HEADER TRANSCRIPTION/DNA 07-SEP-05 2AYB TITLE CRYSTAL STRUCTURE OF HPV6A E2 DNA BINDING DOMAIN BOUND TO A 16 BASE TITLE 2 PAIR DNA TARGET COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*AP*AP*CP*CP*GP*AP*AP*TP*TP*CP*GP*GP*TP*TP*G)-3'; COMPND 3 CHAIN: C, D; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: REGULATORY PROTEIN E2; COMPND 7 CHAIN: A, B; COMPND 8 FRAGMENT: C TERMINAL DOMAIN; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 ORGANISM_SCIENTIFIC: HUMAN PAPILLOMAVIRUS TYPE 6A; SOURCE 5 ORGANISM_TAXID: 37122; SOURCE 6 GENE: E2; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: XL1-BLUE; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PKK223-3 KEYWDS PROTEIN-DNA COMPLEX, DOUBLE HELIX, BETA BARREL, TRANSCRIPTION-DNA KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR E.HOOLEY,R.L.BRADY,K.GASTON REVDAT 6 23-AUG-23 2AYB 1 SEQADV REVDAT 5 04-APR-18 2AYB 1 REMARK REVDAT 4 13-JUL-11 2AYB 1 VERSN REVDAT 3 24-FEB-09 2AYB 1 VERSN REVDAT 2 03-OCT-06 2AYB 1 JRNL REVDAT 1 22-AUG-06 2AYB 0 JRNL AUTH E.HOOLEY,V.FAIRWEATHER,A.R.CLARKE,K.GASTON,R.L.BRADY JRNL TITL THE RECOGNITION OF LOCAL DNA CONFORMATION BY THE HUMAN JRNL TITL 2 PAPILLOMAVIRUS TYPE 6 E2 PROTEIN. JRNL REF NUCLEIC ACIDS RES. V. 34 3897 2006 JRNL REFN ISSN 0305-1048 JRNL PMID 16914454 JRNL DOI 10.1093/NAR/GKL466 REMARK 2 REMARK 2 RESOLUTION. 3.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 3.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 65.23 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 4928 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) : 0.259 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.297 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.600 REMARK 3 FREE R VALUE TEST SET COUNT : 240 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) : 3.29 REMARK 3 REFLECTION IN BIN (WORKING SET) : 362 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.95 REMARK 3 BIN R VALUE (WORKING SET) : 0.2660 REMARK 3 BIN FREE R VALUE SET COUNT : 16 REMARK 3 BIN FREE R VALUE : 0.3560 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1444 REMARK 3 NUCLEIC ACID ATOMS : 650 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 12 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.20000 REMARK 3 B22 (A**2) : 2.20000 REMARK 3 B33 (A**2) : -3.31000 REMARK 3 B12 (A**2) : 1.10000 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): 0.632 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.402 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 33.517 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.942 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.843 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2218 ; 0.014 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3138 ; 2.148 ; 2.303 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 172 ; 9.067 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 70 ;36.318 ;22.286 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 258 ;20.966 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;19.688 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 342 ; 0.111 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1456 