HEADER DNA BINDING PROTEIN 02-APR-19 6R94 TITLE CRYO-EM STRUCTURE OF NCP_THF2(-3) COMPND MOL_ID: 1; COMPND 2 MOLECULE: HUMAN ALPHA-SATELLITE DNA (145-MER); COMPND 3 CHAIN: I; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: HUMAN ALPHA-SATELLITE DNA (145-MER) WITH ABASIC SITES AT COMPND 7 POSITIONS 97-98; COMPND 8 CHAIN: J; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: HISTONE H3.1; COMPND 12 CHAIN: A, E; COMPND 13 SYNONYM: HISTONE H3/A,HISTONE H3/B,HISTONE H3/C,HISTONE H3/D,HISTONE COMPND 14 H3/F,HISTONE H3/H,HISTONE H3/I,HISTONE H3/J,HISTONE H3/K,HISTONE COMPND 15 H3/L; COMPND 16 ENGINEERED: YES; COMPND 17 MOL_ID: 4; COMPND 18 MOLECULE: HISTONE H4; COMPND 19 CHAIN: B, F; COMPND 20 ENGINEERED: YES; COMPND 21 MOL_ID: 5; COMPND 22 MOLECULE: HISTONE H2A TYPE 1-B/E; COMPND 23 CHAIN: C, G; COMPND 24 SYNONYM: HISTONE H2A.2,HISTONE H2A/A,HISTONE H2A/M; COMPND 25 ENGINEERED: YES; COMPND 26 MOL_ID: 6; COMPND 27 MOLECULE: HISTONE H2B TYPE 1-J; COMPND 28 CHAIN: D, H; COMPND 29 SYNONYM: HISTONE H2B.1,HISTONE H2B.R,H2B/R; COMPND 30 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 MOL_ID: 3; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: HIST1H3A, H3FA, HIST1H3B, H3FL, HIST1H3C, H3FC, HIST1H3D, SOURCE 16 H3FB, HIST1H3E, H3FD, HIST1H3F, H3FI, HIST1H3G, H3FH, HIST1H3H, SOURCE 17 H3FK, HIST1H3I, H3FF, HIST1H3J, H3FJ; SOURCE 18 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 19 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 20 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 21 MOL_ID: 4; SOURCE 22 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 23 ORGANISM_COMMON: HUMAN; SOURCE 24 ORGANISM_TAXID: 9606; SOURCE 25 GENE: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, SOURCE 26 H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, SOURCE 27 H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, SOURCE 28 H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, SOURCE 29 H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4; SOURCE 30 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 31 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 32 EXPRESSION_SYSTEM_CELL_LINE: JM109(DE3); SOURCE 33 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 34 MOL_ID: 5; SOURCE 35 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 36 ORGANISM_COMMON: HUMAN; SOURCE 37 ORGANISM_TAXID: 9606; SOURCE 38 GENE: HIST1H2AB, H2AFM, HIST1H2AE, H2AFA; SOURCE 39 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 40 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 41 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 42 MOL_ID: 6; SOURCE 43 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 