PDB Short entry for 5D9I HEADER REPLICATION/DNA 18-AUG-15 5D9I TITLE SV40 LARGE T ANTIGEN ORIGIN BINDING DOMAIN BOUND TO ARTIFICIAL DNA TITLE 2 FORK COMPND MOL_ID: 1; COMPND 2 MOLECULE: LARGE T ANTIGEN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 131-260; COMPND 5 SYNONYM: LT-AG; COMPND 6 EC: 3.6.4.-; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'- COMPND 10 D(*GP*AP*GP*GP*AP*GP*GP*CP*TP*TP*TP*TP*TP*TP*GP*GP*AP*GP*GP*CP*C)- COMPND 11 3'); COMPND 12 CHAIN: X; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: DNA (5'- COMPND 16 D(*AP*CP*TP*CP*CP*TP*CP*CP*GP*AP*AP*AP*AP*AP*AP*CP*CP*TP*CP*CP*GP*GP* COMPND 17 A)-3'); COMPND 18 CHAIN: Y; COMPND 19 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SIMIAN VIRUS 40; SOURCE 3 ORGANISM_COMMON: SV40; SOURCE 4 ORGANISM_TAXID: 10633; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PGEX-1LAMBDAT; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630; SOURCE 12 EXPRESSION_SYSTEM: SYNTHETIC CONSTRUCT; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 32630; SOURCE 14 MOL_ID: 3; SOURCE 15 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 16 ORGANISM_TAXID: 32630; SOURCE 17 EXPRESSION_SYSTEM: SYNTHETIC CONSTRUCT; SOURCE 18 EXPRESSION_SYSTEM_TAXID: 32630 KEYWDS ORIGIN BINDING DOMAIN, REPLICATION, SV40, REPLICATION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR G.MEINKE,A.BOHM,P.A.BULLOCK REVDAT 4 27-SEP-23 5D9I 1 LINK REVDAT 3 25-DEC-19 5D9I 1 REMARK REVDAT 2 20-SEP-17 5D9I 1 REMARK REVDAT 1 09-SEP-15 5D9I 0 JRNL AUTH G.MEINKE,P.J.PHELAN,A.FRADET-TURCOTTE,A.BOHM,J.ARCHAMBAULT, JRNL AUTH 2 P.A.BULLOCK JRNL TITL STRUCTURE-BASED ANALYSIS OF THE INTERACTION BETWEEN THE JRNL TITL 2 SIMIAN VIRUS 40 T-ANTIGEN ORIGIN BINDING DOMAIN AND JRNL TITL 3 SINGLE-STRANDED DNA. JRNL REF J. VIROL. V. 85 818 2011 JRNL REFN ESSN 1098-5514 JRNL PMID 20980496 JRNL DOI 10.1128/JVI.01738-10 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0129 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 88.7 REMARK 3 NUMBER OF REFLECTIONS : 35570 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) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1895 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1541 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 51.90 REMARK 3 BIN R VALUE (WORKING SET) : 0.2240 REMARK 3 BIN FREE R VALUE SET COUNT : 72 REMARK 3 BIN FREE R VALUE : 0.2710 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2162 REMARK 3 NUCLEIC ACID ATOMS : 896 REMARK 3 HETEROGEN ATOMS : 14 REMARK 3 SOLVENT ATOMS : 230 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.15 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.89000 REMARK 3 B22 (A**2) : -0.66000 REMARK 3 B33 (A**2) : -1.13000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.15000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.126 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.123 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.098 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.940 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.945 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3314 ; 0.017 ; 0.017 REMARK 3 BOND LENGTHS OTHERS (A): 2644 ; 0.006 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4678 ; 1.709 ; 1.694 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6145 ; 1.479 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 285 ; 6.625 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 107 ;28.799 ;23.458 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 