 RESOLUTION. 1.76 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) : 1.76 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.81 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 72414 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) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3641 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) : 1.76 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.80 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4725 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.67 REMARK 3 BIN R VALUE (WORKING SET) : 0.2360 REMARK 3 BIN FREE R VALUE SET COUNT : 240 REMARK 3 BIN FREE R VALUE : 0.2870 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4529 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 48 REMARK 3 SOLVENT ATOMS : 584 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.94 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.45000 REMARK 3 B22 (A**2) : 0.79000 REMARK 3 B33 (A**2) : -1.24000 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): 0.107 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.109 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.065 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.961 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4687 ; 0.026 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6338 ; 2.117 ; 1.970 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 561 ; 5.969 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 239 ;36.925 ;24.310 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 831 ;13.153 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 33 ;16.904 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 690 ; 0.187 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3563 ; 0.012 ; 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): 2787 ; 1.372 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4525 ; 2.399 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1900 ; 3.579 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1809 ; 5.581 ; 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 : 1.40 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 3LID COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-FEB-10. REMARK 100 THE DEPOSITION ID IS D_1000057314. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL; NULL REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 6.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : NSLS; NSLS REMARK 200 BEAMLINE : X4A; X4A REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97924 0.97929 0.96784; 0.97921 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; NULL REMARK 200 DETECTOR MANUFACTURER : NULL; NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 72469 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.760 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.76 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.82 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : 0.25600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5% PEG8K, 0.2M NACL, 0.1M NA/K REMARK 280 PHOSPHATE PH6.2, VAPOR DIFFUSION, TEMPERATURE 293K 