HEADER DNA BINDING PROTEIN/DNA 31-JUL-12 3VW4 TITLE CRYSTAL STRUCTURE OF THE DNA-BINDING DOMAIN OF COLE2-P9 REP IN COMPLEX TITLE 2 WITH THE REPLICATION ORIGIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: REP; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: DNA-BINDIG DOMAIN; COMPND 5 SYNONYM: REPLICATION INITIATOR COLE2-REP; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'- COMPND 9 D(P*AP*AP*TP*GP*AP*GP*AP*CP*CP*AP*GP*AP*TP*AP*AP*GP*CP*CP*TP*TP*AP*TP COMPND 10 *C)-3'); COMPND 11 CHAIN: C, E; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA (5'- COMPND 15 D(P*GP*AP*TP*AP*AP*GP*GP*CP*TP*TP*AP*TP*CP*TP*GP*GP*TP*CP*TP*CP*AP*TP COMPND 16 *T)-3'); COMPND 17 CHAIN: D, F; COMPND 18 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: REP; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 OTHER_DETAILS: SYNTHETIC OLIGO DNA; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 OTHER_DETAILS: SYNTHETIC OLIGO DNA KEYWDS HELIX-TURN-HELIX, SPECIFIC DNA-BINDING AND UNWINDING OF DNA DUPLEX, KEYWDS 2 CYTOSOL, REPLICATION INITIATOR PROTEIN, DNA BINDING PROTEIN-DNA KEYWDS 3 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.ITOU,M.YAGURA,T.ITOH,Y.SHIRAKIHARA REVDAT 3 20-MAR-24 3VW4 1 REMARK SEQADV REVDAT 2 28-JAN-15 3VW4 1 JRNL REVDAT 1 31-JUL-13 3VW4 0 JRNL AUTH H.ITOU,M.YAGURA,Y.SHIRAKIHARA,T.ITOH JRNL TITL STRUCTURAL BASIS FOR REPLICATION ORIGIN UNWINDING BY AN JRNL TITL 2 INITIATOR-PRIMASE OF PLASMID COLE2-P9: DUPLEX DNA UNWINDING JRNL TITL 3 BY A SINGLE PROTEIN JRNL REF J.BIOL.CHEM. V. 290 3601 2015 JRNL REFN ISSN 0021-9258 JRNL PMID 25538245 JRNL DOI 10.1074/JBC.M114.595645 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 21787 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) : 0.222 REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1168 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) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.77 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1376 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.68 REMARK 3 BIN R VALUE (WORKING SET) : 0.3180 REMARK 3 BIN FREE R VALUE SET COUNT : 64 REMARK 3 BIN FREE R VALUE : 0.4230 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1972 REMARK 3 NUCLEIC ACID ATOMS : 1665 REMARK 3 HETEROGEN ATOMS : 25 REMARK 3 SOLVENT ATOMS : 27 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.53 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.83000 REMARK 3 B22 (A**2) : 2.00000 REMARK 3 B33 (A**2) : -1.18000 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): 0.440 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.298 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.191 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.645 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.911 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.871 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3920 ; 0.015 ; 