HEADER IMMUNE SYSTEM/DNA 30-JUL-12 3VW3 TITLE ANTIBODY 64M-5 FAB IN COMPLEX WITH A DOUBLE-STRANDED DNA (6-4) TITLE 2 PHOTOPRODUCT COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANTI-(6-4) PHOTOPRODUCT ANTIBODY 64M-5 FAB (LIGHT CHAIN); COMPND 3 CHAIN: L; COMPND 4 MOL_ID: 2; COMPND 5 MOLECULE: ANTI-(6-4) PHOTOPRODUCT ANTIBODY 64M-5 FAB (HEAVY CHAIN); COMPND 6 CHAIN: H; COMPND 7 MOL_ID: 3; COMPND 8 MOLECULE: DNA (5'-D(*GP*CP*GP*AP*GP*TP*GP*AP*(64T)P*(5PY) COMPND 9 P*AP*TP*GP*GP*AP*CP*GP*G)-3'); COMPND 10 CHAIN: A; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 4; COMPND 13 MOLECULE: DNA (5'- COMPND 14 D(*CP*CP*CP*GP*TP*CP*CP*AP*TP*AP*AP*TP*CP*AP*CP*TP*CP*G)-3'); COMPND 15 CHAIN: B; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_TAXID: 10090; SOURCE 4 STRAIN: BALB/C; SOURCE 5 OTHER_DETAILS: HYBRIDOMA; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 8 ORGANISM_TAXID: 10090; SOURCE 9 STRAIN: BALB/C; SOURCE 10 OTHER_DETAILS: HYBRIDOMA; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: DNA WITH (6-4) PHOTOPRODUCT; SOURCE 14 MOL_ID: 4; SOURCE 15 SYNTHETIC: YES; SOURCE 16 OTHER_DETAILS: SYNTHETIC DNA KEYWDS PROTEIN-DNA COMPLEX, DNA (6-4) PHOTOPRODUCT, IMMUNOGLOBULIN, IMMUNE KEYWDS 2 SYSTEM-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.YOKOYAMA,R.MIZUTANI,Y.SATOW REVDAT 4 06-NOV-24 3VW3 1 REMARK REVDAT 3 08-NOV-23 3VW3 1 REMARK LINK REVDAT 2 30-APR-14 3VW3 1 JRNL REVDAT 1 27-MAR-13 3VW3 0 JRNL AUTH H.YOKOYAMA,R.MIZUTANI,Y.SATOW JRNL TITL STRUCTURE OF A DOUBLE-STRANDED DNA (6-4) PHOTOPRODUCT IN JRNL TITL 2 COMPLEX WITH THE 64M-5 ANTIBODY FAB JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 69 504 2013 JRNL REFN ISSN 0907-4449 JRNL PMID 23519658 JRNL DOI 10.1107/S0907444912050007 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH H.YOKOYAMA,R.MIZUTANI,Y.SATOW,K.SATO,Y.KOMATSU,E.OHTSUKA, REMARK 1 AUTH 2 O.NIKAIDO REMARK 1 TITL STRUCTURE OF THE DNA (6-4) PHOTOPRODUCT DTT(6-4)TT IN REMARK 1 TITL 2 COMPLEX WITH THE 64M-2 ANTIBODY FAB FRAGMENT IMPLIES REMARK 1 TITL 3 INCREASED ANTIBODY-BINDING AFFINITY BY THE FLANKING REMARK 1 TITL 4 NUCLEOTIDES REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 68 232 2012 REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 22349224 REMARK 1 DOI 10.1107/S0907444912000327 REMARK 1 REFERENCE 2 REMARK 1 AUTH H.YOKOYAMA,R.MIZUTANI,Y.SATOW,Y.KOMATSU,E.OHTSUKA,O.NIKAIDO REMARK 1 TITL CRYSTAL STRUCTURE OF THE 64M-2 ANTIBODY FAB FRAGMENT IN REMARK 1 TITL 2 COMPLEX WITH A DNA DT(6-4)T PHOTOPRODUCT FORMED BY REMARK 1 TITL 3 ULTRAVIOLET RADIATION REMARK 1 REF J.MOL.BIOL. V. 299 711 2000 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 10835279 REMARK 1 DOI 10.1006/JMBI.2000.3772 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.26 REMARK 3 DATA CUTOFF (SIGMA(F)) : 3.