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 37.05100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 61.57100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.72200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 61.57100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 37.05100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.72200 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -29.0 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 26 REMARK 465 GLU A 27 REMARK 465 LYS A 28 REMARK 465 TYR A 29 REMARK 465 GLN A 30 REMARK 465 ALA A 31 REMARK 465 LEU A 32 REMARK 465 SER A 312 REMARK 465 LEU A 313 REMARK 465 GLU A 314 REMARK 465 HIS A 315 REMARK 465 HIS A 316 REMARK 465 HIS A 317 REMARK 465 HIS A 318 REMARK 465 HIS A 319 REMARK 465 HIS A 320 REMARK 465 MET B 26 REMARK 465 GLU B 27 REMARK 465 LYS B 28 REMARK 465 TYR B 29 REMARK 465 GLN B 30 REMARK 465 ALA B 31 REMARK 465 LEU B 32 REMARK 465 LEU B 33 REMARK 465 ALA B 34 REMARK 465 ASN B 35 REMARK 465 SER B 312 REMARK 465 LEU B 313 REMARK 465 GLU B 314 REMARK 465 HIS B 315 REMARK 465 HIS B 316 REMARK 465 HIS B 317 REMARK 465 HIS B 318 REMARK 465 HIS B 319 REMARK 465 HIS B 320 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 OG SER A 127 O HOH A 486 1.88 REMARK 500 O HOH A 581 O HOH A 582 1.97 REMARK 500 CB TRP B 158 O HOH B 517 2.00 REMARK 500 O HOH B 396 O HOH B 504 2.01 REMARK 500 O HOH A 433 O HOH A 531 2.01 REMARK 500 OD2 ASP A 60 C2 EDO B 6 2.02 REMARK 500 OD2 ASP B 60 O HOH B 455 2.06 REMARK 500 OD2 ASP A 60 O2 EDO B 6 2.12 REMARK 500 O HOH A 372 O HOH A 600 2.14 REMARK 500 ND2 ASN B 36 O HOH B 553 2.18 REMARK 500 CD1 LEU A 308 O HOH B 564 2.18 REMARK 500 OE1 GLU A 231 O HOH A 525 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 OE1 GLN A 262 ND2 ASN B 186 3544 1.92 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 TRP B 158 CB TRP B 158 CG -0.168 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 53 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ASP A 111 CB - CG - OD1 ANGL. DEV. = 6.8 DEGREES REMARK 500 LYS A 222 CB - CG - CD ANGL. DEV. = -24.5 DEGREES REMARK 500 ARG B 53 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ASP B 111 CB - CG - OD1 ANGL. DEV. = 8.8 DEGREES REMARK 500 ILE B 120 CG1 - CB - CG2 ANGL. DEV. = 16.7 DEGREES REMARK 500 TRP B 158 N - CA - CB ANGL. DEV. = -12.0 DEGREES REMARK 500 ARG B 178 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG B 189 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 LYS B 222 CB - CG - CD ANGL. DEV. = -19.0 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 34 -64.26 -12.32 REMARK 500 LYS A 102 -24.86 70.55 REMARK 500 ARG A 303 124.83 -38.31 REMARK 500 LYS B 102 -27.34 74.36 REMARK 500 TYR B 235 39.69 71.71 REMARK 500 GLU B 270 -34.27 -134.04 REMARK 500 VAL B 281 -63.48 70.87 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 PO4 A 321 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 350 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 4 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 5 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 9 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 