HEADER DNA BINDING PROTEIN 20-OCT-20 7DBH TITLE THE MOUSE NUCLEOSOME STRUCTURE CONTAINING H3MM18 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE H3MM18; COMPND 3 CHAIN: A, E; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: HISTONE H4; COMPND 7 CHAIN: B, F; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: HISTONE H2A TYPE 1-B; COMPND 11 CHAIN: C, G; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 4; COMPND 14 MOLECULE: HISTONE H2B TYPE 3-A; COMPND 15 CHAIN: D, H; COMPND 16 ENGINEERED: YES; COMPND 17 MOL_ID: 5; COMPND 18 MOLECULE: DNA (126-MER); COMPND 19 CHAIN: I; COMPND 20 ENGINEERED: YES; COMPND 21 MOL_ID: 6; COMPND 22 MOLECULE: DNA (126-MER); COMPND 23 CHAIN: J; COMPND 24 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_TAXID: 10090; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 8 ORGANISM_COMMON: MOUSE; SOURCE 9 ORGANISM_TAXID: 10090; SOURCE 10 GENE: HIST1H4A, HIST1H4B, H4-53, HIST1H4C, H4-12, HIST1H4D, SOURCE 11 HIST1H4F, HIST1H4H, HIST1H4I, HIST1H4J, HIST1H4K, HIST1H4M, SOURCE 12 HIST2H4A, HIST2H4, HIST4H4; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 15 MOL_ID: 3; SOURCE 16 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 17 ORGANISM_COMMON: MOUSE; SOURCE 18 ORGANISM_TAXID: 10090; SOURCE 19 GENE: HIST1H2AB; SOURCE 20 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 21 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 22 MOL_ID: 4; SOURCE 23 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 24 ORGANISM_COMMON: MOUSE; SOURCE 25 ORGANISM_TAXID: 10090; SOURCE 26 GENE: HIST3H2BA; SOURCE 27 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 28 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 29 MOL_ID: 5; SOURCE 30 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 31 ORGANISM_TAXID: 10090; SOURCE 32 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 33 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 34 MOL_ID: 6; SOURCE 35 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 36 ORGANISM_TAXID: 10090; SOURCE 37 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 38 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS COMPLEX, CHROMATIN, NUCLEOSOME, DNA BINDING PROTEIN, DNA BINDING KEYWDS 2 PROTEIN-DNA COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR S.HIRAI,Y.TAKIZAWA,T.KUJIRAI,H.KURUMIZAKA REVDAT 3 29-MAY-24 7DBH 1 REMARK REVDAT 2 16-FEB-22 7DBH 1 JRNL REVDAT 1 19-JAN-22 7DBH 0 JRNL AUTH S.HIRAI,K.TOMIMATSU,A.MIYAWAKI-KUWAKADO,Y.TAKIZAWA, JRNL AUTH 2 T.KOMATSU,T.TACHIBANA,Y.FUKUSHIMA,Y.TAKEDA,L.NEGISHI, JRNL AUTH 3 T.KUJIRAI,M.KOYAMA,Y.OHKAWA,H.KURUMIZAKA JRNL TITL UNUSUAL NUCLEOSOME FORMATION AND TRANSCRIPTOME INFLUENCE BY JRNL TITL 2 THE HISTONE H3MM18 VARIANT. JRNL REF NUCLEIC ACIDS RES. V. 50 72 2022 JRNL REFN ESSN 1362-4962 JRNL PMID 34929737 JRNL DOI 10.1093/NAR/GKAB1137 REMARK 2 REMARK 2 RESOLUTION. 3.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL 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) : 3.600 REMARK 3 NUMBER OF PARTICLES : 274546 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 7DBH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-OCT-20. REMARK 100 THE DEPOSITION ID IS D_1300018983. 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 : THE MOUSE NUCLEOSOME CONTAINING REMARK 245 H3MM18 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.50 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 : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K 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 : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5660.