0.015 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5644 ; 2.193 ; 1.648 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 240 ; 6.627 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 91 ;30.723 ;19.780 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 348 ;22.801 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;23.066 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 522 ; 0.128 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2411 ; 0.013 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 175 A 239 REMARK 3 ORIGIN FOR THE GROUP (A): 29.9230 16.5810 74.7320 REMARK 3 T TENSOR REMARK 3 T11: 0.0127 T22: 0.0330 REMARK 3 T33: 0.0453 T12: -0.0062 REMARK 3 T13: 0.0035 T23: 0.0086 REMARK 3 L TENSOR REMARK 3 L11: 4.7071 L22: 3.3963 REMARK 3 L33: 2.4524 L12: -3.0529 REMARK 3 L13: -1.3860 L23: 2.1332 REMARK 3 S TENSOR REMARK 3 S11: -0.0062 S12: -0.1959 S13: 0.0868 REMARK 3 S21: -0.0993 S22: 0.0949 S23: -0.0492 REMARK 3 S31: -0.1590 S32: 0.1430 S33: -0.0886 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 269 A 290 REMARK 3 ORIGIN FOR THE GROUP (A): 36.5570 12.9300 12.8900 REMARK 3 T TENSOR REMARK 3 T11: 1.0518 T22: 0.7475 REMARK 3 T33: 0.2422 T12: 0.0570 REMARK 3 T13: 0.0403 T23: 0.0942 REMARK 3 L TENSOR REMARK 3 L11: 7.0135 L22: 12.4873 REMARK 3 L33: 16.3296 L12: 2.7826 REMARK 3 L13: 0.6094 L23: 13.8304 REMARK 3 S TENSOR REMARK 3 S11: -0.5486 S12: 0.4483 S13: 0.1837 REMARK 3 S21: 0.4247 S22: 0.7015 S23: -0.1210 REMARK 3 S31: 0.8559 S32: 0.5646 S33: -0.1529 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 175 B 239 REMARK 3 ORIGIN FOR THE GROUP (A): 2.8790 20.0530 72.2030 REMARK 3 T TENSOR REMARK 3 T11: 0.0076 T22: 0.0264 REMARK 3 T33: 0.0370 T12: -0.0083 REMARK 3 T13: -0.0040 T23: -0.0046 REMARK 3 L TENSOR REMARK 3 L11: 2.5020 L22: 4.0656 REMARK 3 L33: 3.3213 L12: -0.3408 REMARK 3 L13: -0.1534 L23: -2.3367 REMARK 3 S TENSOR REMARK 3 S11: 0.0180 S12: 0.0194 S13: -0.0532 REMARK 3 S21: -0.0892 S22: 0.0407 S23: 0.1192 REMARK 3 S31: 0.1490 S32: -0.1213 S33: -0.0588 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 269 B 290 REMARK 3 ORIGIN FOR THE GROUP (A): -0.7640 19.9100 11.7740 REMARK 3 T TENSOR REMARK 3 T11: 0.9911 T22: 0.9948 REMARK 3 T33: 0.3389 T12: -0.0207 REMARK 3 T13: 0.0645 T23: -0.0509 REMARK 3 L TENSOR REMARK 3 L11: 0.8187 L22: 3.0009 REMARK 3 L33: 14.4801 L12: 0.3551 REMARK 3 L13: 1.8128 L23: -4.6053 REMARK 3 S TENSOR REMARK 3 S11: 0.0518 S12: 0.3260 S13: -0.1289 REMARK 3 S21: -0.0547 S22: 0.6686 S23: 0.2516 REMARK 3 S31: 0.0127 S32: -0.0362 S33: -0.7204 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 USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 3VW4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-AUG-12. REMARK 100 THE DEPOSITION ID IS D_1000095573. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-OCT-11 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9800 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : MONOCHROMATOR AND MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22951 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.13300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.75 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.5M AMMONIUM SULFATE, 1.0M LITHIUM REMARK 280 SULFATE, 0.1M SODIUM-CITRATE, PH 5.6, VAPOR DIFFUSION, HANGING REMARK 280 DROP, 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 23.83100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 136.75400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.91200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 136.75400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.83100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.91200 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 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, D 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7540 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12670 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -63.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, E, F 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 167 REMARK 465 GLY A 168 REMARK 465 HIS A 169 REMARK 465 ASP A 292 REMARK 465 PRO A 293 REMARK 465 ASP A 294 REMARK 465 MET B 167 REMARK 465 GLY B 168 REMARK 465 HIS B 169 REMARK 465 HIS B 170 REMARK 465 CYS B 291 REMARK 465 ASP B 292 REMARK 465 PRO B 293 REMARK 465 ASP B 294 REMARK 465 DA C 23 REMARK 465 DT C 24 REMARK 465 DC C 25 REMARK 465 DA D 33 REMARK 465 DT D 34 REMARK 465 DT D 35 REMARK 465 DT E 24 REMARK 465 DC E 25 REMARK 465 DA F 33 REMARK 465 DT F 34 REMARK 465 DT F 35 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 N2 DG C 8 O2 DC D 30 2.15 REMARK 500 N2 DG E 8 O2 DC F 30 2.17 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 HIS A 173 CG HIS A 173 CD2 0.055 REMARK 500 HIS A 237 CG HIS A 237 CD2 0.068 REMARK 500 HIS B 173 CG HIS B 173 CD2 0.058 REMARK 500 HIS B 178 CG HIS B 178 CD2 0.080 REMARK 500 HIS B 237 CG HIS B 237 CD2 0.054 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 192 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG B 208 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 DA C 4 C3' - O3' - P ANGL. DEV. = 8.9 DEGREES REMARK 500 DG C 6 C3' - O3' - P ANGL. DEV. = 7.7 DEGREES REMARK 500 DA C 7 O5' - P - OP1 ANGL. DEV. = -6.5 DEGREES REMARK 500 DA C 7 C3' - O3' - P ANGL. DEV. = 8.6 DEGREES REMARK 500 DC C 10 C3' - O3' - P ANGL. DEV. = -8.3 DEGREES REMARK 500 DC C 11 C3' - O3' - P ANGL. DEV. = -10.1 DEGREES REMARK 500 DA C 17 O3' - P - O5' ANGL. DEV. = -12.2 DEGREES REMARK 500 DG C 18 O5' - P - OP1 ANGL. DEV. = -7.0 DEGREES REMARK 500 DG C 18 C1' - O4' - C4' ANGL. DEV. = -6.7 DEGREES REMARK 500 DA D 14 O3' - P - O5' ANGL. DEV. = 13.7 DEGREES REMARK 500 DT D 15 O5' - P - OP2 ANGL. DEV. = -8.4 DEGREES REMARK 500 DA D 17 O5' - P - OP1 ANGL. DEV. = -7.2 