389 ;12.164 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;12.281 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 469 ; 0.110 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3144 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 795 ; 0.004 ; 0.020 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): 1105 ; 1.859 ; 1.425 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1103 ; 1.855 ; 1.423 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1392 ; 2.483 ; 2.126 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1393 ; 2.485 ; 2.127 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2209 ; 2.744 ; 1.784 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2209 ; 2.743 ; 1.784 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3284 ; 4.097 ; 2.606 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4077 ; 6.652 ;13.860 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4011 ; 6.606 ;13.568 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 129 259 B 129 259 16448 0.09 0.05 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 129 A 261 REMARK 3 ORIGIN FOR THE GROUP (A): 21.7880 48.3400 31.6780 REMARK 3 T TENSOR REMARK 3 T11: 0.1862 T22: 0.0088 REMARK 3 T33: 0.0075 T12: 0.0011 REMARK 3 T13: 0.0018 T23: -0.0029 REMARK 3 L TENSOR REMARK 3 L11: 0.9180 L22: 1.8849 REMARK 3 L33: 2.2792 L12: -0.2371 REMARK 3 L13: 0.4027 L23: -0.3969 REMARK 3 S TENSOR REMARK 3 S11: -0.0123 S12: -0.0792 S13: 0.0463 REMARK 3 S21: 0.1219 S22: -0.0307 S23: -0.0361 REMARK 3 S31: 0.0183 S32: -0.0549 S33: 0.0430 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 : B 129 B 260 REMARK 3 ORIGIN FOR THE GROUP (A): 23.1660 48.9190 0.7360 REMARK 3 T TENSOR REMARK 3 T11: 0.1580 T22: 0.0082 REMARK 3 T33: 0.0167 T12: 0.0045 REMARK 3 T13: -0.0211 T23: -0.0026 REMARK 3 L TENSOR REMARK 3 L11: 1.0703 L22: 1.8618 REMARK 3 L33: 1.8798 L12: 0.4904 REMARK 3 L13: -0.4291 L23: -0.2025 REMARK 3 S TENSOR REMARK 3 S11: -0.0025 S12: 0.0864 S13: -0.0617 REMARK 3 S21: -0.0737 S22: 0.0051 S23: -0.0706 REMARK 3 S31: -0.0197 S32: -0.0346 S33: -0.0026 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 : X 1 X 21 REMARK 3 ORIGIN FOR THE GROUP (A): 44.2460 84.9630 17.1140 REMARK 3 T TENSOR REMARK 3 T11: 0.3841 T22: 0.2491 REMARK 3 T33: 0.5602 T12: 0.0060 REMARK 3 T13: -0.1294 T23: -0.0185 REMARK 3 L TENSOR REMARK 3 L11: 0.0809 L22: 8.9806 REMARK 3 L33: 0.0850 L12: -0.6503 REMARK 3 L13: -0.0057 L23: -0.4597 REMARK 3 S TENSOR REMARK 3 S11: -0.0538 S12: -0.0282 S13: -0.0544 REMARK 3 S21: 0.4689 S22: -0.0028 S23: -0.3068 REMARK 3 S31: 0.0436 S32: -0.0015 S33: 0.0566 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 : Y 1 Y 23 REMARK 3 ORIGIN FOR THE GROUP (A): 44.4980 84.4500 12.8150 REMARK 3 T TENSOR REMARK 3 T11: 0.4540 T22: 0.2859 REMARK 3 T33: 0.6613 T12: -0.0017 REMARK 3 T13: -0.0288 T23: 0.0170 REMARK 3 L TENSOR REMARK 3 L11: 0.0199 L22: 6.0394 REMARK 3 L33: 0.1022 L12: 0.3129 REMARK 3 L13: -0.0261 L23: -0.6568 REMARK 3 S TENSOR REMARK 3 S11: 0.0320 S12: -0.0036 S13: -0.0179 REMARK 3 S21: -0.0944 S22: -0.2204 S23: -0.6366 REMARK 3 S31: 0.0568 S32: 0.0351 S33: 0.1883 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 5D9I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-AUG-15. REMARK 100 THE DEPOSITION ID IS D_1000212809. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-MAR-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0809 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL 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 : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37425 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 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 (%) : 88.8 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 54.