44 ORGANISM_COMMON: HUMAN; SOURCE 45 ORGANISM_TAXID: 9606; SOURCE 46 GENE: HIST1H2BJ, H2BFR; SOURCE 47 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 48 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 49 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS DNA DAMAGE, NUCLEOSOME, 6-4 PHOTOPRODUCT, DNA BINDING PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR S.MATSUMOTO,S.CAVADINI,R.D.BUNKER,N.H.THOMA REVDAT 4 18-DEC-19 6R94 1 SCALE REVDAT 3 06-NOV-19 6R94 1 REMARK REVDAT 2 17-JUL-19 6R94 1 JRNL REMARK REVDAT 1 12-JUN-19 6R94 0 JRNL AUTH S.MATSUMOTO,S.CAVADINI,R.D.BUNKER,R.S.GRAND,A.POTENZA, JRNL AUTH 2 J.RABL,J.YAMAMOTO,A.D.SCHENK,D.SCHUBELER,S.IWAI,K.SUGASAWA, JRNL AUTH 3 H.KURUMIZAKA,N.H.THOMA JRNL TITL DNA DAMAGE DETECTION IN NUCLEOSOMES INVOLVES DNA REGISTER JRNL TITL 2 SHIFTING. JRNL REF NATURE V. 571 79 2019 JRNL REFN ESSN 1476-4687 JRNL PMID 31142837 JRNL DOI 10.1038/S41586-019-1259-3 REMARK 2 REMARK 2 RESOLUTION. 3.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : EPU, GCTF, COOT, REFMAC, PHENIX, REMARK 3 RELION, RELION, RELION REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 4ZUX REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : FLEXIBLE FIT REMARK 3 REFINEMENT TARGET : CROSS-CORRELATION COEFFICIENT REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 3.500 REMARK 3 NUMBER OF PARTICLES : 78672 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 6R94 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-APR-19. REMARK 100 THE DEPOSITION ID IS D_1292101592. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : THF2 (-3) CONTAINING REMARK 245 NUCLEOSOME; HUMAN DNA; HISTONE REMARK 245 H4; HISTONE H3.1 / 2A / 2B REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 2.00 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.40 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K2 SUMMIT (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : NULL REMARK 245 MAXIMUM DEFOCUS (NM) : NULL REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 0.00 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 40.00 REMARK 245 ILLUMINATION MODE : SPOT SCAN REMARK 245 NOMINAL MAGNIFICATION : 130000 REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. 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: 60530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 77620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -385.