DEGREES REMARK 500 DA D 17 O5' - P - OP2 ANGL. DEV. = 10.6 DEGREES REMARK 500 DG D 19 O5' - P - OP1 ANGL. DEV. = -5.9 DEGREES REMARK 500 DT D 21 C3' - O3' - P ANGL. DEV. = 9.2 DEGREES REMARK 500 DT D 22 C3' - O3' - P ANGL. DEV. = 10.1 DEGREES REMARK 500 DA E 4 C3' - O3' - P ANGL. DEV. = 8.1 DEGREES REMARK 500 DT E 5 C3' - O3' - P ANGL. DEV. = 7.3 DEGREES REMARK 500 DC E 20 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC E 20 C3' - O3' - P ANGL. DEV. = 10.5 DEGREES REMARK 500 DT E 21 O5' - P - OP1 ANGL. DEV. = 12.3 DEGREES REMARK 500 DT E 22 C3' - O3' - P ANGL. DEV. = 11.4 DEGREES REMARK 500 DG F 13 O5' - P - OP1 ANGL. DEV. = 14.7 DEGREES REMARK 500 DT F 15 C3' - O3' - P ANGL. DEV. = 10.2 DEGREES REMARK 500 DA F 17 C3' - C2' - C1' ANGL. DEV. = -6.1 DEGREES REMARK 500 DG F 18 C3' - O3' - P ANGL. DEV. = 9.6 DEGREES REMARK 500 DC F 20 O5' - P - OP1 ANGL. DEV. = 7.7 DEGREES REMARK 500 DT F 22 C3' - O3' - P ANGL. DEV. = 10.3 DEGREES REMARK 500 DT F 24 C3' - O3' - P ANGL. DEV. = 7.5 DEGREES REMARK 500 DG F 27 C3' - O3' - P ANGL. DEV. = 8.8 DEGREES REMARK 500 DG F 28 C5' - C4' - O4' ANGL. DEV. = 7.6 DEGREES REMARK 500 DG F 28 C1' - O4' - C4' ANGL. DEV. = -7.1 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 LYS A 259 41.31 -102.95 REMARK 500 LYS A 273 72.16 43.36 REMARK 500 HIS B 172 -80.09 -33.14 REMARK 500 ILE B 191 -19.79 -49.06 REMARK 500 TRP B 195 57.54 35.14 REMARK 500 VAL B 197 154.65 -46.87 REMARK 500 LYS B 273 68.96 32.38 REMARK 500 ALA B 277 1.77 -62.29 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 SO4 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 304 DBREF 3VW4 A 175 294 UNP Q06B24 Q06B24_ECOLX 175 294 DBREF 3VW4 B 175 294 UNP Q06B24 Q06B24_ECOLX 175 294 DBREF 3VW4 C 3 25 PDB 3VW4 3VW4 3 25 DBREF 3VW4 E 3 25 PDB 3VW4 3VW4 3 25 DBREF 3VW4 D 13 35 PDB 3VW4 3VW4 13 35 DBREF 3VW4 F 13 35 PDB 3VW4 3VW4 13 35 SEQADV 3VW4 MET A 167 UNP Q06B24 EXPRESSION TAG SEQADV 3VW4 GLY A 168 UNP Q06B24 EXPRESSION TAG SEQADV 3VW4 HIS A 169 UNP Q06B24 EXPRESSION TAG SEQADV 3VW4 HIS A 170 UNP Q06B24 EXPRESSION TAG SEQADV 3VW4 HIS A 171 UNP Q06B24 EXPRESSION TAG SEQADV 3VW4 HIS A 172 UNP Q06B24 EXPRESSION TAG SEQADV 3VW4 HIS A 173 UNP Q06B24 EXPRESSION TAG SEQADV 3VW4 HIS A 174 UNP Q06B24 EXPRESSION TAG SEQADV 3VW4 MET B 167 UNP Q06B24 EXPRESSION TAG SEQADV 3VW4 GLY B 168 UNP Q06B24 EXPRESSION TAG SEQADV 3VW4 HIS B 169 UNP Q06B24 EXPRESSION TAG SEQADV 3VW4 HIS B 170 UNP Q06B24 EXPRESSION TAG SEQADV 3VW4 HIS B 171 UNP Q06B24 EXPRESSION TAG SEQADV 3VW4 HIS B 172 UNP Q06B24 EXPRESSION TAG SEQADV 3VW4 HIS B 173 UNP Q06B24 EXPRESSION TAG SEQADV 3VW4 HIS B 174 UNP Q06B24 EXPRESSION TAG SEQRES 1 A 128 MET GLY HIS HIS HIS HIS HIS HIS ARG ASN TYR HIS LEU SEQRES 2 A 128 PHE GLU LYS VAL ARG LYS TRP ALA TYR ARG ALA ILE ARG SEQRES 3 A 128 GLN GLY TRP PRO VAL PHE SER GLN TRP LEU ASP ALA VAL SEQRES 4 A 128 ILE GLN ARG VAL GLU MET TYR ASN ALA SER LEU PRO