HEADER DNA BINDING PROTEIN/DNA 04-JUN-12 4FGN TITLE CRYSTAL STRUCTURE OF THE SV40 LARGE T-ANTIGEN ORIGIN BINING DOMAIN TITLE 2 BOUND TO SITE I DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: LARGE T ANTIGEN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: ORIGIN BINDING DOMAIN, UNP RESIDUES 131-260; COMPND 5 SYNONYM: LT, LT-AG; COMPND 6 EC: 3.6.4.-; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: SITE I DNA; COMPND 10 CHAIN: Z; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: SITE I DNA; COMPND 14 CHAIN: Y; COMPND 15 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: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SIMIAN VIRUS 40; SOURCE 11 ORGANISM_TAXID: 10633; SOURCE 12 OTHER_DETAILS: THIS DNA SEQUENCE IS TERMED SITE 1 IN SV40; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 ORGANISM_SCIENTIFIC: SIMIAN VIRUS 40; SOURCE 16 ORGANISM_TAXID: 10633; SOURCE 17 OTHER_DETAILS: THIS DNA SEQUENCE IS FROM SV40 SITE I KEYWDS ORIGIN BINDING DOMAIN, DNA BINDING PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR G.MEINKE,A.BOHM,P.A.BULLOCK REVDAT 2 27-FEB-13 4FGN 1 JRNL REVDAT 1 23-JAN-13 4FGN 0 JRNL AUTH G.MEINKE,P.J.PHELAN,C.J.HARRISON,P.A.BULLOCK JRNL TITL ANALYSIS OF THE COSTRUCTURE OF THE SIMIAN VIRUS 40 T-ANTIGEN JRNL TITL 2 ORIGIN BINDING DOMAIN WITH SITE I REVEALS A CORRELATION JRNL TITL 3 BETWEEN GAGGC SPACING AND SPIRAL ASSEMBLY. JRNL REF J.VIROL. V. 87 2923 2013 JRNL REFN ISSN 0022-538X JRNL PMID 23269808 JRNL DOI 10.1128/JVI.02549-12 REMARK 2 REMARK 2 RESOLUTION. 3.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.99 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 8841 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) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 444 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) : 3.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.28 REMARK 3 REFLECTION IN BIN (WORKING SET) : 563 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.69 REMARK 3 BIN R VALUE (WORKING SET) : 0.3020 REMARK 3 BIN FREE R VALUE SET COUNT : 29 REMARK 3 BIN FREE R VALUE : 0.2660 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2027 REMARK 3 NUCLEIC ACID ATOMS : 937 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 3 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 137.11 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.22000 REMARK 3 B22 (A**2) : -0.13000 REMARK 3 B33 (A**2) : 0.35000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.504 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.517 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 73.091 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.971 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.952 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3132 ; 0.011 ; 0.017 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4434 ; 1.767 ; 1.737 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 248 ; 8.224 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 98 ;35.384 ;23.061 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 345 ;20.750 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;26.134 