321 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 351 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 6 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 7 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 8 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3LI8 RELATED DB: PDB REMARK 900 RELATED ID: 3LI9 RELATED DB: PDB REMARK 900 RELATED ID: 3LIA RELATED DB: PDB REMARK 900 RELATED ID: 3LIB RELATED DB: PDB REMARK 900 RELATED ID: 3LIC RELATED DB: PDB REMARK 900 RELATED ID: 3LIE RELATED DB: PDB REMARK 900 RELATED ID: 3LIF RELATED DB: PDB DBREF 3LID A 28 313 UNP Q87SR8 Q87SR8_VIBPA 28 313 DBREF 3LID B 28 313 UNP Q87SR8 Q87SR8_VIBPA 28 313 SEQADV 3LID MET A 26 UNP Q87SR8 EXPRESSION TAG SEQADV 3LID GLU A 27 UNP Q87SR8 EXPRESSION TAG SEQADV 3LID GLU A 314 UNP Q87SR8 EXPRESSION TAG SEQADV 3LID HIS A 315 UNP Q87SR8 EXPRESSION TAG SEQADV 3LID HIS A 316 UNP Q87SR8 EXPRESSION TAG SEQADV 3LID HIS A 317 UNP Q87SR8 EXPRESSION TAG SEQADV 3LID HIS A 318 UNP Q87SR8 EXPRESSION TAG SEQADV 3LID HIS A 319 UNP Q87SR8 EXPRESSION TAG SEQADV 3LID HIS A 320 UNP Q87SR8 EXPRESSION TAG SEQADV 3LID MET B 26 UNP Q87SR8 EXPRESSION TAG SEQADV 3LID GLU B 27 UNP Q87SR8 EXPRESSION TAG SEQADV 3LID GLU B 314 UNP Q87SR8 EXPRESSION TAG SEQADV 3LID HIS B 315 UNP Q87SR8 EXPRESSION TAG SEQADV 3LID HIS B 316 UNP Q87SR8 EXPRESSION TAG SEQADV 3LID HIS B 317 UNP Q87SR8 EXPRESSION TAG SEQADV 3LID HIS B 318 UNP Q87SR8 EXPRESSION TAG SEQADV 3LID HIS B 319 UNP Q87SR8 EXPRESSION TAG SEQADV 3LID HIS B 320 UNP Q87SR8 EXPRESSION TAG SEQRES 1 A 295 MET GLU LYS TYR GLN ALA LEU LEU ALA ASN ASN VAL GLU SEQRES 2 A 295 ASN THR ALA LYS GLU ALA LEU HIS GLN LEU ALA TYR THR SEQRES 3 A 295 GLY ARG GLU TYR ASN ASN ILE GLN ASP GLN ILE GLU THR SEQRES 4 A 295 ILE SER ASP LEU LEU GLY HIS SER GLN SER LEU TYR ASP SEQRES 5 A 295 TYR LEU ARG GLU PRO SER LYS ALA ASN LEU THR ILE LEU SEQRES 6 A 295 GLU ASN MET TRP SER SER VAL ALA ARG ASN GLN LYS LEU SEQRES 7 A 295 TYR LYS GLN ILE ARG PHE LEU ASP THR SER GLY THR GLU SEQRES 8 A 295 LYS VAL ARG ILE LYS TYR ASP PHE LYS THR SER ILE ALA SEQRES 9 A 295 GLY PRO SER LEU ILE LEU ARG ASP LYS SER ALA ARG GLU SEQRES 10 A 295 TYR PHE LYS TYR ALA GLN SER LEU ASP ASN GLU GLN ILE SEQRES 11 A 295 SER ALA TRP GLY ILE GLU LEU GLU ARG ASP LYS GLY GLU SEQRES 12 A 295 LEU VAL TYR PRO LEU SER PRO SER LEU ARG ILE LEU MET SEQRES 13 A 295 PRO ILE SER VAL ASN ASP VAL ARG GLN GLY TYR LEU VAL SEQRES 14 A 295 LEU ASN VAL ASP ILE GLU TYR LEU SER SER LEU LEU ASN SEQRES 15 A 295 TYR SER PRO VAL ARG ASP PHE HIS ILE GLU LEU VAL LYS SEQRES 16 A 295 HIS LYS GLY PHE TYR ILE ALA SER PRO ASP GLU SER ARG SEQRES 17 A 295 LEU TYR GLY ASP ILE ILE PRO GLU ARG SER GLN PHE ASN SEQRES 18 A 295 PHE SER ASN MET TYR PRO ASP ILE TRP PRO ARG VAL VAL SEQRES 19 A 295 SER GLU GLN ALA GLY TYR SER TYR SER GLY GLU HIS LEU SEQRES 20 A 295 ILE ALA PHE SER SER ILE LYS PHE VAL SER ASN GLU PRO SEQRES 21 A 295 LEU HIS LEU ILE ILE ASP LEU SER ASN GLU GLN LEU SER SEQRES 22 A 295 LYS ARG ALA THR ARG ASP ILE ASN ASP LEU ILE GLN GLU SEQRES 23 A 295 SER LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 B 295 MET GLU LYS TYR GLN ALA