PDB Short entry for 2BOP HEADER TRANSCRIPTION/DNA 13-JAN-94 2BOP TITLE CRYSTAL STRUCTURE AT 1.7 ANGSTROMS OF THE BOVINE PAPILLOMAVIRUS-1 E2 TITLE 2 DNA-BINDING DOMAIN BOUND TO ITS DNA TARGET CAVEAT 2BOP SER A 326 HAS WRONG CHIRALITY AT ATOM CA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*CP*CP*GP*AP*CP*CP*GP*AP*CP*GP*TP*CP*GP*GP*TP*CP*G )-3'); COMPND 4 CHAIN: B; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: PROTEIN (E2); COMPND 8 CHAIN: A; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 ORGANISM_SCIENTIFIC: BOVINE PAPILLOMAVIRUS TYPE 1; SOURCE 5 ORGANISM_TAXID: 10559; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROTEIN-DNA COMPLEX, DOUBLE HELIX, TRANSCRIPTION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR R.S.HEGDE,S.R.GROSSMAN,L.A.LAIMINS,P.B.SIGLER REVDAT 5 14-FEB-24 2BOP 1 REMARK LINK REVDAT 4 20-NOV-19 2BOP 1 CAVEAT REMARK LINK REVDAT 3 24-FEB-09 2BOP 1 VERSN REVDAT 2 01-APR-03 2BOP 1 JRNL REVDAT 1 31-JAN-94 2BOP 0 JRNL AUTH R.S.HEGDE,S.R.GROSSMAN,L.A.LAIMINS,P.B.SIGLER JRNL TITL CRYSTAL STRUCTURE AT 1.7 A OF THE BOVINE PAPILLOMAVIRUS-1 E2 JRNL TITL 2 DNA-BINDING DOMAIN BOUND TO ITS DNA TARGET. JRNL REF NATURE V. 359 505 1992 JRNL REFN ISSN 0028-0836 JRNL PMID 1328886 JRNL DOI 10.1038/359505A0 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NUCLSQ REMARK 3 AUTHORS : WESTHOF,DUMAS,MORAS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 22798 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.201 REMARK 3 R VALUE (WORKING SET) : NULL REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 677 REMARK 3 NUCLEIC ACID ATOMS : 344 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 121 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 SUGAR-BASE BOND DISTANCE (A) : NULL ; NULL REMARK 3 SUGAR-BASE BOND ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 PHOSPHATE BONDS DISTANCE (A) : NULL ; NULL REMARK 3 PHOSPHATE BOND ANGLE, H-BOND (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION CONTACT (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION CONTACT (A) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 SUGAR-BASE BONDS (A**2) : NULL ; NULL REMARK 3 SUGAR-BASE ANGLES (A**2) : NULL ; NULL REMARK 3 PHOSPHATE BONDS (A**2) : NULL ; NULL REMARK 3 PHOSPHATE BOND ANGLE, H-BOND (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2BOP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000177845. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 7.50 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : SDMS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL 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 (%): 43.