HEADER DNA BINDING PROTEIN/DNA 04-NOV-18 6IPU TITLE HUMAN NUCLEOSOME CORE PARTICLE CONTAINING 145 BP OF DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE H3.1; COMPND 3 CHAIN: A, E; COMPND 4 SYNONYM: HISTONE H3/A,HISTONE H3/B,HISTONE H3/C,HISTONE H3/D,HISTONE COMPND 5 H3/F,HISTONE H3/H,HISTONE H3/I,HISTONE H3/J,HISTONE H3/K,HISTONE COMPND 6 H3/L; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: HISTONE H4; COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: HISTONE H2A TYPE 1-B/E; COMPND 14 CHAIN: C, G; COMPND 15 SYNONYM: HISTONE H2A.2,HISTONE H2A/A,HISTONE H2A/M; COMPND 16 ENGINEERED: YES; COMPND 17 MOL_ID: 4; COMPND 18 MOLECULE: HISTONE H2B TYPE 1-J; COMPND 19 CHAIN: D, H; COMPND 20 SYNONYM: HISTONE H2B.1,HISTONE H2B.R,H2B/R; COMPND 21 ENGINEERED: YES; COMPND 22 MOL_ID: 5; COMPND 23 MOLECULE: HISTONE H4; COMPND 24 CHAIN: F; COMPND 25 ENGINEERED: YES; COMPND 26 MOL_ID: 6; COMPND 27 MOLECULE: DNA (145-MER); COMPND 28 CHAIN: I; COMPND 29 ENGINEERED: YES; COMPND 30 MOL_ID: 7; COMPND 31 MOLECULE: DNA (145-MER); COMPND 32 CHAIN: J; COMPND 33 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: HIST1H3A, H3FA, HIST1H3B, H3FL, HIST1H3C, H3FC, HIST1H3D, SOURCE 6 H3FB, HIST1H3E, H3FD, HIST1H3F, H3FI, HIST1H3G, H3FH, HIST1H3H, SOURCE 7 H3FK, HIST1H3I, H3FF, HIST1H3J, H3FJ; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 GENE: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, SOURCE 15 H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, SOURCE 16 H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, SOURCE 17 H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, SOURCE 18 H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4; SOURCE 19 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 20 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 21 MOL_ID: 3; SOURCE 22 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 23 ORGANISM_COMMON: HUMAN; SOURCE 24 ORGANISM_TAXID: 9606; SOURCE 25 GENE: HIST1H2AB, H2AFM, HIST1H2AE, H2AFA; SOURCE 26 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 27 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 28 MOL_ID: 4; SOURCE 29 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 30 ORGANISM_COMMON: HUMAN; SOURCE 31 ORGANISM_TAXID: 9606; SOURCE 32 GENE: HIST1H2BJ, H2BFR; SOURCE 33 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 34 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 35 MOL_ID: 5; SOURCE 36 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 37 ORGANISM_COMMON: HUMAN; SOURCE 38 ORGANISM_TAXID: 9606; SOURCE 39 GENE: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, SOURCE 40 H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, SOURCE 41 H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, SOURCE 42 H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, SOURCE 43 H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4; SOURCE 44 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 45 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 46 MOL_ID: 6; SOURCE 47 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 48 ORGANISM_COMMON: HUMAN; SOURCE 49 ORGANISM_TAXID: 9606; SOURCE 50 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 51 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 