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 2FUF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM TRIS, 300 MM NH4CL, 28% REMARK 280 POLYETHYLENE GLYCOL [PEG] 4000, 20 MM CACL2, PH 8.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 47.09600 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.69650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 47.09600 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 31.69650 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, X, Y 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 262 REMARK 465 SER B 261 REMARK 465 SER B 262 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 DG X 1 O5' 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 OD1 ASN A 191 CE1 HIS A 201 4546 1.89 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 TYR A 190 -125.06 57.29 REMARK 500 THR A 217 35.20 -96.26 REMARK 500 SER A 219 171.11 66.36 REMARK 500 ASP A 239 130.71 -36.07 REMARK 500 ASP A 239 130.61 -35.22 REMARK 500 SER B 180 52.99 39.30 REMARK 500 TYR B 190 -124.26 55.16 REMARK 500 THR B 217 37.41 -95.53 REMARK 500 SER B 219 172.00 65.88 REMARK 500 ASP B 239 131.75 -36.46 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 301 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA B 212 O REMARK 620 2 CME B 216 OH 98.4 REMARK 620 3 CME B 216 O 122.3 120.0 REMARK 620 4 HOH B 433 O 116.2 133.2 67.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA Y 101 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG X 18 OP2 REMARK 620 2 DG X 19 O6 93.6 REMARK 620 3 HOH X 112 O 18.1 92.3 REMARK 620 4 HOH X 120 O 20.1 94.4 2.9 REMARK 620 5 DG Y 22 OP2 20.8 92.4 2.7 2.1 REMARK 620 6 HOH Y 201 O 22.0 92.4 4.0 2.8 1.2 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA Y 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT Y 102 DBREF 5D9I A 131 260 UNP P03070 LT_SV40 131 260 DBREF 5D9I B 131 260 UNP P03070 LT_SV40 131 260 DBREF 5D9I X 1 21 PDB 5D9I 5D9I 1 21 DBREF 5D9I Y 1 23 PDB 5D9I 5D9I 1 23 SEQADV 5D9I GLY A 129 UNP P03070 EXPRESSION TAG SEQADV 5D9I SER A 130 UNP P03070 EXPRESSION TAG SEQADV 5D9I SER A 261 UNP P03070 EXPRESSION TAG SEQADV 5D9I SER A 262 UNP P03070 EXPRESSION TAG SEQADV 5D9I GLY B 129 UNP P03070 EXPRESSION TAG SEQADV 5D9I SER B 130 UNP P03070 EXPRESSION TAG SEQADV 5D9I SER B 261 UNP P03070 EXPRESSION TAG SEQADV 5D9I SER B 262 UNP P03070 EXPRESSION TAG SEQRES 1 A 134 GLY SER LYS VAL GLU ASP PRO LYS ASP PHE PRO SER GLU SEQRES 2 A 134 LEU LEU SER PHE LEU SER HIS ALA VAL PHE SER ASN ARG SEQRES 3 A 134 THR LEU ALA CYS PHE ALA ILE TYR THR THR LYS GLU LYS SEQRES 4 A 134 ALA ALA LEU LEU TYR LYS LYS ILE MET GLU LYS TYR SER SEQRES 5 A 134 VAL THR PHE ILE SER ARG HIS ASN SER TYR ASN HIS ASN SEQRES 6 A 134 ILE LEU PHE PHE LEU THR PRO HIS ARG HIS ARG VAL SER SEQRES 7 A 134 ALA ILE ASN ASN TYR ALA GLN LYS LEU CME THR PHE SER SEQRES 8 A 134 PHE LEU ILE CYS LYS GLY VAL ASN LYS GLU TYR LEU MET SEQRES 9 A 134 TYR SER ALA LEU THR ARG ASP PRO PHE SER VAL ILE GLU SEQRES 10 A 134 GLU SER LEU PRO GLY GLY LEU LYS GLU HIS ASP PHE ASN SEQRES 11 A 134 PRO GLU SER SER SEQRES 1 B 134 GLY SER LYS VAL GLU ASP PRO LYS ASP PHE PRO SER GLU SEQRES 2 B 134 LEU LEU SER PHE LEU SER HIS ALA VAL PHE SER ASN ARG SEQRES 3 B 134 THR LEU ALA CYS PHE ALA ILE TYR THR THR LYS GLU LYS SEQRES 4 