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 448 ; 0.102 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2062 ; 0.008 ; 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 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED 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 133 A 258 REMARK 3 ORIGIN FOR THE GROUP (A): 1.5594 42.2545 -0.2878 REMARK 3 T TENSOR REMARK 3 T11: 0.3479 T22: 0.6030 REMARK 3 T33: 0.8232 T12: -0.0302 REMARK 3 T13: 0.2384 T23: -0.0679 REMARK 3 L TENSOR REMARK 3 L11: 4.3163 L22: 14.3332 REMARK 3 L33: 11.8625 L12: -2.8324 REMARK 3 L13: -1.0743 L23: 2.3666 REMARK 3 S TENSOR REMARK 3 S11: 0.0745 S12: -0.2827 S13: -0.9794 REMARK 3 S21: 0.8123 S22: -0.7172 S23: 0.6496 REMARK 3 S31: 0.5555 S32: -0.3503 S33: 0.6427 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 134 B 257 REMARK 3 ORIGIN FOR THE GROUP (A): 3.1383 5.6793 -17.5268 REMARK 3 T TENSOR REMARK 3 T11: 1.2112 T22: 1.5418 REMARK 3 T33: 0.7115 T12: -0.4074 REMARK 3 T13: -0.4374 T23: -0.1961 REMARK 3 L TENSOR REMARK 3 L11: 10.8722 L22: 11.1175 REMARK 3 L33: 3.7342 L12: 2.9635 REMARK 3 L13: 1.3241 L23: 0.2369 REMARK 3 S TENSOR REMARK 3 S11: 0.9076 S12: -0.6183 S13: -0.5681 REMARK 3 S21: -0.2245 S22: -0.7337 S23: 1.4421 REMARK 3 S31: 1.6383 S32: -1.9481 S33: -0.1738 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 : Z 1 Z 23 REMARK 3 ORIGIN FOR THE GROUP (A): 17.6876 27.3756 -20.0936 REMARK 3 T TENSOR REMARK 3 T11: 1.0534 T22: 0.6879 REMARK 3 T33: 0.7649 T12: 0.2711 REMARK 3 T13: 0.1618 T23: -0.0419 REMARK 3 L TENSOR REMARK 3 L11: 4.5856 L22: 8.9030 REMARK 3 L33: 3.2417 L12: -5.0544 REMARK 3 L13: -0.7161 L23: 3.2412 REMARK 3 S TENSOR REMARK 3 S11: 0.6374 S12: 0.3198 S13: 0.9739 REMARK 3 S21: -1.2909 S22: -0.4605 S23: -1.7934 REMARK 3 S31: -0.3216 S32: 0.3427 S33: -0.1769 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): 16.4447 29.9636 -20.6853 REMARK 3 T TENSOR REMARK 3 T11: 0.9832 T22: 0.6251 REMARK 3 T33: 0.7814 T12: 0.2006 REMARK 3 T13: 0.2339 T23: -0.0533 REMARK 3 L TENSOR REMARK 3 L11: 2.5926 L22: 4.0713 REMARK 3 L33: 4.1954 L12: -2.6339 REMARK 3 L13: 1.4469 L23: 0.4706 REMARK 3 S TENSOR REMARK 3 S11: 0.9031 S12: 0.5819 S13: 0.0307 REMARK 3 S21: -1.4441 S22: -0.7736 S23: 0.2976 REMARK 3 S31: -0.2765 S32: 0.1121 S33: -0.1295 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 4FGN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JUN-12. REMARK 100 THE RCSB ID CODE IS RCSB072876. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 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) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9304 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.31 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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_EP REMARK 200 STARTING MODEL: 2NTC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM ACETATE PH 4.6, .2M REMARK 280 AMMONIUM SULFATE, 30 % PEG 4000, 10 MM CACL2, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 66.05600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 66.05600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 29.30200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 69.83600 