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 573129.690 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.6 REMARK 3 NUMBER OF REFLECTIONS : 20294 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 SET) : 0.247 REMARK 3 FREE R VALUE : 0.290 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1993 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.66 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2916 REMARK 3 BIN R VALUE (WORKING SET) : 0.3240 REMARK 3 BIN FREE R VALUE : 0.4210 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 322 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.023 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3307 REMARK 3 NUCLEIC ACID ATOMS : 732 REMARK 3 HETEROGEN ATOMS : 7 REMARK 3 SOLVENT ATOMS : 144 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 49.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -7.77000 REMARK 3 B22 (A**2) : -7.77000 REMARK 3 B33 (A**2) : 15.53000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.35 REMARK 3 ESD FROM SIGMAA (A) : 0.26 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.44 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.44 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.120 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 4.860 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 7.010 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 7.020 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 9.400 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.30 REMARK 3 BSOL : 48.13 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : T64B.PARAM REMARK 3 PARAMETER FILE 4 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 5 : NCO_XPLOR_PAR.TXT REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : T64B.TOP REMARK 3 TOPOLOGY FILE 4 : WATER.TOP REMARK 3 TOPOLOGY FILE 5 : NCO_XPLOR_TOP.TXT REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 3VW3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-AUG-12. REMARK 100 THE DEPOSITION ID IS D_1000095572. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAR-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8000 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20541 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 200 DATA REDUNDANCY : 10.50 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 60.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.24000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 16.00 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1KEG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12% PEG 3350, 0.1M MAGNESIUM ACETATE, REMARK 280 10MM COBALT HEXAMINE CHLORIDE, 0.1M TRIS-HCL, PH 8.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 121.82900 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 34.21500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 34.21500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 182.74350 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 34.21500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 34.21500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 60.91450 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 34.21500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 34.21500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 182.74350 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 