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.50, VAPOR DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: R 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 Z,X,Y REMARK 290 3555 Y,Z,X REMARK 290 4555 -Y,-X,-Z REMARK 290 5555 -X,-Z,-Y REMARK 290 6555 -Z,-Y,-X 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 0.472551 0.282816 0.834692 0.00000 REMARK 290 SMTRY2 2 0.881303 -0.151645 -0.447558 0.00000 REMARK 290 SMTRY3 2 0.000000 0.947111 -0.320906 0.00000 REMARK 290 SMTRY1 3 0.472551 0.881303 0.000000 0.00000 REMARK 290 SMTRY2 3 0.282816 -0.151645 0.947111 0.00000 REMARK 290 SMTRY3 3 0.834692 -0.447558 -0.320906 0.00000 REMARK 290 SMTRY1 4 -0.472551 -0.881303 0.000000 0.00000 REMARK 290 SMTRY2 4 -0.881303 0.472551 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -0.320906 -0.947111 0.00000 REMARK 290 SMTRY3 5 0.000000 -0.947111 0.320906 0.00000 REMARK 290 SMTRY1 6 -0.472551 -0.282816 -0.834692 0.00000 REMARK 290 SMTRY2 6 -0.282816 -0.848355 0.447558 0.00000 REMARK 290 SMTRY3 6 -0.834692 0.447558 0.320906 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 APPLY THE FOLLOWING TO CHAINS: B, 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 BIOMT1 2 -0.472551 -0.881303 0.000000 220.78034 REMARK 350 BIOMT2 2 -0.881303 0.472551 0.000000 132.13431 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 53.92111 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 OP2 DC B 9 O HOH B 621 1.84 REMARK 500 OD1 ASN A 400 O HOH A 545 1.86 REMARK 500 OD1 ASN A 366 YB YB A 499 1.96 REMARK 500 O HOH A 527 O HOH A 547 1.97 REMARK 500 ND1 HIS A 351 O HOH A 568 2.00 REMARK 500 O HOH A 528 O HOH A 550 2.01 REMARK 500 O HOH A 560 O HOH A 598 2.04 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 O HOH A 569 O HOH A 569 4776 1.65 REMARK 500 O HOH A 540 O HOH A 587 4776 2.07 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 DC B 2 P DC B 2 OP2 -0.156 REMARK 500 DC B 2 C3' DC B 2 C2' -0.071 REMARK 500 DC B 2 O4' DC B 2 C4' -0.068 REMARK 500 DC B 2 O3' DG B 3 P 0.078 REMARK 500 DA B 4 P DA B 4 O5' -0.060 REMARK 500 DC B 6 P DC B 6 OP2 -0.155 REMARK 500 DG B 7 P DG B 7 OP1 0.148 REMARK 500 DA B 8 P DA B 8 OP2 -0.186 REMARK 500 DA B 8 P DA B 8 O5' 0.107 REMARK 500 DA B 8 O4' DA B 8 C4' -0.062 REMARK 500 DA B 8 C6 DA B 8 N1 0.046 REMARK 500 DC B 9 P DC B 9 OP2 -0.130 REMARK 500 DC B 9 P DC B 9 O5' 0.233 REMARK 500 DC B 9 O4' DC B 9 C4' -0.068 REMARK 500 DC B 9 O3' DG B 10 P 0.141 REMARK 500 DG B 10 P DG B 10 O5' 0.062 REMARK 500 DG B 10 O3' DT B 11 P -0.122 REMARK 500 DT B 11 P DT B 11 OP1 -0.226 REMARK 500 DT B 11 P DT B 11 O5' 0.107 REMARK 500 DT B 11 C4 DT B 11 O4 0.074 REMARK 500 DC B 12 O4' DC B 12 C4' -0.071 REMARK 500 DG B 14 C5 DG B 14 N7 0.038 REMARK 500 DG B 14 N7 DG B 14 C8 -0.041 REMARK 500 DG B 14 O3' DT B 15 P 0.074 REMARK 500 DC B 16 P DC B 16 OP2 -0.119 REMARK 500 DC B 16 P DC B 16 O5' -0.125 REMARK 500 DC B 16 C2' DC B 16 C1' 0.074 REMARK 500 DC B 16 O4' DC B 16 C4' -0.065 REMARK 500 DC B 16 O3' DG B 17 P 0.108 REMARK 500 DG B 17 P DG B 17 OP1 0.169 REMARK 500 DG B 17 P DG B 17 O5' -0.192 REMARK 500 DG B 17 C6 DG B 17 N1 -0.051 REMARK 500 DG B 17 C8 DG B 17 N9 -0.049 REMARK 500 SER A 326 CB SER A 326 OG 0.083 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 DC B 1 O5' - C5' - C4' ANGL. DEV. = -5.5 DEGREES REMARK 500 DC B 1 O4' - C1' - N1 ANGL. DEV. = -4.4 DEGREES REMARK 500 DC B 1 