LEU LEU ALA ASN ASN VAL GLU SEQRES 2 B 295 ASN THR ALA LYS GLU ALA LEU HIS GLN LEU ALA TYR THR SEQRES 3 B 295 GLY ARG GLU TYR ASN ASN ILE GLN ASP GLN ILE GLU THR SEQRES 4 B 295 ILE SER ASP LEU LEU GLY HIS SER GLN SER LEU TYR ASP SEQRES 5 B 295 TYR LEU ARG GLU PRO SER LYS ALA ASN LEU THR ILE LEU SEQRES 6 B 295 GLU ASN MET TRP SER SER VAL ALA ARG ASN GLN LYS LEU SEQRES 7 B 295 TYR LYS GLN ILE ARG PHE LEU ASP THR SER GLY THR GLU SEQRES 8 B 295 LYS VAL ARG ILE LYS TYR ASP PHE LYS THR SER ILE ALA SEQRES 9 B 295 GLY PRO SER LEU ILE LEU ARG ASP LYS SER ALA ARG GLU SEQRES 10 B 295 TYR PHE LYS TYR ALA GLN SER LEU ASP ASN GLU GLN ILE SEQRES 11 B 295 SER ALA TRP GLY ILE GLU LEU GLU ARG ASP LYS GLY GLU SEQRES 12 B 295 LEU VAL TYR PRO LEU SER PRO SER LEU ARG ILE LEU MET SEQRES 13 B 295 PRO ILE SER VAL ASN ASP VAL ARG GLN GLY TYR LEU VAL SEQRES 14 B 295 LEU ASN VAL ASP ILE GLU TYR LEU SER SER LEU LEU ASN SEQRES 15 B 295 TYR SER PRO VAL ARG ASP PHE HIS ILE GLU LEU VAL LYS SEQRES 16 B 295 HIS LYS GLY PHE TYR ILE ALA SER PRO ASP GLU SER ARG SEQRES 17 B 295 LEU TYR GLY ASP ILE ILE PRO GLU ARG SER GLN PHE ASN SEQRES 18 B 295 PHE SER ASN MET TYR PRO ASP ILE TRP PRO ARG VAL VAL SEQRES 19 B 295 SER GLU GLN ALA GLY TYR SER TYR SER GLY GLU HIS LEU SEQRES 20 B 295 ILE ALA PHE SER SER ILE LYS PHE VAL SER ASN GLU PRO SEQRES 21 B 295 LEU HIS LEU ILE ILE ASP LEU SER ASN GLU GLN LEU SER SEQRES 22 B 295 LYS ARG ALA THR ARG ASP ILE ASN ASP LEU ILE GLN GLU SEQRES 23 B 295 SER LEU GLU HIS HIS HIS HIS HIS HIS HET PO4 A 321 5 HET CL A 350 1 HET EDO A 2 4 HET EDO A 3 4 HET EDO A 4 4 HET EDO A 5 4 HET EDO A 9 4 HET PO4 B 321 5 HET CL B 351 1 HET EDO B 1 4 HET EDO B 6 4 HET EDO B 7 4 HET EDO B 8 4 HETNAM PO4 PHOSPHATE ION HETNAM CL CHLORIDE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 PO4 2(O4 P 3-) FORMUL 4 CL 2(CL 1-) FORMUL 5 EDO 9(C2 H6 O2) FORMUL 16 HOH *584(H2 O) HELIX 1 1 LEU A 33 HIS A 71 1 39 HELIX 2 2 SER A 72 GLU A 81 1 10 HELIX 3 3 SER A 83 LYS A 102 1 20 HELIX 4 4 ARG A 141 LEU A 150 1 10 HELIX 5 5 ILE A 199 ASN A 207 1 9 HELIX 6 6 ASP A 230 LEU A 234 5 5 HELIX 7 7 ILE A 239 SER A 243 5 5 HELIX 8 8 ASN A 246 TYR A 251 1 6 HELIX 9 9 ILE A 254 SER A 260 1 7 HELIX 10 10 ASN A 294 ARG A 300 1 7 HELIX 11 11 ASP A 304 ILE A 309 1 6 HELIX 12 12 ASN B 36 HIS B 71 1 36 HELIX 13 13 SER B 72 GLU B 81 1 10 HELIX 14 14 SER B 83 LYS B 102 1 20 HELIX 15 15 ARG B 141 LEU B 150 1 10 HELIX 16 16 ILE B 199 ASN B 207 1 9 HELIX 17 17 ASP B 230 LEU B 234 5 5 HELIX 18 18 ILE B 239 SER B 243 5 5 HELIX 19 19 ASN B 246 TYR B 251 1 6 HELIX 20 20 ILE B 254 VAL B 259 1 6 HELIX 21 21 ASN B 294 ARG B 300 1 7 HELIX 22 22 ALA B 301 ARG B 303 5 3 HELIX 23 23 ASP B 304 GLU B 311 1 8 SHEET 1 A 6 ILE A 128 PRO A 131 0 SHEET 2 A 6 GLU A 116 ASP A 123 -1 N LYS A 121 O GLY A 130 SHEET 3 A 6 TYR A 104 ASP A 111 -1 N PHE A 109 O LYS A 117 SHEET 4 A 6 VAL A 188 ASP A 198 -1 O TYR A 192 N LEU A 110 SHEET 5 A 6 PRO A 175 VAL A 185 -1 N ILE A 183 O GLN A 190 SHEET 6 A 6 SER A 156 ALA A 157 -1 N SER A 156 O LEU A 180 SHEET 1 B 6 ILE A 128 PRO A 131 0 SHEET 2 B 6 GLU A 116 ASP A 123 -1 N LYS A 121 O GLY A 130 SHEET 3 B 6 TYR A 104 ASP