34.21500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 34.21500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 60.91450 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 121.82900 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: 8000 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: L, H, 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 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 ASP L 1 REMARK 465 GLU L 213 REMARK 465 ASN H 135 REMARK 465 VAL H 193 REMARK 465 PRO H 194 REMARK 465 SER H 195 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LEU L 3 CG CD1 CD2 REMARK 480 ARG L 24 CG CD NE CZ NH1 NH2 REMARK 480 SER L 63 OG REMARK 480 ILE L 106 CG1 CG2 CD1 REMARK 480 LEU L 125 CG CD1 CD2 REMARK 480 THR L 126 OG1 CG2 REMARK 480 SER L 127 OG REMARK 480 GLN L 156 CG CD OE1 NE2 REMARK 480 ASN L 157 CG OD1 ND2 REMARK 480 LEU L 181 CG CD1 CD2 REMARK 480 LYS L 183 CG CD CE NZ REMARK 480 THR L 197 OG1 CG2 REMARK 480 ASN L 212 CG OD1 ND2 REMARK 480 SER H 113 OG REMARK 480 VAL H 144 CG1 CG2 REMARK 480 SER H 167 OG REMARK 480 THR H 199 OG1 CG2 REMARK 480 SER H 203 OG REMARK 480 GLU H 204 CG CD OE1 OE2 REMARK 480 THR H 205 OG1 CG2 REMARK 480 THR H 207 OG1 CG2 REMARK 480 ASN H 209 CG OD1 ND2 REMARK 480 SER H 215 OG REMARK 480 SER H 216 OG REMARK 480 THR H 217 OG1 CG2 REMARK 480 ASP H 220 CG OD1 OD2 REMARK 480 LYS H 222 CG CD CE NZ REMARK 480 ILE H 223 CG1 CG2 CD1 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 15 O4' - C1' - N1 ANGL. DEV. = 2.3 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 L 27E -2.24 -58.73 REMARK 500 VAL L 51 -53.08 71.45 REMARK 500 ARG L 61 2.97 -66.51 REMARK 500 HIS L 93 -118.97 62.81 REMARK 500 PRO L 113 108.57 -57.96 REMARK 500 SER L 116 112.62 -160.37 REMARK 500 ASN L 138 86.80 45.18 REMARK 500 ASP L 151 44.43 70.99 REMARK 500 ASN L 190 -38.25 -135.95 REMARK 500 PRO L 204 175.16 -57.00 REMARK 500 ARG L 211 23.71 -51.99 REMARK 500 THR H 9 153.14 -37.74 REMARK 500 ASN H 54 13.89 -142.37 REMARK 500 SER H 74 -16.88 -49.45 REMARK 500 ALA H 88 -179.08 173.33 REMARK 500 SER H 100 141.56 178.84 REMARK 500 ALA H 100J -172.16 -179.98 REMARK 500 SER H 128 71.49 59.35 REMARK 500 ALA H 129 -2.84 -146.08 REMARK 500 PRO H 149 -169.22 -103.10 REMARK 500 GLN H 179 76.52 -114.96 REMARK 500 SER H 180 87.33 68.35 REMARK 500 ASP H 183 -14.96 60.27 REMARK 500 PRO H 227 174.19 -44.45 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 NCO H 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1KEG RELATED DB: PDB REMARK 900 THE RELATED ANTIBODY FAB IN COMPLEX WITH DNA (6-4) PHOTOPRODUCT REMARK 900 RELATED ID: 1EHL RELATED DB: PDB REMARK 900 THE RELATED ANTIBODY FAB IN COMPLEX WITH DNA (6-4) PHOTOPRODUCT DBREF 3VW3 L 1 213 PDB 3VW3 3VW3 1 213 DBREF 3VW3 H 1 228 PDB 3VW3 3VW3 1 228 DBREF 3VW3 A 1 18 PDB 3VW3 3VW3 1 18 DBREF 3VW3 B 1 18 PDB 3VW3 3VW3 1 18 SEQRES 1 L 217 ASP VAL LEU MET THR GLN THR PRO LEU SER LEU PRO VAL SEQRES 2 L 217 SER LEU GLY ASP GLN ALA SER ILE SER CYS ARG SER SER SEQRES 3 L 217 GLN ASN ILE VAL HIS SER ASN GLY TYR THR TYR LEU GLU