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: I, J, A, B, C, D, E, F, G, H 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 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 ARG A 3 REMARK 465 THR A 4 REMARK 465 LYS A 5 REMARK 465 GLN A 6 REMARK 465 THR A 7 REMARK 465 ALA A 8 REMARK 465 ARG A 9 REMARK 465 LYS A 10 REMARK 465 SER A 11 REMARK 465 THR A 12 REMARK 465 GLY A 13 REMARK 465 GLY A 14 REMARK 465 LYS A 15 REMARK 465 ALA A 16 REMARK 465 PRO A 17 REMARK 465 ARG A 18 REMARK 465 LYS A 19 REMARK 465 GLN A 20 REMARK 465 LEU A 21 REMARK 465 ALA A 22 REMARK 465 THR A 23 REMARK 465 LYS A 24 REMARK 465 ALA A 25 REMARK 465 ALA A 26 REMARK 465 ARG A 27 REMARK 465 LYS A 28 REMARK 465 SER A 29 REMARK 465 ALA A 30 REMARK 465 PRO A 31 REMARK 465 ALA A 32 REMARK 465 THR A 33 REMARK 465 GLY A 34 REMARK 465 GLY A 35 REMARK 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 SER B 2 REMARK 465 GLY B 3 REMARK 465 ARG B 4 REMARK 465 GLY B 5 REMARK 465 LYS B 6 REMARK 465 GLY B 7 REMARK 465 GLY B 8 REMARK 465 LYS B 9 REMARK 465 GLY B 10 REMARK 465 LEU B 11 REMARK 465 GLY B 12 REMARK 465 LYS B 13 REMARK 465 GLY B 14 REMARK 465 GLY B 15 REMARK 465 ALA B 16 REMARK 465 LYS B 17 REMARK 465 ARG B 18 REMARK 465 HIS B 19 REMARK 465 GLY C -2 REMARK 465 SER C -1 REMARK 465 HIS C 0 REMARK 465 MET C 1 REMARK 465 SER C 2 REMARK 465 GLY C 3 REMARK 465 ARG C 4 REMARK 465 GLY C 5 REMARK 465 LYS C 6 REMARK 465 GLN C 7 REMARK 465 GLY C 8 REMARK 465 HIS C 124 REMARK 465 HIS C 125 REMARK 465 LYS C 126 REMARK 465 ALA C 127 REMARK 465 LYS C 128 REMARK 465 GLY C 129 REMARK 465 LYS C 130 REMARK 465 GLY D -5 REMARK 465 SER D -4 REMARK 465 HIS D -3 REMARK 465 MET D -2 REMARK 465 PRO D -1 REMARK 465 GLU D 0 REMARK 465 PRO D 1 REMARK 465 ALA D 2 REMARK 465 LYS D 3 REMARK 465 SER D 4 REMARK 465 ALA D 5 REMARK 465 PRO D 6 REMARK 465 ALA D 7 REMARK 465 PRO D 8 REMARK 465 LYS D 9 REMARK 465 LYS D 10 REMARK 465 GLY D 11 REMARK 465 SER D 12 REMARK 465 LYS D 13 REMARK 465 LYS D 14 REMARK 465 ALA D 15 REMARK 465 VAL D 16 REMARK 465 THR D 17 REMARK 465 LYS D 18 REMARK 465 ALA D 19 REMARK 465 GLN D 20 REMARK 465 LYS D 21 REMARK 465 LYS D 22 REMARK 465 ASP D 23 REMARK 465 GLY D 24 REMARK 465 LYS D 25 REMARK 465 LYS D 26 REMARK 465 GLY E -2 REMARK 465 SER E -1 REMARK 465 HIS E 0 REMARK 465 MET E 1 REMARK 465 ALA E 2 REMARK 465 ARG E 3 REMARK 465 THR E 4 REMARK 465 LYS E 5 REMARK 465 GLN E 6 REMARK 465 THR E 7 REMARK 465 ALA E 8 REMARK 465 ARG E 9 REMARK 465 LYS E 10 REMARK 465 SER E 11 REMARK 465 THR E 12 REMARK 465 GLY E 13 REMARK 465 GLY E 14 REMARK 465 LYS E 15 REMARK 465 ALA E 16 REMARK 465 PRO E 17 REMARK 465 ARG E 18 REMARK 465 LYS E 19 REMARK 465 GLN E 20 REMARK 465 LEU E 21 REMARK 465 ALA E 22 REMARK 465 THR E 23 REMARK 465 LYS E 24 REMARK 465 ALA E 25 REMARK 465 ALA E 26 REMARK 465 ARG E 27 REMARK 465 LYS E 28 REMARK 465 SER E 29 REMARK 465 ALA E 30 REMARK 465 PRO E 31 REMARK 465 ALA E 32 REMARK 465 THR E 33 