B 134 ALA ALA LEU LEU TYR LYS LYS ILE MET GLU LYS TYR SER SEQRES 5 B 134 VAL THR PHE ILE SER ARG HIS ASN SER TYR ASN HIS ASN SEQRES 6 B 134 ILE LEU PHE PHE LEU THR PRO HIS ARG HIS ARG VAL SER SEQRES 7 B 134 ALA ILE ASN ASN TYR ALA GLN LYS LEU CME THR PHE SER SEQRES 8 B 134 PHE LEU ILE CYS LYS GLY VAL ASN LYS GLU TYR LEU MET SEQRES 9 B 134 TYR SER ALA LEU THR ARG ASP PRO PHE SER VAL ILE GLU SEQRES 10 B 134 GLU SER LEU PRO GLY GLY LEU LYS GLU HIS ASP PHE ASN SEQRES 11 B 134 PRO GLU SER SER SEQRES 1 X 21 DG DA DG DG DA DG DG DC DT DT DT DT DT SEQRES 2 X 21 DT DG DG DA DG DG DC DC SEQRES 1 Y 23 DA DC DT DC DC DT DC DC DG DA DA DA DA SEQRES 2 Y 23 DA DA DC DC DT DC DC DG DG DA MODRES 5D9I CME A 216 CYS MODIFIED RESIDUE MODRES 5D9I CME B 216 CYS MODIFIED RESIDUE HET CME A 216 10 HET CME B 216 10 HET EDO A 301 4 HET CA B 301 1 HET EDO B 302 4 HET CA Y 101 1 HET ACT Y 102 4 HETNAM CME S,S-(2-HYDROXYETHYL)THIOCYSTEINE HETNAM EDO 1,2-ETHANEDIOL HETNAM CA CALCIUM ION HETNAM ACT ACETATE ION HETSYN EDO ETHYLENE GLYCOL FORMUL 1 CME 2(C5 H11 N O3 S2) FORMUL 5 EDO 2(C2 H6 O2) FORMUL 6 CA 2(CA 2+) FORMUL 9 ACT C2 H3 O2 1- FORMUL 10 HOH *230(H2 O) HELIX 1 AA1 GLY A 129 ASP A 134 1 6 HELIX 2 AA2 PRO A 139 LEU A 146 5 8 HELIX 3 AA3 THR A 164 SER A 180 1 17 HELIX 4 AA4 ARG A 204 CME A 216 1 13 HELIX 5 AA5 LYS A 228 THR A 237 1 10 HELIX 6 AA6 LYS A 253 ASN A 258 5 6 HELIX 7 AA7 SER B 130 ASP B 134 1 5 HELIX 8 AA8 PRO B 139 LEU B 146 5 8 HELIX 9 AA9 THR B 164 SER B 180 1 17 HELIX 10 AB1 VAL B 205 CME B 216 1 12 HELIX 11 AB2 LYS B 228 THR B 237 1 10 HELIX 12 AB3 LYS B 253 ASN B 258 5 6 SHEET 1 AA1 5 LEU A 221 GLY A 225 0 SHEET 2 AA1 5 LEU A 156 THR A 163 -1 N TYR A 162 O ILE A 222 SHEET 3 AA1 5 HIS A 192 HIS A 203 -1 O LEU A 195 N ILE A 161 SHEET 4 AA1 5 PHE A 183 SER A 189 -1 N HIS A 187 O ILE A 194 SHEET 5 AA1 5 PHE A 241 GLU A 246 -1 O ILE A 244 N ARG A 186 SHEET 1 AA2 5 LEU B 221 GLY B 225 0 SHEET 2 AA2 5 THR B 155 THR B 163 -1 N TYR B 162 O ILE B 222 SHEET 3 AA2 5 HIS B 192 ARG B 204 -1 O LEU B 195 N ILE B 161 SHEET 4 AA2 5 PHE B 183 SER B 189 -1 N HIS B 187 O ILE B 194 SHEET 5 AA2 5 PHE B 241 GLU B 246 -1 O ILE B 244 N ARG B 186 LINK OD1 ASN A 191 ND1BHIS A 201 1555 4546 1.48 LINK C LEU A 215 N CME A 216 1555 1555 1.33 LINK C CME A 216 N THR A 217 1555 1555 1.32 LINK C LEU B 215 N CME B 216 1555 1555 1.32 LINK C CME B 216 N THR B 217 1555 1555 1.32 LINK O ALA B 212 CA CA B 301 1555 1555 2.56 LINK OH CME B 216 CA CA B 301 1555 1555 2.70 LINK O CME B 216 CA CA B 301 1555 1555 2.83 LINK CA CA B 301 O HOH B 433 1555 1555 2.25 LINK OP2 DG X 18 CA CA Y 101 1555 1565 2.19 LINK O6 DG X 19 CA CA Y 101 1555 1565 2.27 LINK O HOH X 112 CA CA Y 101 1545 1555 2.33 LINK O HOH X 120 CA CA Y 101 1545 1555 2.18 LINK OP2 DG Y 22 CA CA Y 101 1555 1555 2.35 LINK CA CA Y 101 O HOH Y 201 1555 1555 2.44 CISPEP 1 ASP A 239 PRO A 240 0 4.70 CISPEP 2 ASP A 239 PRO A 240 0 4.87 CISPEP 3 ASP B 239 PRO B 240 0 6.37 SITE 1 AC1 4 ASN A 209 ILE A 222 CYS A 223 HOH A 413 SITE 1 AC2 5 LYS B 167 ALA B 212 GLN B 213 CME B 216 SITE 2 AC2 5 HOH B 433 SITE 1 AC3 5 ASN B 209 ILE B 222 CYS B 223 HOH B 436 SITE 2 AC3 5 HOH B 438 SITE 1 AC4 6 DG X 18 DG X 19 HOH X 112 HOH X 120 SITE 2 AC4 6 DG Y 22 HOH Y 201 SITE 1 AC5 5 ASN B 153 DA X 17 DG X 18 DG Y 22 SITE 2 AC5 5 HOH Y 201 CRYST1 94.192 63.393 64.891 90.00 92.42 90.00 C 1 2 1 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 0.010617 0.000000 0.000449 0.00000 SCALE2 0.000000 0.015775 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015424 0.00000