VAL SEQRES 5 A 128 PRO LEU SER PRO ALA GLU CYS ARG ALA ILE GLY LYS SER SEQRES 6 A 128 ILE ALA LYS TYR THR HIS ARG LYS PHE SER PRO GLU GLY SEQRES 7 A 128 PHE SER ALA VAL GLN ALA ALA ARG GLY ARG LYS GLY GLY SEQRES 8 A 128 THR LYS SER LYS ARG ALA ALA VAL PRO THR SER ALA ARG SEQRES 9 A 128 SER LEU LYS PRO TRP GLU ALA LEU GLY ILE SER ARG ALA SEQRES 10 A 128 THR TYR TYR ARG LYS LEU LYS CYS ASP PRO ASP SEQRES 1 B 128 MET GLY HIS HIS HIS HIS HIS HIS ARG ASN TYR HIS LEU SEQRES 2 B 128 PHE GLU LYS VAL ARG LYS TRP ALA TYR ARG ALA ILE ARG SEQRES 3 B 128 GLN GLY TRP PRO VAL PHE SER GLN TRP LEU ASP ALA VAL SEQRES 4 B 128 ILE GLN ARG VAL GLU MET TYR ASN ALA SER LEU PRO VAL SEQRES 5 B 128 PRO LEU SER PRO ALA GLU CYS ARG ALA ILE GLY LYS SER SEQRES 6 B 128 ILE ALA LYS TYR THR HIS ARG LYS PHE SER PRO GLU GLY SEQRES 7 B 128 PHE SER ALA VAL GLN ALA ALA ARG GLY ARG LYS GLY GLY SEQRES 8 B 128 THR LYS SER LYS ARG ALA ALA VAL PRO THR SER ALA ARG SEQRES 9 B 128 SER LEU LYS PRO TRP GLU ALA LEU GLY ILE SER ARG ALA SEQRES 10 B 128 THR TYR TYR ARG LYS LEU LYS CYS ASP PRO ASP SEQRES 1 C 23 DA DA DT DG DA DG DA DC DC DA DG DA DT SEQRES 2 C 23 DA DA DG DC DC DT DT DA DT DC SEQRES 1 D 23 DG DA DT DA DA DG DG DC DT DT DA DT DC SEQRES 2 D 23 DT DG DG DT DC DT DC DA DT DT SEQRES 1 E 23 DA DA DT DG DA DG DA DC DC DA DG DA DT SEQRES 2 E 23 DA DA DG DC DC DT DT DA DT DC SEQRES 1 F 23 DG DA DT DA DA DG DG DC DT DT DA DT DC SEQRES 2 F 23 DT DG DG DT DC DT DC DA DT DT HET SO4 A 301 5 HET SO4 B 301 5 HET SO4 B 302 5 HET SO4 B 303 5 HET SO4 B 304 5 HETNAM SO4 SULFATE ION FORMUL 7 SO4 5(O4 S 2-) FORMUL 12 HOH *27(H2 O) HELIX 1 1 HIS A 172 ILE A 191 1 20 HELIX 2 2 VAL A 197 LEU A 216 1 20 HELIX 3 3 SER A 221 PHE A 240 1 20 HELIX 4 4 SER A 241 LYS A 259 1 19 HELIX 5 5 SER A 268 LYS A 273 1 6 HELIX 6 6 LYS A 273 LEU A 278 1 6 HELIX 7 7 SER A 281 CYS A 291 1 11 HELIX 8 8 HIS B 174 ILE B 191 1 18 HELIX 9 9 VAL B 197 ALA B 214 1 18 HELIX 10 10 SER B 221 PHE B 240 1 20 HELIX 11 11 SER B 241 SER B 260 1 20 HELIX 12 12 SER B 268 LYS B 273 1 6 HELIX 13 13 TRP B 275 GLY B 279 5 5 HELIX 14 14 SER B 281 LYS B 290 1 10 SITE 1 AC1 4 HIS A 172 HIS A 173 HIS A 174 ARG A 175 SITE 1 AC2 6 HIS B 171 HIS B 172 HIS B 173 HIS B 174 SITE 2 AC2 6 ARG B 175 HOH B 407 SITE 1 AC3 5 HIS A 173 HIS B 174 ASN B 176 TYR B 177 SITE 2 AC3 5 DG F 13 SITE 1 AC4 2 PRO B 222 ARG B 226 SITE 1 AC5 4 GLN A 193 GLY A 194 TRP B 186 ARG B 208 CRYST1 47.662 61.824 273.508 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 0.020981 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016175 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003656 0.00000 MTRIX1 1 1.000000 0.000000 0.000000 0.00000 1 MTRIX2 1 0.000000 1.000000 0.000000 0.00000 1 MTRIX3 1 0.000000 0.000000 1.000000 0.00000 1 MTRIX1 2 -0.976328 0.113415 -0.184178 43.76983 1 MTRIX2 2 -0.113122 -0.993507 -0.012130 37.72441 1 MTRIX3 2 -0.184358 0.008991 0.982818 4.07547 1