REMARK 465 GLY E 34 REMARK 465 GLY E 35 REMARK 465 GLY F -2 REMARK 465 SER F -1 REMARK 465 HIS F 0 REMARK 465 MET F 1 REMARK 465 SER F 2 REMARK 465 GLY F 3 REMARK 465 ARG F 4 REMARK 465 GLY F 5 REMARK 465 LYS F 6 REMARK 465 GLY F 7 REMARK 465 GLY F 8 REMARK 465 LYS F 9 REMARK 465 GLY F 10 REMARK 465 LEU F 11 REMARK 465 GLY F 12 REMARK 465 LYS F 13 REMARK 465 GLY F 14 REMARK 465 GLY F 15 REMARK 465 ALA F 16 REMARK 465 GLY G -2 REMARK 465 SER G -1 REMARK 465 HIS G 0 REMARK 465 MET G 1 REMARK 465 SER G 2 REMARK 465 GLY G 3 REMARK 465 ARG G 4 REMARK 465 GLY G 5 REMARK 465 LYS G 6 REMARK 465 GLN G 7 REMARK 465 GLY G 8 REMARK 465 ALA G 127 REMARK 465 LYS G 128 REMARK 465 GLY G 129 REMARK 465 LYS G 130 REMARK 465 GLY H -2 REMARK 465 SER H -1 REMARK 465 HIS H 0 REMARK 465 MET H 1 REMARK 465 PRO H 2 REMARK 465 GLU H 3 REMARK 465 PRO H 4 REMARK 465 ALA H 5 REMARK 465 LYS H 6 REMARK 465 SER H 7 REMARK 465 ALA H 8 REMARK 465 PRO H 9 REMARK 465 ALA H 10 REMARK 465 PRO H 11 REMARK 465 LYS H 12 REMARK 465 LYS H 13 REMARK 465 GLY H 14 REMARK 465 SER H 15 REMARK 465 LYS H 16 REMARK 465 LYS H 17 REMARK 465 ALA H 18 REMARK 465 VAL H 19 REMARK 465 THR H 20 REMARK 465 LYS H 21 REMARK 465 ALA H 22 REMARK 465 GLN H 23 REMARK 465 LYS H 24 REMARK 465 LYS H 25 REMARK 465 ASP H 26 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 NH1 ARG E 70 OD1 ASN F 26 2.11 REMARK 500 OD2 ASP D 66 OH TYR F 99 2.18 REMARK 500 NH1 ARG A 70 OD1 ASN B 26 2.18 REMARK 500 OH TYR C 40 OE1 GLU D 69 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DA I 43 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DT I 45 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DC I 47 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DA I 57 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DC I 75 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DG I 97 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DA I 98 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DT I 139 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DT J 38 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DC J 47 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG J 58 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG J 77 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DC J 83 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DG J 99 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DA J 138 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 VAL A 36 CG1 - CB - CG2 ANGL. DEV. = 10.4 DEGREES REMARK 500 SER H 33 CB - CA - C ANGL. DEV. = 12.6 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 111 113.14 -165.73 REMARK 500 LYS D 28 131.32 -170.88 REMARK 500 ASP