52 MOL_ID: 7; SOURCE 53 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 54 ORGANISM_COMMON: HUMAN; SOURCE 55 ORGANISM_TAXID: 9606; SOURCE 56 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 57 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NUCLEOSOME, DNA BINDING PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR L.DEFALCO,C.A.DAVEY REVDAT 2 22-NOV-23 6IPU 1 LINK REVDAT 1 15-JAN-20 6IPU 0 JRNL AUTH D.SHARMA,L.DE FALCO,S.PADAVATTAN,C.RAO,S.GEIFMAN-SHOCHAT, JRNL AUTH 2 C.F.LIU,C.A.DAVEY JRNL TITL PARP1 EXHIBITS ENHANCED ASSOCIATION AND CATALYTIC EFFICIENCY JRNL TITL 2 WITH GAMMA H2A.X-NUCLEOSOME. JRNL REF NAT COMMUN V. 10 5751 2019 JRNL REFN ESSN 2041-1723 JRNL PMID 31848352 JRNL DOI 10.1038/S41467-019-13641-0 REMARK 2 REMARK 2 RESOLUTION. 1.99 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 94.16 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 145312 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) : 0.237 REMARK 3 R VALUE (WORKING SET) : 0.236 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3035 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) : 1.99 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.04 REMARK 3 REFLECTION IN BIN (WORKING SET) : 10328 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.71 REMARK 3 BIN R VALUE (WORKING SET) : 0.3800 REMARK 3 BIN FREE R VALUE SET COUNT : 210 REMARK 3 BIN FREE R VALUE : 0.3890 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6117 REMARK 3 NUCLEIC ACID ATOMS : 5939 REMARK 3 HETEROGEN ATOMS : 7 REMARK 3 SOLVENT ATOMS : 114 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 74.55 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.76000 REMARK 3 B22 (A**2) : -3.11000 REMARK 3 B33 (A**2) : 1.35000 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): 0.168 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.152 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.166 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.418 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.939 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 12859 ; 0.008 ; 0.015 REMARK 3 BOND LENGTHS OTHERS (A): 9663 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 18602 ; 1.474 ; 1.538 REMARK 3 BOND ANGLES OTHERS (DEGREES): 22363 ; 1.426 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 761 ; 5.191 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 273 ;33.301 ;21.172 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1191 ;16.771 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 88 ;21.693 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1823 ; 0.200 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 10312 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 2861 ; 0.002 ; 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): 3068 ; 3.042 ; 4.959 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3067 ; 3.041 ; 4.956 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3821 ; 4.560 ; 7.399 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3822 ; 4.560 ; 7.403 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 9791 ; 4.022 ; 9.004 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 9790 ; 4.022 ; 9.004 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 14782 ; 6.308 ;13.534 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 16489 ;10.006 ;81.014 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 16479 ;10.008 ;81.034 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 6IPU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-NOV-18. REMARK 100 THE DEPOSITION ID IS D_1300009685. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-SEP-17 REMARK 200 TEMPERATURE (KELVIN) : 98.15 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 148453 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.990 REMARK 200 RESOLUTION RANGE LOW (A) : 94.160 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 12.20 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.99 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9 REMARK 200 DATA REDUNDANCY IN SHELL : 11.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.300 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: 2NZD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MANGANESE CHLORIDE, POTASSIUM REMARK 280 CHLORIDE, POTASSIUM CACODYLATE, PH 6.0, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 53.78000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 91.74000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 54.85500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 91.74000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 53.78000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 54.85500 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: DECAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DECAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 58440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 72620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -445.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H, I, J 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 O GLN A 125 NH1 ARG A 134 1.87 REMARK 500 O ARG E 134 O HOH E 201 2.07 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 ARG C 81 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ARG C 81 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG E 69 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG E 128 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG G 88 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 ARG G 88 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 DT I -50 C1' - O4' - C4' ANGL. DEV. = -9.0 DEGREES REMARK 500 DT I -50 N1 - C1' - C2' ANGL. DEV. = 14.6 DEGREES REMARK 500 DT I -50 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DA I -49 C3' - C2' - C1' ANGL. DEV. = -5.7 DEGREES REMARK 500 DA I -49 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DG I -40 C1' - O4' - C4' ANGL. DEV. = -7.2 DEGREES REMARK 500 DG I -40 N9 - C1' - C2' ANGL. DEV. = 11.2 DEGREES REMARK 500 DG I -40 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DA I -19 C3' - C2' - C1' ANGL. DEV. = -5.2 DEGREES REMARK 500 DA J 28 C3' - C2' - C1' ANGL. DEV. = -5.3 DEGREES REMARK 500 DG J 29 C3' - C2' - C1' ANGL. DEV. = -5.2 DEGREES REMARK 500 DG J 60 N9 - C1' - C2' ANGL. DEV. = 10.0 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 ASN C 110 114.63 -169.41 REMARK 500 LYS C 118 -149.92 68.15 REMARK 500 ARG E 134 34.99 -154.86 REMARK 500 ARG F 17 -55.90 -124.11 REMARK 500 