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1024 ; 0.250 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1414 ; 0.320 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 75 ; 0.161 ; 0.200 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): 44 ; 0.179 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 4 ; 0.198 ; 0.200 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): 891 ; 0.552 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1430 ; 1.020 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1696 ; 1.021 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1708 ; 1.742 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 283 A 364 1 REMARK 3 1 B 283 B 364 1 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 1 A (A): 693 ; NULL ; NULL REMARK 3 TIGHT THERMAL 1 A (A**2): 693 ; NULL ; NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 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 : B 281 B 366 REMARK 3 ORIGIN FOR THE GROUP (A): -13.6070 18.0505 -14.8703 REMARK 3 T TENSOR REMARK 3 T11: 0.0067 T22: 0.0851 REMARK 3 T33: -0.0595 T12: -0.0672 REMARK 3 T13: 0.0808 T23: -0.0142 REMARK 3 L TENSOR REMARK 3 L11: 2.0086 L22: 2.4985 REMARK 3 L33: 2.7172 L12: -0.3197 REMARK 3 L13: 0.1951 L23: -0.1690 REMARK 3 S TENSOR REMARK 3 S11: -0.1516 S12: 0.2636 S13: -0.2337 REMARK 3 S21: -0.1494 S22: 0.1538 S23: 0.0433 REMARK 3 S31: 0.3387 S32: 0.0745 S33: -0.0022 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 281 A 366 REMARK 3 ORIGIN FOR THE GROUP (A): -8.8454 20.8860 3.3446 REMARK 3 T TENSOR REMARK 3 T11: 0.0014 T22: 0.0705 REMARK 3 T33: -0.0412 T12: -0.0733 REMARK 3 T13: 0.0264 T23: 0.0793 REMARK 3 L TENSOR REMARK 3 L11: 2.4077 L22: 1.7972 REMARK 3 L33: 3.2064 L12: -0.5251 REMARK 3 L13: -0.2787 L23: 0.2356 REMARK 3 S TENSOR REMARK 3 S11: 0.0860 S12: -0.2957 S13: -0.0930 REMARK 3 S21: 0.0453 S22: -0.1333 S23: -0.2217 REMARK 3 S31: 0.1975 S32: 0.2542 S33: 0.0473 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 2AYB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-SEP-05. REMARK 100 THE DEPOSITION ID IS D_1000034449. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAY-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : BRUKER X8 PROTEUM REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.548 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER SMART 6000 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4928 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.200 REMARK 200 RESOLUTION RANGE LOW (A) : 65.230 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 22.50 REMARK 200 R MERGE (I) : 0.13800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.8000 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) : 3.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 22.50 REMARK 200 R MERGE FOR SHELL (I) : 0.38700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.200 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: PROTEIN OF PDB ENTRY 1R8H DNA OF PDB ENTRY 1JJ4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TRI-SODIUM CITRATE DIHYDRATE, PH 6.