D 49 74.97 -102.81 REMARK 500 ALA D 122 35.14 -97.18 REMARK 500 ARG F 18 -63.28 -93.59 REMARK 500 ARG F 20 66.47 60.78 REMARK 500 ASN G 111 112.09 -164.40 REMARK 500 LYS G 119 -77.64 -52.98 REMARK 500 LYS G 120 -175.66 172.91 REMARK 500 HIS G 124 34.47 -94.17 REMARK 500 ASP H 52 62.75 -102.68 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 ARG A 135 -11.98 REMARK 500 GLY B 102 -11.53 REMARK 500 ARG E 135 12.89 REMARK 500 GLY F 102 11.11 REMARK 500 ALA H 125 -12.86 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-4768 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF NCP_THF2(-3) DBREF 6R94 I 1 145 PDB 6R94 6R94 1 145 DBREF 6R94 J 1 145 PDB 6R94 6R94 1 145 DBREF 6R94 A 1 136 UNP P68431 H31_HUMAN 1 136 DBREF 6R94 B 1 103 UNP P62805 H4_HUMAN 1 103 DBREF 6R94 C 1 130 UNP P04908 H2A1B_HUMAN 1 130 DBREF 6R94 D -2 123 UNP P06899 H2B1J_HUMAN 1 126 DBREF 6R94 E 1 136 UNP P68431 H31_HUMAN 1 136 DBREF 6R94 F 1 103 UNP P62805 H4_HUMAN 1 103 DBREF 6R94 G 1 130 UNP P04908 H2A1B_HUMAN 1 130 DBREF 6R94 H 1 126 UNP P06899 H2B1J_HUMAN 1 126 SEQADV 6R94 GLY A -2 UNP P68431 EXPRESSION TAG SEQADV 6R94 SER A -1 UNP P68431 EXPRESSION TAG SEQADV 6R94 HIS A 0 UNP P68431 EXPRESSION TAG SEQADV 6R94 GLY B -2 UNP P62805 EXPRESSION TAG SEQADV 6R94 SER B -1 UNP P62805 EXPRESSION TAG SEQADV 6R94 HIS B 0 UNP P62805 EXPRESSION TAG SEQADV 6R94 GLY C -2 UNP P04908 EXPRESSION TAG SEQADV 6R94 SER C -1 UNP P04908 EXPRESSION TAG SEQADV 6R94 HIS C 0 UNP P04908 EXPRESSION TAG SEQADV 6R94 GLY D -5 UNP P06899 EXPRESSION TAG SEQADV 6R94 SER D -4 UNP P06899 EXPRESSION TAG SEQADV 6R94 HIS D -3 UNP P06899 EXPRESSION TAG SEQADV 6R94 GLY E -2 UNP P68431 EXPRESSION TAG SEQADV 6R94 SER E -1 UNP P68431 EXPRESSION TAG SEQADV 6R94 HIS E 0 UNP P68431 EXPRESSION TAG SEQADV 6R94 GLY F -2 UNP P62805 EXPRESSION TAG SEQADV 6R94 SER F -1 UNP P62805 EXPRESSION TAG SEQADV 6R94 HIS F 0 UNP P62805 EXPRESSION TAG SEQADV 6R94 GLY G -2 UNP P04908 EXPRESSION TAG SEQADV 6R94 SER G -1 UNP P04908 EXPRESSION TAG SEQADV 6R94 HIS G 0 UNP P04908 EXPRESSION TAG SEQADV 6R94 GLY H -2 UNP P06899 EXPRESSION TAG SEQADV 6R94 SER H -1 UNP P06899 EXPRESSION TAG SEQADV 6R94 HIS H 0 UNP P06899 EXPRESSION TAG 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 DT 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 DG DT 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 DA 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 DT 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 DA DC 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 3DR 3DR 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 DA 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 SEQRES 1 A 139 GLY SER HIS MET