HIS F 18 123.90 66.89 REMARK 500 LYS F 77 33.40 71.03 REMARK 500 ASN G 110 113.69 -167.26 REMARK 500 LYS G 118 -70.60 -109.71 REMARK 500 ALA H 121 89.40 -170.88 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 DT I -50 0.07 SIDE CHAIN 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 MN D 201 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 VAL D 45 O REMARK 620 2 HOH D 301 O 96.7 REMARK 620 3 HOH D 308 O 82.5 177.6 REMARK 620 4 ASP E 77 OD1 26.9 112.5 65.9 REMARK 620 5 HOH E 219 O 168.2 95.1 85.8 145.3 REMARK 620 6 HOH F 205 O 89.4 87.5 90.2 69.4 92.1 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 CL C 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN D 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL G 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN I 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN I 102 DBREF 6IPU A 38 135 UNP P68431 H31_HUMAN 39 136 DBREF 6IPU B 21 102 UNP P62805 H4_HUMAN 22 103 DBREF 6IPU C 13 119 UNP P04908 H2A1B_HUMAN 14 120 DBREF 6IPU D 28 122 UNP P06899 H2B1J_HUMAN 32 126 DBREF 6IPU E 38 135 UNP P68431 H31_HUMAN 39 136 DBREF 6IPU F 16 102 UNP P62805 H4_HUMAN 17 103 DBREF 6IPU G 13 119 UNP P04908 H2A1B_HUMAN 14 120 DBREF 6IPU H 28 122 UNP P06899 H2B1J_HUMAN 32 126 DBREF 6IPU I -72 72 PDB 6IPU 6IPU -72 72 DBREF 6IPU J -72 72 PDB 6IPU 6IPU -72 72 SEQRES 1 A 98 PRO HIS ARG TYR ARG PRO GLY THR VAL ALA LEU ARG GLU SEQRES 2 A 98 ILE ARG ARG TYR GLN LYS SER THR GLU LEU LEU ILE ARG SEQRES 3 A 98 LYS LEU PRO PHE GLN ARG LEU VAL ARG GLU ILE ALA GLN SEQRES 4 A 98 ASP PHE LYS THR ASP LEU ARG PHE GLN SER SER ALA VAL SEQRES 5 A 98 MET ALA LEU GLN GLU ALA CYS GLU ALA TYR LEU VAL GLY SEQRES 6 A 98 LEU PHE GLU ASP THR ASN LEU CYS ALA ILE HIS ALA LYS SEQRES 7 A 98 ARG VAL THR ILE MET PRO LYS ASP ILE GLN LEU ALA ARG SEQRES 8 A 98 ARG ILE ARG GLY GLU ARG ALA SEQRES 1 B 82 VAL LEU ARG ASP ASN ILE GLN GLY ILE THR LYS PRO ALA SEQRES 2 B 82 ILE ARG ARG LEU ALA ARG ARG GLY GLY VAL LYS ARG ILE SEQRES 3 B 82 SER GLY LEU ILE TYR GLU GLU THR ARG GLY VAL LEU LYS SEQRES 4 B 82 VAL PHE LEU GLU ASN VAL ILE ARG ASP ALA VAL THR TYR SEQRES 5 B 82 THR GLU HIS ALA LYS ARG LYS THR VAL THR ALA MET ASP SEQRES 6 B 82 VAL VAL TYR ALA LEU LYS ARG GLN GLY ARG THR LEU TYR SEQRES 7 B 82 GLY PHE GLY GLY SEQRES 1 C 107 LYS ALA LYS THR ARG SER SER ARG ALA GLY LEU GLN PHE SEQRES 2 C 107 PRO VAL GLY ARG VAL HIS ARG LEU LEU ARG LYS GLY ASN SEQRES 3 C 107 TYR SER GLU ARG VAL GLY ALA GLY ALA PRO VAL TYR LEU SEQRES 4 C 107 ALA ALA VAL LEU GLU TYR LEU THR ALA GLU ILE LEU GLU SEQRES 5 C 107 LEU ALA GLY ASN ALA ALA ARG ASP ASN LYS LYS THR ARG SEQRES 6 C 107 ILE ILE PRO ARG HIS LEU GLN LEU ALA ILE ARG ASN ASP SEQRES 7 C 107 GLU GLU LEU ASN LYS LEU LEU GLY ARG VAL THR ILE ALA SEQRES 8 C 107 GLN GLY GLY VAL LEU PRO ASN ILE GLN ALA VAL LEU LEU SEQRES 9 C 107 PRO LYS LYS SEQRES 1 D 95 ARG SER ARG LYS GLU SER TYR SER ILE TYR VAL TYR LYS SEQRES 2 D 95 VAL LEU LYS GLN VAL HIS PRO ASP THR GLY ILE SER SER SEQRES 3 D 95 LYS ALA MET GLY ILE MET ASN SER PHE VAL ASN ASP ILE SEQRES 4 D 95 PHE GLU ARG ILE ALA GLY GLU ALA SER ARG LEU ALA HIS SEQRES 5 D 95 TYR ASN LYS ARG SER THR ILE THR SER ARG GLU ILE GLN SEQRES 6 D 95 THR ALA VAL ARG LEU LEU LEU PRO GLY GLU LEU ALA LYS SEQRES 7 D 95 HIS ALA VAL