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 29.30200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 69.83600 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 66.05600 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 29.30200 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 69.83600 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 66.05600 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 29.30200 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 69.83600 REMARK 290 SMTRY3 8 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: 4860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, Z, Y, 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH B 301 LIES ON A SPECIAL POSITION. 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 GLY A 129 REMARK 465 SER A 130 REMARK 465 LYS A 131 REMARK 465 VAL A 132 REMARK 465 PRO A 259 REMARK 465 GLU A 260 REMARK 465 GLY B 129 REMARK 465 SER B 130 REMARK 465 LYS B 131 REMARK 465 VAL B 132 REMARK 465 GLU B 133 REMARK 465 ASN B 258 REMARK 465 PRO B 259 REMARK 465 GLU B 260 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 LYS A 136 CG CD CE NZ REMARK 470 LYS B 136 CG CD CE NZ REMARK 470 LYS B 167 CG CD CE NZ REMARK 470 LYS B 214 CG CD CE NZ REMARK 470 LYS B 228 CG CD CE NZ 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 148 CG HIS A 148 CD2 0.059 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 DA Z 9 C3' - O3' - P ANGL. DEV. = 7.8 DEGREES REMARK 500 DA Z 13 C3' - O3' - P ANGL. DEV. = 7.5 DEGREES REMARK 500 DA Z 14 C3' - O3' - P ANGL. DEV. = 9.7 DEGREES REMARK 500 DC Z 16 C3' - O3' - P ANGL. DEV. = -8.4 DEGREES REMARK 500 DA Y 2 C3' - O3' - P ANGL. DEV. = -8.1 DEGREES REMARK 500 DT Y 9 C3' - O3' - P ANGL. DEV. = 9.2 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 135 130.90 -37.48 REMARK 500 SER A 140 -66.13 -1.63 REMARK 500 ALA A 149 105.22 -52.32 REMARK 500 PHE A 151 47.07 -105.55 REMARK 500 THR A 163 -167.31 -165.28 REMARK 500 SER A 189 98.49 -160.08 REMARK 500 LEU A 215 31.22 -89.57 REMARK 500 CYS A 216 98.03 -168.08 REMARK 500 PHE A 218 -36.56 -137.72 REMARK 500 LEU A 221 119.82 -161.15 REMARK 500 ILE A 244 -80.60 -126.42 REMARK 500 SER A 247 -86.80 -55.44 REMARK 500 SER B 140 -57.72 -24.99 REMARK 500 ARG B 154 120.48 -38.27 REMARK 500 LYS B 173 -78.88 -75.82 REMARK 500 ASN B 191 18.05 46.66 REMARK 500 HIS B 192 -154.54 -112.28 REMARK 500 SER B 219 -117.26 69.93 REMARK 500 LEU B 221 104.98 -174.48 REMARK 500 CYS B 223 119.10 -169.79 REMARK 500 MET B 232 -72.33 -65.00 REMARK 500 PRO B 249 127.40 -34.16 REMARK 500 LYS B 253 -128.46 -83.48 REMARK 500 GLU B 254 -67.40 -106.73 REMARK 500 HIS B 255 -56.43 -2.91 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 PHE A 257 ASN A 258 149.86 REMARK 500 THR B 217 PHE B 218 148.93 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2FUF RELATED DB: PDB REMARK 900 APO-LARGE T-ANTIGEN ORIGIN BINDING DOMAIN REMARK 900 RELATED ID: 2NTC RELATED DB: PDB REMARK 900 LARGE T-ANTIGEN ORIGIN BINDING DOMAIN IN COMPLEX WITH REMARK 900 SUBSET OF SITE II DNA (P1, P3) REMARK 900 RELATED ID: 2ITL RELATED DB: PDB REMARK 900 LARGE T-ANTIGEN ORIGIN BINDING DOMAIN IN COMPLEX