ALA ARG THR LYS GLN THR ALA ARG LYS SEQRES 2 A 139 SER THR GLY GLY LYS ALA PRO ARG LYS GLN LEU ALA THR SEQRES 3 A 139 LYS ALA ALA ARG LYS SER ALA PRO ALA THR GLY GLY VAL SEQRES 4 A 139 LYS LYS PRO HIS ARG TYR ARG PRO GLY THR VAL ALA LEU SEQRES 5 A 139 ARG GLU ILE ARG ARG TYR GLN LYS SER THR GLU LEU LEU SEQRES 6 A 139 ILE ARG LYS LEU PRO PHE GLN ARG LEU VAL ARG GLU ILE SEQRES 7 A 139 ALA GLN ASP PHE LYS THR ASP LEU ARG PHE GLN SER SER SEQRES 8 A 139 ALA VAL MET ALA LEU GLN GLU ALA CYS GLU ALA TYR LEU SEQRES 9 A 139 VAL GLY LEU PHE GLU ASP THR ASN LEU CYS ALA ILE HIS SEQRES 10 A 139 ALA LYS ARG VAL THR ILE MET PRO LYS ASP ILE GLN LEU SEQRES 11 A 139 ALA ARG ARG ILE ARG GLY GLU ARG ALA SEQRES 1 B 106 GLY SER HIS MET SER GLY ARG GLY LYS GLY GLY LYS GLY SEQRES 2 B 106 LEU GLY LYS GLY GLY ALA LYS ARG HIS ARG LYS VAL LEU SEQRES 3 B 106 ARG ASP ASN ILE GLN GLY ILE THR LYS PRO ALA ILE ARG SEQRES 4 B 106 ARG LEU ALA ARG ARG GLY GLY VAL LYS ARG ILE SER GLY SEQRES 5 B 106 LEU ILE TYR GLU GLU THR ARG GLY VAL LEU LYS VAL PHE SEQRES 6 B 106 LEU GLU ASN VAL ILE ARG ASP ALA VAL THR TYR THR GLU SEQRES 7 B 106 HIS ALA LYS ARG LYS THR VAL THR ALA MET ASP VAL VAL SEQRES 8 B 106 TYR ALA LEU LYS ARG GLN GLY ARG THR LEU TYR GLY PHE SEQRES 9 B 106 GLY GLY SEQRES 1 C 133 GLY SER HIS MET SER GLY ARG GLY LYS GLN GLY GLY LYS SEQRES 2 C 133 ALA ARG ALA LYS ALA LYS THR ARG SER SER ARG ALA GLY SEQRES 3 C 133 LEU GLN PHE PRO VAL GLY ARG VAL HIS ARG LEU LEU ARG SEQRES 4 C 133 LYS GLY ASN TYR SER GLU ARG VAL GLY ALA GLY ALA PRO SEQRES 5 C 133 VAL TYR LEU ALA ALA VAL LEU GLU TYR LEU THR ALA GLU SEQRES 6 C 133 ILE LEU GLU LEU ALA GLY ASN ALA ALA ARG ASP ASN LYS SEQRES 7 C 133 LYS THR ARG ILE ILE PRO ARG HIS LEU GLN LEU ALA ILE SEQRES 8 C 133 ARG ASN ASP GLU GLU LEU ASN LYS LEU LEU GLY ARG VAL SEQRES 9 C 133 THR ILE ALA GLN GLY GLY VAL LEU PRO ASN ILE GLN ALA SEQRES 10 C 133 VAL LEU LEU PRO LYS LYS THR GLU SER HIS HIS LYS ALA SEQRES 11 C 133 LYS GLY LYS SEQRES 1 D 129 GLY SER HIS MET PRO GLU PRO ALA LYS SER ALA PRO ALA SEQRES 2 D 129 PRO LYS LYS GLY SER LYS LYS ALA VAL THR LYS ALA GLN SEQRES 3 D 129 LYS LYS ASP GLY LYS LYS ARG LYS ARG SER ARG LYS GLU SEQRES 4 D 129 SER TYR SER ILE TYR VAL TYR LYS VAL LEU LYS GLN VAL SEQRES 5 D 129 HIS PRO ASP THR GLY ILE SER SER LYS ALA MET GLY ILE SEQRES 6 D 129 MET ASN SER PHE VAL ASN ASP ILE PHE GLU ARG ILE ALA SEQRES 7 D 129 GLY GLU ALA SER ARG LEU ALA HIS TYR ASN LYS ARG SER SEQRES 8 D 129 THR ILE THR SER ARG GLU ILE GLN THR ALA VAL ARG LEU SEQRES 9 D 129 LEU LEU PRO GLY GLU LEU ALA LYS HIS ALA VAL SER GLU SEQRES 10 D 129 GLY THR LYS ALA VAL THR LYS TYR THR SER ALA LYS SEQRES 1 E 139 GLY SER HIS MET ALA ARG THR LYS GLN THR