SER GLU GLY THR LYS ALA VAL THR LYS TYR SEQRES 8 D 95 THR SER ALA LYS SEQRES 1 E 98 PRO HIS ARG TYR ARG PRO GLY THR VAL ALA LEU ARG GLU SEQRES 2 E 98 ILE ARG ARG TYR GLN LYS SER THR GLU LEU LEU ILE ARG SEQRES 3 E 98 LYS LEU PRO PHE GLN ARG LEU VAL ARG GLU ILE ALA GLN SEQRES 4 E 98 ASP PHE LYS THR ASP LEU ARG PHE GLN SER SER ALA VAL SEQRES 5 E 98 MET ALA LEU GLN GLU ALA CYS GLU ALA TYR LEU VAL GLY SEQRES 6 E 98 LEU PHE GLU ASP THR ASN LEU CYS ALA ILE HIS ALA LYS SEQRES 7 E 98 ARG VAL THR ILE MET PRO LYS ASP ILE GLN LEU ALA ARG SEQRES 8 E 98 ARG ILE ARG GLY GLU ARG ALA SEQRES 1 F 87 LYS ARG HIS ARG LYS VAL LEU ARG ASP ASN ILE GLN GLY SEQRES 2 F 87 ILE THR LYS PRO ALA ILE ARG ARG LEU ALA ARG ARG GLY SEQRES 3 F 87 GLY VAL LYS ARG ILE SER GLY LEU ILE TYR GLU GLU THR SEQRES 4 F 87 ARG GLY VAL LEU LYS VAL PHE LEU GLU ASN VAL ILE ARG SEQRES 5 F 87 ASP ALA VAL THR TYR THR GLU HIS ALA LYS ARG LYS THR SEQRES 6 F 87 VAL THR ALA MET ASP VAL VAL TYR ALA LEU LYS ARG GLN SEQRES 7 F 87 GLY ARG THR LEU TYR GLY PHE GLY GLY SEQRES 1 G 107 LYS ALA LYS THR ARG SER SER ARG ALA GLY LEU GLN PHE SEQRES 2 G 107 PRO VAL GLY ARG VAL HIS ARG LEU LEU ARG LYS GLY ASN SEQRES 3 G 107 TYR SER GLU ARG VAL GLY ALA GLY ALA PRO VAL TYR LEU SEQRES 4 G 107 ALA ALA VAL LEU GLU TYR LEU THR ALA GLU ILE LEU GLU SEQRES 5 G 107 LEU ALA GLY ASN ALA ALA ARG ASP ASN LYS LYS THR ARG SEQRES 6 G 107 ILE ILE PRO ARG HIS LEU GLN LEU ALA ILE ARG ASN ASP SEQRES 7 G 107 GLU GLU LEU ASN LYS LEU LEU GLY ARG VAL THR ILE ALA SEQRES 8 G 107 GLN GLY GLY VAL LEU PRO ASN ILE GLN ALA VAL LEU LEU SEQRES 9 G 107 PRO LYS LYS SEQRES 1 H 95 ARG SER ARG LYS GLU SER TYR SER ILE TYR VAL TYR LYS SEQRES 2 H 95 VAL LEU LYS GLN VAL HIS PRO ASP THR GLY ILE SER SER SEQRES 3 H 95 LYS ALA MET GLY ILE MET ASN SER PHE VAL ASN ASP ILE SEQRES 4 H 95 PHE GLU ARG ILE ALA GLY GLU ALA SER ARG LEU ALA HIS SEQRES 5 H 95 TYR ASN LYS ARG SER THR ILE THR SER ARG GLU ILE GLN SEQRES 6 H 95 THR ALA VAL ARG LEU LEU LEU PRO GLY GLU LEU ALA LYS SEQRES 7 H 95 HIS ALA VAL SER GLU GLY THR LYS ALA VAL THR LYS TYR SEQRES 8 H 95 THR SER ALA LYS SEQRES 1 I 145 DA DT DC DA DA DT DA DT DC DC DA DC DC SEQRES 2 I 145 DT DG DC DA DG DA DT DA DC DT DA DC DC SEQRES 3 I 145 DA DA DA DA DG DT DG DT DA DT DT DT DG SEQRES 4 I 145 DG DA DA DA DC DT DG DC DT DC DC DA DT SEQRES 5 I 145 DC DA DA DA DA DG DG DC DA DT DG DT DT SEQRES 6 I 145 DC DA DG DC DT DG DA DA DT DC DA DG DC SEQRES 7 I 145 DT DG DA DA DC DA DT DG DC DC DT DT DT SEQRES 8 I 145 DT DG DA DT DG DG DA DG DC DA DG DT DT SEQRES 9 I 145 DT DC DC DA DA DA DT DA DC DA DC DT DT SEQRES 10 I 145 DT DT DG DG DT DA DG DT DA DT DC DT DG SEQRES 11 I 145 DC DA DG DG DT DG DG DA DT DA DT DT DG SEQRES 12 I 145 DA DT SEQRES 1 J 145 DA DT DC DA DA DT DA DT DC DC DA DC DC SEQRES 2 J 145 DT DG DC DA DG DA DT DA DC DT DA DC DC SEQRES 3 J 145 DA DA DA DA DG DT DG DT DA DT DT DT DG SEQRES 4 J 145 DG DA DA DA DC DT DG DC DT DC DC DA DT SEQRES 5 J 145 DC DA DA DA DA DG DG DC DA DT DG DT DT SEQRES 6 J 145 DC DA DG DC DT DG DA DT DT DC DA DG DC SEQRES 7 J 145 DT DG DA DA DC DA DT DG DC DC DT DT DT SEQRES 8 J 145 DT DG DA DT DG DG DA DG DC DA DG DT DT SEQRES 9 J 145 DT DC DC DA DA DA DT DA DC DA DC DT DT SEQRES 10 J 145 DT DT DG DG DT DA DG DT DA DT DC DT DG SEQRES 11 J 145 