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.47533 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 64.95067 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 48.71300 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 81.18833 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 16.23767 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A PROTEIN DIMER BOUND TO DOUBLE REMARK 300 STRANDED DNA 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: C, D, A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 C 11 CG2 THR A 316 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 DC C 5 O3' DC C 5 C3' -0.038 REMARK 500 DA C 8 O3' DA C 8 C3' -0.042 REMARK 500 DT C 9 O3' DT C 9 C3' -0.040 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 C 1 O5' - C5' - C4' ANGL. DEV. = -6.4 DEGREES REMARK 500 DC C 1 O4' - C4' - C3' ANGL. DEV. = -5.6 DEGREES REMARK 500 DC C 1 C1' - O4' - C4' ANGL. DEV. = -16.0 DEGREES REMARK 500 DC C 1 C4' - C3' - C2' ANGL. DEV. = -5.6 DEGREES REMARK 500 DC C 1 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DA C 2 P - O5' - C5' ANGL. DEV. = -11.2 DEGREES REMARK 500 DA C 2 C3' - C2' - C1' ANGL. DEV. = -5.0 DEGREES REMARK 500 DA C 2 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DC C 5 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DG C 6 O4' - C1' - N9 ANGL. DEV. = 6.3 DEGREES REMARK 500 DG C 6 C3' - O3' - P ANGL. DEV. = 10.6 DEGREES REMARK 500 DA C 7 C5' - C4' - O4' ANGL. DEV. = 7.4 DEGREES REMARK 500 DA C 7 C3' - C2' - C1' ANGL. DEV. = -5.3 DEGREES REMARK 500 DA C 7 O4' - C1' - N9 ANGL. DEV. = 8.0 DEGREES REMARK 500 DT C 9 C6 - C5 - C7 ANGL. DEV. = -7.2 DEGREES REMARK 500 DT C 10 N3 - C4 - O4 ANGL. DEV. = 3.8 DEGREES REMARK 500 DT C 10 C5 - C4 - O4 ANGL. DEV. = -6.2 DEGREES REMARK 500 DG C 12 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 DG C 12 C3' - O3' - P ANGL. DEV. = 12.6 DEGREES REMARK 500 DG C 13 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 DG C 13 C3' - O3' - P ANGL. DEV. = 9.7 DEGREES REMARK 500 DT C 15 O5' - C5' - C4' ANGL. DEV. = -5.1 DEGREES REMARK 500 DT C 15 C3' - C2' - C1' ANGL. DEV. = -6.3 DEGREES REMARK 500 DG C 16 O4' - C1' - N9 ANGL. DEV. = -5.4 DEGREES REMARK 500 DC D 1 O4' - C4' - C3' ANGL. DEV. = -6.8 DEGREES REMARK 500 DC D 1 C1' - O4' - C4' ANGL. DEV. = -13.9 DEGREES REMARK 500 DC D 1 C4' - C3' - C2' ANGL. DEV. = -4.5 DEGREES REMARK 500 DC D 1 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DA D 2 C3' - C2' - C1' ANGL. DEV. = -7.9 DEGREES REMARK 500 DA D 2 C8 - N9 - C4 ANGL. DEV. = 2.8 DEGREES REMARK 500 DC D 5 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DG D 6 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 DG D 6 C3' - O3' - P ANGL. DEV. = 11.6 DEGREES REMARK 500 DA D 7 C5' - C4' - O4' ANGL. DEV. = 7.0 DEGREES REMARK 500 DA D 7 C3' - C2' - C1' ANGL. DEV. = -5.4 DEGREES REMARK 500 DA D 7 O4' - C1' - N9 ANGL. DEV. = 11.4 DEGREES REMARK 500 DA D 8 C3' - C2' - C1' ANGL. DEV. = -5.5 DEGREES REMARK 500 DT D 9 C6 - C5 - C7 ANGL. DEV. = -5.8 DEGREES REMARK 500 DT D 10 C5 - C4 - O4 ANGL. DEV. = -5.1 DEGREES REMARK 500 DT D 10 C3' - O3' - P ANGL. DEV. = 8.8 DEGREES REMARK 500 DC D 11 O4' - C1' - C2' ANGL. DEV. = 3.3 DEGREES REMARK 500 DC D 11 O4' - C1' - N1 ANGL. DEV. = -4.7 DEGREES REMARK 500 DG