ALA ARG LYS SEQRES 2 E 139 SER THR GLY GLY LYS ALA PRO ARG LYS GLN LEU ALA THR SEQRES 3 E 139 LYS ALA ALA ARG LYS SER ALA PRO ALA THR GLY GLY VAL SEQRES 4 E 139 LYS LYS PRO HIS ARG TYR ARG PRO GLY THR VAL ALA LEU SEQRES 5 E 139 ARG GLU ILE ARG ARG TYR GLN LYS SER THR GLU LEU LEU SEQRES 6 E 139 ILE ARG LYS LEU PRO PHE GLN ARG LEU VAL ARG GLU ILE SEQRES 7 E 139 ALA GLN ASP PHE LYS THR ASP LEU ARG PHE GLN SER SER SEQRES 8 E 139 ALA VAL MET ALA LEU GLN GLU ALA CYS GLU ALA TYR LEU SEQRES 9 E 139 VAL GLY LEU PHE GLU ASP THR ASN LEU CYS ALA ILE HIS SEQRES 10 E 139 ALA LYS ARG VAL THR ILE MET PRO LYS ASP ILE GLN LEU SEQRES 11 E 139 ALA ARG ARG ILE ARG GLY GLU ARG ALA SEQRES 1 F 106 GLY SER HIS MET SER GLY ARG GLY LYS GLY GLY LYS GLY SEQRES 2 F 106 LEU GLY LYS GLY GLY ALA LYS ARG HIS ARG LYS VAL LEU SEQRES 3 F 106 ARG ASP ASN ILE GLN GLY ILE THR LYS PRO ALA ILE ARG SEQRES 4 F 106 ARG LEU ALA ARG ARG GLY GLY VAL LYS ARG ILE SER GLY SEQRES 5 F 106 LEU ILE TYR GLU GLU THR ARG GLY VAL LEU LYS VAL PHE SEQRES 6 F 106 LEU GLU ASN VAL ILE ARG ASP ALA VAL THR TYR THR GLU SEQRES 7 F 106 HIS ALA LYS ARG LYS THR VAL THR ALA MET ASP VAL VAL SEQRES 8 F 106 TYR ALA LEU LYS ARG GLN GLY ARG THR LEU TYR GLY PHE SEQRES 9 F 106 GLY GLY SEQRES 1 G 133 GLY SER HIS MET SER GLY ARG GLY LYS GLN GLY GLY LYS SEQRES 2 G 133 ALA ARG ALA LYS ALA LYS THR ARG SER SER ARG ALA GLY SEQRES 3 G 133 LEU GLN PHE PRO VAL GLY ARG VAL HIS ARG LEU LEU ARG SEQRES 4 G 133 LYS GLY ASN TYR SER GLU ARG VAL GLY ALA GLY ALA PRO SEQRES 5 G 133 VAL TYR LEU ALA ALA VAL LEU GLU TYR LEU THR ALA GLU SEQRES 6 G 133 ILE LEU GLU LEU ALA GLY ASN ALA ALA ARG ASP ASN LYS SEQRES 7 G 133 LYS THR ARG ILE ILE PRO ARG HIS LEU GLN LEU ALA ILE SEQRES 8 G 133 ARG ASN ASP GLU GLU LEU ASN LYS LEU LEU GLY ARG VAL SEQRES 9 G 133 THR ILE ALA GLN GLY GLY VAL LEU PRO ASN ILE GLN ALA SEQRES 10 G 133 VAL LEU LEU PRO LYS LYS THR GLU SER HIS HIS LYS ALA SEQRES 11 G 133 LYS GLY LYS SEQRES 1 H 129 GLY SER HIS MET PRO GLU PRO ALA LYS SER ALA PRO ALA SEQRES 2 H 129 PRO LYS LYS GLY SER LYS LYS ALA VAL THR LYS ALA GLN SEQRES 3 H 129 LYS LYS ASP GLY LYS LYS ARG LYS ARG SER ARG LYS GLU SEQRES 4 H 129 SER TYR SER ILE TYR VAL TYR LYS VAL LEU LYS GLN VAL SEQRES 5 H 129 HIS PRO ASP THR GLY ILE SER SER LYS ALA MET GLY ILE SEQRES 6 H 129 MET ASN SER PHE VAL ASN ASP ILE PHE GLU ARG ILE ALA SEQRES 7 H 129 GLY GLU ALA SER ARG LEU ALA HIS TYR ASN LYS ARG SER SEQRES 8 H 129 THR ILE THR SER ARG GLU ILE GLN THR ALA VAL ARG LEU SEQRES 9 H 129 LEU LEU PRO GLY GLU LEU ALA LYS HIS ALA VAL SER GLU SEQRES 10 H 129 GLY THR LYS ALA VAL THR LYS TYR THR SER ALA LYS HET 3DR I 97 19 HET 3DR I 98 19 HET 3DR J 97 19 HET 3DR J 98 19 HETNAM 3DR 