SEQRES 4 L 217 TRP TYR LEU GLN LYS PRO GLY GLN SER PRO LYS LEU LEU SEQRES 5 L 217 ILE TYR THR VAL SER ASN ARG PHE SER GLY VAL PRO ASP SEQRES 6 L 217 ARG PHE SER GLY SER GLY SER GLY THR ASP PHE THR LEU SEQRES 7 L 217 LYS ILE SER ARG VAL GLU ALA GLU ASP LEU GLY VAL TYR SEQRES 8 L 217 TYR CYS PHE ARG GLY SER HIS VAL PRO THR PHE GLY GLY SEQRES 9 L 217 GLY THR LYS LEU GLU ILE LYS ARG ALA ASP ALA ALA PRO SEQRES 10 L 217 THR VAL SER ILE PHE PRO PRO SER SER GLU GLN LEU THR SEQRES 11 L 217 SER GLY GLY ALA SER VAL VAL CYS PHE LEU ASN ASN PHE SEQRES 12 L 217 TYR PRO LYS ASP ILE ASN VAL LYS TRP LYS ILE ASP GLY SEQRES 13 L 217 SER GLU ARG GLN ASN GLY VAL LEU ASN SER TRP THR ASP SEQRES 14 L 217 GLN ASP SER LYS ASP SER THR TYR SER MET SER SER THR SEQRES 15 L 217 LEU THR LEU THR LYS ASP GLU TYR GLU ARG HIS ASN SER SEQRES 16 L 217 TYR THR CYS GLU ALA THR HIS LYS THR SER THR SER PRO SEQRES 17 L 217 ILE VAL LYS SER PHE ASN ARG ASN GLU SEQRES 1 H 220 GLU VAL GLN LEU GLN GLN SER GLY THR VAL LEU ALA ARG SEQRES 2 H 220 PRO GLY ALA SER VAL LYS MET SER CYS LYS ALA SER GLY SEQRES 3 H 220 TYR THR PHE THR ASN TYR TRP MET HIS TRP ILE LYS GLN SEQRES 4 H 220 ARG PRO GLY GLN GLY LEU GLU TRP ILE GLY THR ILE TYR SEQRES 5 H 220 PRO GLY ASN SER ASP THR THR TYR SER GLN LYS PHE LYS SEQRES 6 H 220 GLY LYS ALA LYS LEU THR ALA VAL THR SER THR SER THR SEQRES 7 H 220 ALA TYR MET GLU LEU SER SER LEU THR ASN GLU ASP SER SEQRES 8 H 220 ALA VAL TYR TYR CYS SER ARG ARG ASN TYR GLY SER SER SEQRES 9 H 220 TYR ALA MET ASP TYR TRP GLY GLN GLY THR SER VAL THR SEQRES 10 H 220 VAL SER SER ALA LYS THR THR PRO PRO SER VAL TYR PRO SEQRES 11 H 220 LEU ALA PRO GLY SER ALA ALA GLN THR ASN SER MET VAL SEQRES 12 H 220 THR LEU GLY CYS LEU VAL LYS GLY TYR PHE PRO GLU PRO SEQRES 13 H 220 VAL THR VAL THR TRP ASN SER GLY SER LEU SER SER GLY SEQRES 14 H 220 VAL HIS THR PHE PRO ALA VAL LEU GLN SER ASP LEU TYR SEQRES 15 H 220 THR LEU SER SER SER VAL THR VAL PRO SER SER THR TRP SEQRES 16 H 220 PRO SER GLU THR VAL THR CYS ASN VAL ALA HIS PRO ALA SEQRES 17 H 220 SER SER THR LYS VAL ASP LYS LYS ILE VAL PRO ARG SEQRES 1 A 18 DG DC DG DA DG DT DG DA 64T 5PY DA DT DG SEQRES 2 A 18 DG DA DC DG DG SEQRES 1 B 18 DC DC DC DG DT DC DC DA DT DA DA DT DC SEQRES 2 B 18 DA DC DT DC DG MODRES 3VW3 64T A 9 DT 5-HYDROXY-THYMIDINE-5'-MONOPHOSPHATE MODRES 3VW3 5PY A 10 DT HET 64T A 9 21 HET 5PY A 10 19 HET NCO H 301 7 HETNAM 64T 5-HYDROXY-THYMIDINE-5'-MONOPHOSPHATE HETNAM 5PY 1-(2'-DEOXY-5'-O-PHOSPHONO-BETA-D-ERYTHRO- HETNAM 2 5PY PENTOFURANOSYL)-5-METHYLPYRIMIDIN-2(1H)-ONE HETNAM NCO COBALT HEXAMMINE(III) FORMUL 3 64T C10 H17 N2 O9 P FORMUL 3 5PY C10 H15 N2 O7 P FORMUL 5 NCO CO H18 N6 3+ FORMUL 6 HOH *144(H2 O) HELIX 1 1 GLU L 79 LEU L 83 5 5 HELIX 2 2 SER L 121 SER L 127 1 7 HELIX 3 3 LYS L 183 HIS L 189 1 7 HELIX 4 4 THR H 28 TYR H 32 5 5 HELIX 5 5 GLN H 61 LYS H 64 5 4 HELIX 6 6 THR H 73 THR H 75 5 3 HELIX 7 7 THR H 83 SER H 87 5 5 SHEET 1 A 4 MET L 4 THR L 7 0 SHEET 2 A 4 ALA L 19 SER L 25 -1 O SER L 22 N THR L 7 SHEET 3 A 4 ASP L 70 ILE L 75 -1 O PHE L 71 N CYS L 23 SHEET 4 A 4 PHE L 62 SER L 