C6 - N1 - C2 ANGL. DEV. = 3.0 DEGREES REMARK 500 DC B 1 C4 - C5 - C6 ANGL. DEV. = 3.7 DEGREES REMARK 500 DC B 1 C5 - C6 - N1 ANGL. DEV. = -4.6 DEGREES REMARK 500 DC B 1 N1 - C2 - O2 ANGL. DEV. = 4.8 DEGREES REMARK 500 DC B 1 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 DC B 2 O4' - C1' - C2' ANGL. DEV. = -5.8 DEGREES REMARK 500 DC B 2 N1 - C2 - N3 ANGL. DEV. = -4.3 DEGREES REMARK 500 DC B 2 C2 - N3 - C4 ANGL. DEV. = 7.2 DEGREES REMARK 500 DC B 2 N3 - C4 - C5 ANGL. DEV. = -2.9 DEGREES REMARK 500 DG B 3 O5' - P - OP2 ANGL. DEV. = 8.0 DEGREES REMARK 500 DG B 3 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 DG B 3 N3 - C4 - C5 ANGL. DEV. = -3.6 DEGREES REMARK 500 DG B 3 C5 - C6 - O6 ANGL. DEV. = -3.7 DEGREES REMARK 500 DA B 4 O5' - P - OP2 ANGL. DEV. = 8.0 DEGREES REMARK 500 DA B 4 C5' - C4' - C3' ANGL. DEV. = 7.3 DEGREES REMARK 500 DA B 4 N1 - C2 - N3 ANGL. DEV. = -3.7 DEGREES REMARK 500 DA B 4 C2 - N3 - C4 ANGL. DEV. = 4.0 DEGREES REMARK 500 DA B 4 C5 - N7 - C8 ANGL. DEV. = -3.2 DEGREES REMARK 500 DC B 5 C5' - C4' - C3' ANGL. DEV. = 9.2 DEGREES REMARK 500 DC B 5 C1' - O4' - C4' ANGL. DEV. = -6.0 DEGREES REMARK 500 DC B 5 N3 - C4 - C5 ANGL. DEV. = -2.7 DEGREES REMARK 500 DC B 6 O5' - P - OP2 ANGL. DEV. = 8.8 DEGREES REMARK 500 DC B 6 C2 - N3 - C4 ANGL. DEV. = 3.8 DEGREES REMARK 500 DG B 7 O3' - P - OP1 ANGL. DEV. = 11.5 DEGREES REMARK 500 DG B 7 OP1 - P - OP2 ANGL. DEV. = -19.2 DEGREES REMARK 500 DG B 7 O5' - P - OP2 ANGL. DEV. = -9.2 DEGREES REMARK 500 DG B 7 O5' - C5' - C4' ANGL. DEV. = -6.7 DEGREES REMARK 500 DG B 7 P - O5' - C5' ANGL. DEV. = -12.9 DEGREES REMARK 500 DG B 7 N1 - C2 - N2 ANGL. DEV. = 5.4 DEGREES REMARK 500 DG B 7 N3 - C2 - N2 ANGL. DEV. = -5.8 DEGREES REMARK 500 DG B 7 C5 - C6 - O6 ANGL. DEV. = -5.5 DEGREES REMARK 500 DA B 8 O3' - P - OP2 ANGL. DEV. = 10.6 DEGREES REMARK 500 DA B 8 O5' - P - OP1 ANGL. DEV. = -6.5 DEGREES REMARK 500 DA B 8 O5' - C5' - C4' ANGL. DEV. = -6.6 DEGREES REMARK 500 DA B 8 P - O5' - C5' ANGL. DEV. = -10.7 DEGREES REMARK 500 DC B 9 O3' - P - OP2 ANGL. DEV. = 10.5 DEGREES REMARK 500 DC B 9 O5' - P - OP1 ANGL. DEV. = -12.5 DEGREES REMARK 500 DC B 9 O5' - C5' - C4' ANGL. DEV. = -8.1 DEGREES REMARK 500 DC B 9 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 DC B 9 C2 - N3 - C4 ANGL. DEV. = 4.2 DEGREES REMARK 500 DC B 9 N3 - C4 - C5 ANGL. DEV. = -4.4 DEGREES REMARK 500 DG B 10 OP1 - P - OP2 ANGL. DEV. = 15.7 DEGREES REMARK 500 DG B 10 O5' - C5' - C4' ANGL. DEV. = -6.1 DEGREES REMARK 500 DG B 10 C6 - N1 - C2 ANGL. DEV. = -5.3 DEGREES REMARK 500 DG B 10 N1 - C2 - N3 ANGL. DEV. = 3.9 DEGREES REMARK 500 DG B 10 C5 - C6 - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 DG B 10 N1 - C6 - O6 ANGL. DEV. = -6.0 DEGREES REMARK 500 DT B 11 O3' - P - OP1 ANGL. DEV. = 8.3 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 100 ANGLE DEVIATIONS. 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 GLU A 354 -71.51 -84.84 REMARK 500 ALA A 364 -157.27 -110.