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE HETSYN 3DR ABASIC DIDEOXYRIBOSE FORMUL 1 3DR 4(C5 H11 O6 P) HELIX 1 AA1 THR A 46 SER A 58 1 13 HELIX 2 AA2 ARG A 64 ASP A 78 1 15 HELIX 3 AA3 GLN A 86 ALA A 115 1 30 HELIX 4 AA4 MET A 121 GLY A 133 1 13 HELIX 5 AA5 ASN B 26 ILE B 30 5 5 HELIX 6 AA6 THR B 31 GLY B 42 1 12 HELIX 7 AA7 LEU B 50 LYS B 78 1 29 HELIX 8 AA8 THR B 83 GLN B 94 1 12 HELIX 9 AA9 THR C 17 GLY C 23 1 7 HELIX 10 AB1 VAL C 28 LYS C 37 1 10 HELIX 11 AB2 ALA C 46 ASN C 74 1 29 HELIX 12 AB3 ILE C 80 ASN C 90 1 11 HELIX 13 AB4 ASP C 91 LEU C 98 1 8 HELIX 14 AB5 GLN C 113 LEU C 117 5 5 HELIX 15 AB6 TYR D 35 HIS D 47 1 13 HELIX 16 AB7 SER D 53 ASN D 82 1 30 HELIX 17 AB8 THR D 88 LEU D 100 1 13 HELIX 18 AB9 PRO D 101 ALA D 122 1 22 HELIX 19 AC1 GLY E 45 SER E 58 1 14 HELIX 20 AC2 ARG E 64 LYS E 80 1 17 HELIX 21 AC3 GLN E 86 ALA E 115 1 30 HELIX 22 AC4 MET E 121 GLY E 133 1 13 HELIX 23 AC5 ASN F 26 ILE F 30 5 5 HELIX 24 AC6 THR F 31 GLY F 42 1 12 HELIX 25 AC7 LEU F 50 ALA F 77 1 28 HELIX 26 AC8 THR F 83 GLN F 94 1 12 HELIX 27 AC9 THR G 17 GLY G 23 1 7 HELIX 28 AD1 PRO G 27 LYS G 37 1 11 HELIX 29 AD2 ALA G 46 ASN G 74 1 29 HELIX 30 AD3 ILE G 80 ASN G 90 1 11 HELIX 31 AD4 ASP G 91 LEU G 98 1 8 HELIX 32 AD5 GLN G 113 LEU G 117 5 5 HELIX 33 AD6 TYR H 38 HIS H 50 1 13 HELIX 34 AD7 SER H 56 ASN H 85 1 30 HELIX 35 AD8 THR H 91 LEU H 103 1 13 HELIX 36 AD9 PRO H 104 ALA H 125 1 22 SHEET 1 AA1 2 ARG A 84 PHE A 85 0 SHEET 2 AA1 2 THR B 81 VAL B 82 1 O VAL B 82 N ARG A 84 SHEET 1 AA2 2 THR A 119 ILE A 120 0 SHEET 2 AA2 2 ARG B 46 ILE B 47 1 O ARG B 46 N ILE A 120 SHEET 1 AA3 2 THR B 97 TYR B 99 0 SHEET 2 AA3 2 VAL G 101 ILE G 103 1 O THR G 102 N THR B 97 SHEET 1 AA4 2 ARG C 43 VAL C 44 0 SHEET 2 AA4 2 THR D 86 ILE D 87 1 O ILE D 87 N ARG C 43 SHEET 1 AA5 2 ARG C 78 ILE C 79 0 SHEET 2 AA5 2 GLY D 51 ILE D 52 1 O GLY D 51 N ILE C 79 SHEET 1 AA6 2 VAL C 101 ILE C 103 0 SHEET 2 AA6 2 THR F 97 TYR F 99 1 O TYR F 99 N THR C 102 SHEET 1 AA7 2 ARG E 84 PHE E 85 0 SHEET 2 AA7 2 THR F 81 VAL F 82 1 O VAL F 82 N ARG E 84 SHEET 1 AA8 2 THR E 119 ILE E 120 0 SHEET 2 AA8 2 ARG F 46 ILE F 47 1 O ARG F 46 N ILE E 120 SHEET 1 AA9 2 ARG G 43 VAL G 44 0 SHEET 2 AA9 2 THR H 89 ILE H 90 1 O ILE H 90 N ARG G 43 SHEET 1 AB1 2 ARG G 78 ILE G 79 0 SHEET 2 AB1 2 GLY H 54 ILE H 55 1 O GLY H 54 N ILE G 79 LINK O3' DG I 96 P B3DR I 97 1555 1555 1.61 LINK O3'B3DR I 97 P B3DR I 98 1555 1555 1.61 LINK O3'B3DR I 98 P DG I 99 1555 1555 1.61 LINK O3' DG J 96 P A3DR J 97 1555 1555 1.61 LINK O3'A3DR J 97 P A3DR J 98 1555 1555 1.61 LINK O3'A3DR J 98 P DG J 99 1555 1555 1.61 CISPEP 1 LYS D 28 ARG D 29 0 -2.05 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000