A 111 -1 N PHE A 109 O LYS A 117 SHEET 4 B 6 VAL A 188 ASP A 198 -1 O TYR A 192 N LEU A 110 SHEET 5 B 6 PRO A 175 VAL A 185 -1 N ILE A 183 O GLN A 190 SHEET 6 B 6 GLU A 161 LEU A 162 -1 N GLU A 161 O SER A 176 SHEET 1 C 2 ARG A 164 ASP A 165 0 SHEET 2 C 2 GLU A 168 LEU A 169 -1 O GLU A 168 N ASP A 165 SHEET 1 D 2 TYR A 208 SER A 209 0 SHEET 2 D 2 PHE A 214 HIS A 215 -1 O PHE A 214 N SER A 209 SHEET 1 E 5 TYR A 225 ALA A 227 0 SHEET 2 E 5 GLU A 217 LYS A 220 -1 N LEU A 218 O ILE A 226 SHEET 3 E 5 LEU A 286 SER A 293 -1 O ILE A 289 N GLU A 217 SHEET 4 E 5 HIS A 271 ILE A 278 -1 N ILE A 278 O LEU A 286 SHEET 5 E 5 GLY A 264 TYR A 267 -1 N SER A 266 O ILE A 273 SHEET 1 F 6 ILE B 128 PRO B 131 0 SHEET 2 F 6 GLU B 116 ASP B 123 -1 N LYS B 121 O GLY B 130 SHEET 3 F 6 TYR B 104 ASP B 111 -1 N PHE B 109 O LYS B 117 SHEET 4 F 6 VAL B 188 ASP B 198 -1 O TYR B 192 N LEU B 110 SHEET 5 F 6 PRO B 175 VAL B 185 -1 N ILE B 183 O GLN B 190 SHEET 6 F 6 SER B 156 ALA B 157 -1 N SER B 156 O LEU B 180 SHEET 1 G 6 ILE B 128 PRO B 131 0 SHEET 2 G 6 GLU B 116 ASP B 123 -1 N LYS B 121 O GLY B 130 SHEET 3 G 6 TYR B 104 ASP B 111 -1 N PHE B 109 O LYS B 117 SHEET 4 G 6 VAL B 188 ASP B 198 -1 O TYR B 192 N LEU B 110 SHEET 5 G 6 PRO B 175 VAL B 185 -1 N ILE B 183 O GLN B 190 SHEET 6 G 6 GLU B 161 LEU B 162 -1 N GLU B 161 O SER B 176 SHEET 1 H 2 ARG B 164 ASP B 165 0 SHEET 2 H 2 GLU B 168 LEU B 169 -1 O GLU B 168 N ASP B 165 SHEET 1 I 2 TYR B 208 SER B 209 0 SHEET 2 I 2 PHE B 214 HIS B 215 -1 O PHE B 214 N SER B 209 SHEET 1 J 5 TYR B 225 ALA B 227 0 SHEET 2 J 5 GLU B 217 LYS B 220 -1 N LEU B 218 O ILE B 226 SHEET 3 J 5 LEU B 286 SER B 293 -1 O ILE B 289 N GLU B 217 SHEET 4 J 5 HIS B 271 ILE B 278 -1 N LEU B 272 O LEU B 292 SHEET 5 J 5 ALA B 263 TYR B 267 -1 N GLY B 264 O PHE B 275 CISPEP 1 TYR A 171 PRO A 172 0 -0.66 CISPEP 2 ILE A 309 GLN A 310 0 -8.06 CISPEP 3 TYR B 171 PRO B 172 0 0.54 SITE 1 AC1 10 GLN A 106 ARG A 108 LYS A 138 ARG A 141 SITE 2 AC1 10 TYR A 143 GLU A 163 ARG A 164 ARG A 178 SITE 3 AC1 10 ASN A 196 HOH A 334 SITE 1 AC2 3 LYS A 138 ARG A 141 GLY A 167 SITE 1 AC3 6 TYR A 78 PRO A 82 ASP A 111 LYS A 117 SITE 2 AC3 6 HOH A 382 HOH A 515 SITE 1 AC4 5 HOH A 25 TYR A 171 ILE A 238 PRO A 240 SITE 2 AC4 5 HOH A 570 SITE 1 AC5 4 TYR A 146 ALA A 157 HOH A 535 HOH A 571 SITE 1 AC6 4 ILE A 160 LYS A 220 TYR A 235 ASP A 237 SITE 1 AC7 5 LEU A 79 ARG A 80 VAL A 185 GLN A 190 SITE 2 AC7 5 SER B 149 SITE 1 AC8 10 GLN B 106 ARG B 108 LYS B 138 ARG B 141 SITE 2 AC8 10 TYR B 143 GLU B 163 ARG B 164 ARG B 178 SITE 3 AC8 10 ASN B 196 HOH B 366 SITE 1 AC9 4 LYS B 138 ARG B 141 LYS B 166 GLY B 167 SITE 1 BC1 5 ILE B 160 LYS B 220 ILE B 226 TYR B 235 SITE 2 BC1 5 ASP B 237 SITE 1 BC2 5 ASP A 60 GLN B 47 TYR B 50 SER B 209 SITE 2 BC2 5 ARG B 212 SITE 1 BC3 5 GLY B 159 ILE B 160 LYS B 220 SER B 282 SITE 2 BC3 5 HOH B 431 SITE 1 BC4 5 ARG A 257 HOH A 345 TYR B 78 LEU B 79 SITE 2 BC4 5 LYS B 117 CRYST1 74.102 79.444 123.142 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 0.013495 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012587 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008121 0.00000