DC DA DG DG DT DG DG DA DT DA DT DT DG SEQRES 12 J 145 DA DT HET CL C 201 1 HET MN D 201 1 HET CL G 201 1 HET MN I 101 1 HET MN I 102 1 HET MN J 101 1 HET MN J 102 1 HETNAM CL CHLORIDE ION HETNAM MN MANGANESE (II) ION FORMUL 11 CL 2(CL 1-) FORMUL 12 MN 5(MN 2+) FORMUL 18 HOH *114(H2 O) HELIX 1 AA1 GLY A 44 SER A 57 1 14 HELIX 2 AA2 ARG A 63 ASP A 77 1 15 HELIX 3 AA3 GLN A 85 ALA A 114 1 30 HELIX 4 AA4 MET A 120 GLY A 132 1 13 HELIX 5 AA5 ASN B 25 ILE B 29 5 5 HELIX 6 AA6 THR B 30 GLY B 41 1 12 HELIX 7 AA7 LEU B 49 ALA B 76 1 28 HELIX 8 AA8 THR B 82 GLN B 93 1 12 HELIX 9 AA9 THR C 16 GLY C 22 1 7 HELIX 10 AB1 PRO C 26 GLY C 37 1 12 HELIX 11 AB2 GLY C 46 ASN C 73 1 28 HELIX 12 AB3 ILE C 79 ASP C 90 1 12 HELIX 13 AB4 ASP C 90 LEU C 97 1 8 HELIX 14 AB5 GLN C 112 LEU C 116 5 5 HELIX 15 AB6 TYR D 34 HIS D 46 1 13 HELIX 16 AB7 SER D 52 ASN D 81 1 30 HELIX 17 AB8 THR D 87 LEU D 99 1 13 HELIX 18 AB9 PRO D 100 ALA D 121 1 22 HELIX 19 AC1 GLY E 44 SER E 57 1 14 HELIX 20 AC2 ARG E 63 LYS E 79 1 17 HELIX 21 AC3 GLN E 85 ALA E 114 1 30 HELIX 22 AC4 MET E 120 ARG E 131 1 12 HELIX 23 AC5 ASP F 24 ILE F 29 5 6 HELIX 24 AC6 THR F 30 GLY F 41 1 12 HELIX 25 AC7 LEU F 49 ALA F 76 1 28 HELIX 26 AC8 THR F 82 GLN F 93 1 12 HELIX 27 AC9 THR G 16 GLY G 22 1 7 HELIX 28 AD1 PRO G 26 GLY G 37 1 12 HELIX 29 AD2 ALA G 45 ASN G 73 1 29 HELIX 30 AD3 ILE G 79 ASN G 89 1 11 HELIX 31 AD4 ASP G 90 LEU G 97 1 8 HELIX 32 AD5 GLN G 112 LEU G 116 5 5 HELIX 33 AD6 TYR H 34 HIS H 46 1 13 HELIX 34 AD7 SER H 52 ASN H 81 1 30 HELIX 35 AD8 THR H 87 LEU H 99 1 13 HELIX 36 AD9 PRO H 100 SER H 120 1 21 SHEET 1 AA1 2 ARG A 83 PHE A 84 0 SHEET 2 AA1 2 THR B 80 VAL B 81 1 O VAL B 81 N ARG A 83 SHEET 1 AA2 2 THR A 118 ILE A 119 0 SHEET 2 AA2 2 ARG B 45 ILE B 46 1 O ARG B 45 N ILE A 119 SHEET 1 AA3 2 THR B 96 TYR B 98 0 SHEET 2 AA3 2 VAL G 100 ILE G 102 1 O THR G 101 N TYR B 98 SHEET 1 AA4 2 ARG C 42 VAL C 43 0 SHEET 2 AA4 2 THR D 85 ILE D 86 1 O ILE D 86 N ARG C 42 SHEET 1 AA5 2 ARG C 77 ILE C 78 0 SHEET 2 AA5 2 GLY D 50 ILE D 51 1 O GLY D 50 N ILE C 78 SHEET 1 AA6 2 VAL C 100 ILE C 102 0 SHEET 2 AA6 2 THR F 96 TYR F 98 1 O TYR F 98 N THR C 101 SHEET 1 AA7 2 ARG E 83 PHE E 84 0 SHEET 2 AA7 2 THR F 80 VAL F 81 1 O VAL F 81 N ARG E 83 SHEET 1 AA8 2 THR E 118 ILE E 119 0 SHEET 2 AA8 2 ARG F 45 ILE F 46 1 O ARG F 45 N ILE E 119 SHEET 1 AA9 2 ARG G 42 VAL G 43 0 SHEET 2 AA9 2 THR H 85 ILE H 86 1 O ILE H 86 N ARG G 42 SHEET 1 AB1 2 ARG G 77 ILE G 78 0 SHEET 2 AB1 2 GLY H 50 ILE H 51 1 O GLY H 50 N ILE G 78 LINK O VAL D 45 MN MN D 201 1555 1555 2.14 LINK MN MN D 201 O HOH D 301 1555 1555 2.10 LINK MN MN D 201 O HOH D 308 1555 1555 2.11 LINK MN MN D 201 OD1 ASP E 77 3755 1555 2.18 LINK MN MN D 201 O HOH E 219 1555 3745 2.21 LINK MN MN D 201 O HOH F 205 1555 3745 2.04 SITE 1 AC1 4 GLY C 46 ALA C 47 THR D 87 SER D 88 SITE 1 AC2 6 VAL D 45 HOH D 301 HOH D 308 ASP E 77 SITE 2 AC2 6 HOH E 219 HOH F 205 SITE 1 AC3 5 GLY G 44 GLY G 46 ALA G 47 THR H 87 SITE 2 AC3 5 SER H 88 SITE 1 AC4 1 DG I 60 SITE 1 AC5 1 DG I 29 CRYST1 107.560 109.710 183.480 90.00 90.00 90.00 P 21 21 21 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 0.009297 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009115 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005450 0.00000