67 -1 N SER L 65 O THR L 72 SHEET 1 B 6 SER L 10 VAL L 13 0 SHEET 2 B 6 THR L 102 ILE L 106 1 O LYS L 103 N LEU L 11 SHEET 3 B 6 GLY L 84 ARG L 90 -1 N GLY L 84 O LEU L 104 SHEET 4 B 6 LEU L 33 GLN L 38 -1 N GLU L 34 O PHE L 89 SHEET 5 B 6 LYS L 45 TYR L 49 -1 O LYS L 45 N LEU L 37 SHEET 6 B 6 ASN L 53 ARG L 54 -1 O ASN L 53 N TYR L 49 SHEET 1 C 4 SER L 10 VAL L 13 0 SHEET 2 C 4 THR L 102 ILE L 106 1 O LYS L 103 N LEU L 11 SHEET 3 C 4 GLY L 84 ARG L 90 -1 N GLY L 84 O LEU L 104 SHEET 4 C 4 THR L 97 PHE L 98 -1 O THR L 97 N ARG L 90 SHEET 1 D 4 THR L 114 PHE L 118 0 SHEET 2 D 4 GLY L 129 PHE L 139 -1 O VAL L 133 N PHE L 118 SHEET 3 D 4 TYR L 173 THR L 182 -1 O LEU L 179 N VAL L 132 SHEET 4 D 4 VAL L 159 THR L 164 -1 N LEU L 160 O THR L 178 SHEET 1 E 4 SER L 153 ARG L 155 0 SHEET 2 E 4 ILE L 144 ILE L 150 -1 N TRP L 148 O ARG L 155 SHEET 3 E 4 SER L 191 HIS L 198 -1 O GLU L 195 N LYS L 147 SHEET 4 E 4 ILE L 205 ASN L 210 -1 O LYS L 207 N CYS L 194 SHEET 1 F 4 GLN H 3 GLN H 6 0 SHEET 2 F 4 VAL H 18 SER H 25 -1 O LYS H 23 N GLN H 5 SHEET 3 F 4 THR H 77 LEU H 82 -1 O ALA H 78 N CYS H 22 SHEET 4 F 4 ALA H 67 VAL H 72 -1 N THR H 70 O TYR H 79 SHEET 1 G 6 VAL H 10 ALA H 12 0 SHEET 2 G 6 THR H 107 VAL H 111 1 O THR H 110 N ALA H 12 SHEET 3 G 6 ALA H 88 ASN H 96 -1 N ALA H 88 O VAL H 109 SHEET 4 G 6 MET H 34 GLN H 39 -1 N ILE H 37 O TYR H 91 SHEET 5 G 6 GLU H 46 ILE H 51 -1 O ILE H 51 N MET H 34 SHEET 6 G 6 THR H 57 TYR H 59 -1 O THR H 58 N THR H 50 SHEET 1 H 4 VAL H 10 ALA H 12 0 SHEET 2 H 4 THR H 107 VAL H 111 1 O THR H 110 N ALA H 12 SHEET 3 H 4 ALA H 88 ASN H 96 -1 N ALA H 88 O VAL H 109 SHEET 4 H 4 ALA H 100J TRP H 103 -1 O ALA H 100J N ASN H 96 SHEET 1 I 4 TYR H 122 LEU H 124 0 SHEET 2 I 4 LEU H 140 TYR H 147 -1 O GLY H 141 N LEU H 124 SHEET 3 I 4 TYR H 185 VAL H 191 -1 O LEU H 187 N VAL H 144 SHEET 4 I 4 VAL H 171 THR H 173 -1 N HIS H 172 O SER H 190 SHEET 1 J 4 TYR H 122 LEU H 124 0 SHEET 2 J 4 LEU H 140 TYR H 147 -1 O GLY H 141 N LEU H 124 SHEET 3 J 4 TYR H 185 VAL H 191 -1 O LEU H 187 N VAL H 144 SHEET 4 J 4 VAL H 177 LEU H 178 -1 N VAL H 177 O THR H 186 SHEET 1 K 3 THR H 153 TRP H 157 0 SHEET 2 K 3 THR H 207 HIS H 212 -1 O ALA H 211 N THR H 153 SHEET 3 K 3 THR H 217 LYS H 222 -1 O LYS H 221 N CYS H 208 SSBOND 1 CYS L 23 CYS L 88 1555 1555 2.04 SSBOND 2 CYS L 134 CYS L 194 1555 1555 2.03 SSBOND 3 CYS H 22 CYS H 92 1555 1555 2.04 SSBOND 4 CYS H 142 CYS H 208 1555 1555 2.03 LINK O3' DA A 8 P 64T A 9 1555 1555 1.60 LINK O3' 64T A 9 P 5PY A 10 1555 1555 1.60 LINK C6 64T A 9 C4 5PY A 10 1555 1555 1.53 LINK O3' 5PY A 10 P DA A 11 1555 1555 1.61 CISPEP 1 THR L 7 PRO L 8 0 -0.40 CISPEP 2 TYR L 140 PRO L 141 0 0.09 CISPEP 3 PHE H 148 PRO H 149 0 -0.35 CISPEP 4 GLU H 150 PRO H 151 0 -0.31 CISPEP 5 TRP H 200 PRO H 202 0 -0.67 SITE 1 AC1 4 DA A 11 ASP H 56 THR H 57 THR H 58 CRYST1 68.430 68.430 243.658 90.00 90.00 90.00 P 43 21 2 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 0.014613 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014613 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004104 0.00000