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DC B 6 0.06 SIDE CHAIN REMARK 500 DA B 8 0.06 SIDE CHAIN REMARK 500 DC B 9 0.08 SIDE CHAIN REMARK 500 DC B 12 0.11 SIDE CHAIN REMARK 500 GLN A 371 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ASN A 348 13.08 REMARK 500 GLY A 381 11.57 REMARK 500 LYS A 391 -10.60 REMARK 500 GLY A 403 11.32 REMARK 500 ALA A 406 12.53 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 YTTERBIUM WAS USED IN THE CRYSTALLIZATION AND PHASING OF THIS REMARK 600 STRUCTURE. IT HAS NO ROLE IN DNA-BINDING OR DNA SEQUENCE REMARK 600 RECOGNITION. 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 YB B 500 YB REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 612 O REMARK 620 2 HOH B 613 O 65.2 REMARK 620 3 HOH B 620 O 104.6 68.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 YB A 499 YB REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 354 OE1 REMARK 620 2 GLU A 354 OE2 54.4 REMARK 620 3 ASP A 365 OD1 43.3 26.4 REMARK 620 4 GLU A 369 OE1 41.5 24.0 3.6 REMARK 620 5 GLU A 369 OE2 39.3 24.0 5.7 2.4 REMARK 620 N 1 2 3 4 REMARK 700 REMARK 700 SHEET REMARK 700 THE PROTEIN FORMS A DIMERIC BARREL. THE FOUR STRANDS OF REMARK 700 EACH BETA SHEET DESCRIBED BELOW COMPRISE A HALF BARREL. REMARK 700 THE OTHER HALF IS GENERATED BY A CRYSTALLOGRAPHIC TWO-FOLD. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE YB A 499 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE YB B 500 DBREF 2BOP A 326 410 UNP P03122 VE2_BPV1 326 410 DBREF 2BOP B 1 17 PDB 2BOP 2BOP 1 17 SEQRES 1 B 17 DC DC DG DA DC DC DG DA DC DG DT DC DG SEQRES 2 B 17 DG DT DC DG SEQRES 1 A 85 SER CYS PHE ALA LEU ILE SER GLY THR ALA ASN GLN VAL SEQRES 2 A 85 LYS CYS TYR ARG PHE ARG VAL LYS LYS ASN HIS ARG HIS SEQRES 3 A 85 ARG TYR GLU ASN CYS THR THR THR TRP PHE THR VAL ALA SEQRES 4 A 85 ASP ASN GLY ALA GLU ARG GLN GLY GLN ALA GLN ILE LEU SEQRES 5 A 85 ILE THR PHE GLY SER PRO SER GLN ARG GLN ASP PHE LEU SEQRES 6 A 85 LYS HIS VAL PRO LEU PRO PRO GLY MET ASN ILE SER GLY SEQRES 7 A 85 PHE THR ALA SER LEU ASP PHE HET YB B 500 1 HET YB A 499 1 HETNAM YB YTTERBIUM (III) ION FORMUL 3 YB 2(YB 3+) FORMUL 5 HOH *121(H2 O) HELIX 1 A1 THR A 334 HIS A 349 1 16 HELIX 2 A2 SER A 382 VAL A 393 1 12 SHEET 1 B 4 TYR A 353 ASP A 365 0 SHEET 2 B 4 GLU A 369 GLY A 381 -1 SHEET 3 B 4 SER A 326 THR A 334 -1 SHEET 4 B 4 MET A 399 PHE A 410 -1 LINK YB YB B 500 O HOH B 612 1555 4776 2.67 LINK YB YB B 500 O HOH B 613 1555 4776 2.64 LINK YB YB B 500 O HOH B 620 1555 4776 2.67 LINK OE1 GLU A 354 YB YB A 499 1555 5776 2.45 LINK OE2 GLU A 354 YB YB A 499 1555 5776 2.28 LINK OD1 ASP A 365 YB YB A 499 1555 1555 2.26 LINK OE1 GLU A 369 YB YB A 499 1555 1555 2.41 LINK OE2 GLU A 369 YB YB A 499 1555 1555 2.31 SITE 1 AC1 4 GLU A 354 ASP A 365 ASN A 366 GLU A 369 SITE 1 AC2 3 HOH B 612 HOH B 613 HOH B 620 CRYST1 64.600 64.600 64.600 61.80 61.80 61.80 R 3 2 6 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 0.015480 -0.008300 -0.005951 0.00000 SCALE2 0.000000 0.017565 -0.005951 0.00000 SCALE3 0.000000 0.000000 0.018546 0.00000