D 12 C3' - O3' - P ANGL. DEV. = 9.5 DEGREES REMARK 500 DG D 13 C3' - O3' - P ANGL. DEV. = 9.9 DEGREES REMARK 500 DT D 15 O4' - C4' - C3' ANGL. DEV. = -2.9 DEGREES REMARK 500 DT D 15 O4' - C1' - N1 ANGL. DEV. = -5.9 DEGREES REMARK 500 DG D 16 O4' - C1' - N9 ANGL. DEV. = -5.8 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 SER A 282 30.57 -91.76 REMARK 500 HIS A 306 12.16 -146.12 REMARK 500 ASP A 311 -80.75 -123.71 REMARK 500 HIS A 326 -141.52 -133.95 REMARK 500 LYS A 327 -11.49 -153.48 REMARK 500 THR A 353 0.68 -67.65 REMARK 500 HIS A 364 -68.34 15.64 REMARK 500 SER B 282 31.08 -93.69 REMARK 500 HIS B 306 14.08 -144.27 REMARK 500 ASP B 311 -79.58 -124.25 REMARK 500 HIS B 326 -140.99 -134.49 REMARK 500 LYS B 327 -12.41 -155.19 REMARK 500 HIS B 364 -70.90 15.83 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 MET A 363 HIS A 364 130.17 REMARK 500 MET B 363 HIS B 364 129.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2AYE RELATED DB: PDB REMARK 900 RELATED ID: 2AYG RELATED DB: PDB DBREF 2AYB A 281 366 UNP Q84294 VE2_HPV6A 282 368 DBREF 2AYB B 281 366 UNP Q84294 VE2_HPV6A 282 368 DBREF 2AYB C 1 16 PDB 2AYB 2AYB 1 16 DBREF 2AYB D 1 16 PDB 2AYB 2AYB 1 16 SEQADV 2AYB MET A 361 UNP Q84294 LEU 365 VARIANT SEQADV 2AYB MET B 361 UNP Q84294 LEU 365 VARIANT SEQRES 1 C 16 DC DA DA DC DC DG DA DA DT DT DC DG DG SEQRES 2 C 16 DT DT DG SEQRES 1 D 16 DC DA DA DC DC DG DA DA DT DT DC DG DG SEQRES 2 D 16 DT DT DG SEQRES 1 A 87 SER SER ALA THR PRO ILE VAL GLN PHE GLN GLY GLU SER SEQRES 2 A 87 ASN CYS LEU LYS CYS PHE ARG TYR ARG LEU ASN ASP LYS SEQRES 3 A 87 HIS ARG HIS LEU PHE ASP LEU ILE SER SER THR TRP HIS SEQRES 4 A 87 TRP ALA SER PRO LYS ALA PRO HIS LYS HIS ALA ILE VAL SEQRES 5 A 87 THR VAL THR TYR HIS SER GLU GLU GLN ARG GLN GLN PHE SEQRES 6 A 87 LEU ASN VAL VAL LYS ILE PRO PRO THR ILE ARG HIS LYS SEQRES 7 A 87 LEU GLY PHE MET SER MET HIS LEU LEU SEQRES 1 B 87 SER SER ALA THR PRO ILE VAL GLN PHE GLN GLY GLU SER SEQRES 2 B 87 ASN CYS LEU LYS CYS PHE ARG TYR ARG LEU ASN ASP LYS SEQRES 3 B 87 HIS ARG HIS LEU PHE ASP LEU ILE SER SER THR TRP HIS SEQRES 4 B 87 TRP ALA SER PRO LYS ALA PRO HIS LYS HIS ALA ILE VAL SEQRES 5 B 87 THR VAL THR TYR HIS SER GLU GLU GLN ARG GLN GLN PHE SEQRES 6 B 87 LEU ASN VAL VAL LYS ILE PRO PRO THR ILE ARG HIS LYS SEQRES 7 B 87 LEU GLY PHE MET SER MET HIS LEU LEU FORMUL 5 HOH *12(H2 O) HELIX 1 1 GLU A 292 HIS A 306 1 16 HELIX 2 2 ARG A 307 PHE A 310 5 4 HELIX 3 3 SER A 337 VAL A 348 1 12 HELIX 4 4 HIS A 364 LEU A 366 5 3 HELIX 5 5 GLU B 292 HIS B 306 1 16 HELIX 6 6 ARG B 307 PHE B 310 5 4 HELIX 7 7 SER B 337 VAL B 348 1 12 HELIX 8 8 HIS B 364 LEU B 366 5 3 SHEET 1 A 3 ALA A 329 THR A 334 0 SHEET 2 A 3 ALA A 283 GLY A 291 -1 N VAL A 287 O VAL A 333 SHEET 3 A 3 ARG A 355 SER A 362 -1 O MET A 361 N THR A 284 SHEET 1 B 3 ALA B 329 THR B 334 0 SHEET 2 B 3 ALA B 283 GLY B 291 -1 N PHE B 289 O VAL B 331 SHEET 3 B 3 ARG B 355 SER B 362 -1 O MET B 361 N THR B 284 CRYST1 75.247 75.247 97.426 90.00 90.00 120.00 P 61 12 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 0.013290 0.007670 0.000000 0.00000 SCALE2 0.000000 0.015340 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010260 0.00000