WITH SITE REMARK 900 II DNA (P1-P4) DBREF 4FGN A 131 260 UNP P03070 LT_SV40 131 260 DBREF 4FGN B 131 260 UNP P03070 LT_SV40 131 260 DBREF 4FGN Z 1 23 PDB 4FGN 4FGN 1 23 DBREF 4FGN Y 1 23 PDB 4FGN 4FGN 1 23 SEQADV 4FGN GLY A 129 UNP P03070 EXPRESSION TAG SEQADV 4FGN SER A 130 UNP P03070 EXPRESSION TAG SEQADV 4FGN GLY B 129 UNP P03070 EXPRESSION TAG SEQADV 4FGN SER B 130 UNP P03070 EXPRESSION TAG SEQRES 1 A 132 GLY SER LYS VAL GLU ASP PRO LYS ASP PHE PRO SER GLU SEQRES 2 A 132 LEU LEU SER PHE LEU SER HIS ALA VAL PHE SER ASN ARG SEQRES 3 A 132 THR LEU ALA CYS PHE ALA ILE TYR THR THR LYS GLU LYS SEQRES 4 A 132 ALA ALA LEU LEU TYR LYS LYS ILE MET GLU LYS TYR SER SEQRES 5 A 132 VAL THR PHE ILE SER ARG HIS ASN SER TYR ASN HIS ASN SEQRES 6 A 132 ILE LEU PHE PHE LEU THR PRO HIS ARG HIS ARG VAL SER SEQRES 7 A 132 ALA ILE ASN ASN TYR ALA GLN LYS LEU CYS THR PHE SER SEQRES 8 A 132 PHE LEU ILE CYS LYS GLY VAL ASN LYS GLU TYR LEU MET SEQRES 9 A 132 TYR SER ALA LEU THR ARG ASP PRO PHE SER VAL ILE GLU SEQRES 10 A 132 GLU SER LEU PRO GLY GLY LEU LYS GLU HIS ASP PHE ASN SEQRES 11 A 132 PRO GLU SEQRES 1 B 132 GLY SER LYS VAL GLU ASP PRO LYS ASP PHE PRO SER GLU SEQRES 2 B 132 LEU LEU SER PHE LEU SER HIS ALA VAL PHE SER ASN ARG SEQRES 3 B 132 THR LEU ALA CYS PHE ALA ILE TYR THR THR LYS GLU LYS SEQRES 4 B 132 ALA ALA LEU LEU TYR LYS LYS ILE MET GLU LYS TYR SER SEQRES 5 B 132 VAL THR PHE ILE SER ARG HIS ASN SER TYR ASN HIS ASN SEQRES 6 B 132 ILE LEU PHE PHE LEU THR PRO HIS ARG HIS ARG VAL SER SEQRES 7 B 132 ALA ILE ASN ASN TYR ALA GLN LYS LEU CYS THR PHE SER SEQRES 8 B 132 PHE LEU ILE CYS LYS GLY VAL ASN LYS GLU TYR LEU MET SEQRES 9 B 132 TYR SER ALA LEU THR ARG ASP PRO PHE SER VAL ILE GLU SEQRES 10 B 132 GLU SER LEU PRO GLY GLY LEU LYS GLU HIS ASP PHE ASN SEQRES 11 B 132 PRO GLU SEQRES 1 Z 23 DA DG DG DC DC DT DC DC DA DA DA DA DA SEQRES 2 Z 23 DA DG DC DC DT DC DC DT DC DA SEQRES 1 Y 23 DG DA DG DG DA DG DG DC DT DT DT DT DT SEQRES 2 Y 23 DT DG DG DA DG DG DC DC DT DT FORMUL 5 HOH *3(H2 O) HELIX 1 1 GLU A 141 LEU A 146 5 6 HELIX 2 2 THR A 164 TYR A 179 1 16 HELIX 3 3 ARG A 204 LYS A 214 1 11 HELIX 4 4 LYS A 228 ARG A 238 1 11 HELIX 5 5 GLY A 250 GLU A 254 5 5 HELIX 6 6 PRO B 139 LEU B 146 5 8 HELIX 7 7 ALA B 168 SER B 180 1 13 HELIX 8 8 ARG B 204 CYS B 216 1 13 HELIX 9 9 LYS B 228 ARG B 238 1 11 SHEET 1 A 5 LEU A 221 GLY A 225 0 SHEET 2 A 5 LEU A 156 THR A 163 -1 N ALA A 160 O LYS A 224 SHEET 3 A 5 ASN A 193 HIS A 203 -1 O HIS A 203 N LEU A 156 SHEET 4 A 5 PHE A 183 ASN A 188 -1 N HIS A 187 O ILE A 194 SHEET 5 A 5 VAL A 243 GLU A 246 -1 O ILE A 244 N ARG A 186 SHEET 1 B 4 LEU B 156 THR B 163 0 SHEET 2 B 4 ASN B 193 HIS B 203 -1 O HIS B 203 N LEU B 156 SHEET 3 B 4 PHE B 183 ASN B 188 -1 N SER B 185 O PHE B 196 SHEET 4 B 4 SER B 242 GLU B 246 -1 O SER B 242 N ASN B 188 CISPEP 1 ASP A 239 PRO A 240 0 12.73 CISPEP 2 ASP B 239 PRO B 240 0 0.19 CRYST1 58.604 139.672 132.112 90.00 90.00 90.00 C 2 2 21 16 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 0.017064 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007160 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007569 0.00000 MASTER 470 0 0 9 9 0 0 6 0 0 0 26 END