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL 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 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 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 -3 REMARK 465 SER A -2 REMARK 465 HIS A -1 REMARK 465 MET A 0 REMARK 465 ALA A 1 REMARK 465 ARG A 2 REMARK 465 THR A 3 REMARK 465 LYS A 4 REMARK 465 GLN A 5 REMARK 465 THR A 6 REMARK 465 ALA A 7 REMARK 465 ARG A 8 REMARK 465 LYS A 9 REMARK 465 SER A 10 REMARK 465 THR A 11 REMARK 465 GLY A 12 REMARK 465 ASP A 13 REMARK 465 LYS A 14 REMARK 465 ALA A 15 REMARK 465 PRO A 16 REMARK 465 ARG A 17 REMARK 465 LYS A 18 REMARK 465 GLN A 19 REMARK 465 LEU A 20 REMARK 465 ALA A 21 REMARK 465 THR A 22 REMARK 465 LYS A 23 REMARK 465 ALA A 24 REMARK 465 ALA A 25 REMARK 465 ARG A 26 REMARK 465 LYS A 27 REMARK 465 SER A 28 REMARK 465 ALA A 29 REMARK 465 PRO A 30 REMARK 465 SER A 31 REMARK 465 THR A 32 REMARK 465 GLY A 33 REMARK 465 GLY A 34 REMARK 465 VAL A 35 REMARK 465 LYS A 36 REMARK 465 LYS A 37 REMARK 465 PRO A 38 REMARK 465 HIS A 39 REMARK 465 CYS A 40 REMARK 465 TYR A 41 REMARK 465 ARG A 42 REMARK 465 PRO A 43 REMARK 465 GLY A 44 REMARK 465 THR A 45 REMARK 465 VAL A 46 REMARK 465 ALA A 47 REMARK 465 LEU A 48 REMARK 465 ARG A 49 REMARK 465 GLU A 50 REMARK 465 ILE A 51 REMARK 465 ARG A 52 REMARK 465 SER A 53 REMARK 465 TYR A 54 REMARK 465 GLU A 133 REMARK 465 CYS A 134 REMARK 465 ALA A 135 REMARK 465 GLY B -3 REMARK 465 SER B -2 REMARK 465 HIS B -1 REMARK 465 MET B 0 REMARK 465 SER B 1 REMARK 465 GLY B 2 REMARK 465 ARG B 3 REMARK 465 GLY B 4 REMARK 465 LYS B 5 REMARK 465 GLY B 6 REMARK 465 GLY B 7 REMARK 465 LYS B 8 REMARK 465 GLY B 9 REMARK 465 LEU B 10 REMARK 465 GLY B 11 REMARK 465 LYS B 12 REMARK 465 GLY B 13 REMARK 465 GLY B 14 REMARK 465 ALA B 15 REMARK 465 LYS B 16 REMARK 465 ARG B 17 REMARK 465 HIS B 18 REMARK 465 ARG B 19 REMARK 465 GLY B 102 REMARK 465 GLY C -3 REMARK 465 SER C -2 REMARK 465 HIS C -1 REMARK 465 MET C 0 REMARK 465 SER C 1 REMARK 465 GLY C 2 REMARK 465 ARG C 3 REMARK 465 GLY C 4 REMARK 465 LYS C 5 REMARK 465 GLN C 6 REMARK 465 GLY C 7 REMARK 465 GLY C 8 REMARK 465 LYS C 9 REMARK 465 ALA C 10 REMARK 465 ARG C 11 REMARK 465 ALA C 12 REMARK 465 LYS C 13 REMARK 465 ALA C 14 REMARK 465 LYS C 15 REMARK 465 ASN C 110 REMARK 465 ILE C 111 REMARK 465 GLN C 112 REMARK 465 ALA C 113 REMARK 465 VAL C 114 REMARK 465 LEU C 115 REMARK 465 LEU C 116 REMARK 465 PRO C 117 REMARK 465 LYS C 118 REMARK 465 LYS C 119 REMARK 465 THR C 120 REMARK 465 GLU C 121 REMARK 465 SER C 122 REMARK 465 HIS C 123 REMARK 465 HIS C 124 REMARK 465 LYS C 125 REMARK 465 ALA C 126 REMARK 465 LYS C 127 REMARK 465 GLY C 128 REMARK 465 LYS C 129 REMARK 465 GLY D -3 REMARK 465 SER D -2 REMARK 465 HIS D -1 REMARK 465 MET D 0 REMARK 465 PRO D 1 REMARK 465 GLU D 2 REMARK 465 PRO D 3 REMARK 465 SER D 4 REMARK 465 ARG D 5 REMARK 465 SER D 6 REMARK 465 THR D 7 REMARK 465 PRO D 8 REMARK 465 ALA D 9 REMARK 465 PRO D 10 REMARK 465 LYS D 11 REMARK 465 LYS D 12 REMARK 465 GLY D 13 REMARK 465 SER D 14 REMARK 465 LYS D 15 REMARK 465 LYS D 16 REMARK 465 ALA D 17 REMARK 465 ILE D 18 REMARK 465 THR D 19 REMARK 465 LYS D 20 REMARK 465 ALA D 21 REMARK 465 GLN D 22 REMARK 465 LYS D 23 REMARK 465 LYS D 24 REMARK 465 ASP D 25 REMARK 465 GLY D 26 REMARK 465 LYS D 27 REMARK 465 LYS D 28 REMARK 465 ARG D 29 REMARK 465 LYS D 30 REMARK 465 ARG D 31 REMARK 465 GLY D 32 REMARK 465 LYS D 125 REMARK 465 GLY E -3 REMARK 465 SER E -2 REMARK 465 HIS E -1 REMARK 465 MET E 0 REMARK 465 ALA E 1 REMARK 465 ARG E 2 REMARK 465 THR E 3 REMARK 465 LYS E 4 REMARK 465 GLN E 5 REMARK 465 THR E 6 REMARK 465 ALA E 7 REMARK 465 ARG E 8 REMARK 465 LYS E 9 REMARK 465 SER E 10 REMARK 465 THR E 11 REMARK 465 GLY E 12 REMARK 465 ASP E 13 REMARK 465 LYS E 14 REMARK 465 ALA E 15 REMARK 465 PRO E 16 REMARK 465 ARG E 17 REMARK 465 LYS E 18 REMARK 465 GLN E 19 REMARK 465 LEU E 20 REMARK 465 ALA E 21 REMARK 465 THR E 22 REMARK 465 LYS E 23 REMARK 465 ALA E 24 REMARK 465 ALA E 25 REMARK 465 ARG E 26 REMARK 465 LYS E 27 REMARK 465 SER E 28 REMARK 465 ALA E 29 REMARK 465 PRO E 30 REMARK 465 SER E 31 REMARK 465 THR E 32 REMARK 465 GLY E 33 REMARK 465 GLY E 34 REMARK 465 VAL E 35 REMARK 465 LYS E 36 REMARK 465 LYS E 37 REMARK 465 PRO E 38 REMARK 465 HIS E 39 REMARK 465 CYS E 40 REMARK 465 TYR E 41 REMARK 465 ARG E 42 REMARK 465 PRO E 43 REMARK 465 GLY E 44 REMARK 465 THR E 45 REMARK 465 VAL E 46 REMARK 465 ALA E 47 REMARK 465 GLU E 133 REMARK 465 CYS E 134 REMARK 465 ALA E 135 REMARK 465 GLY F -3 REMARK 465 SER F -2 REMARK 465 HIS F -1 REMARK 465 MET F 0 REMARK 465 SER F 1 REMARK 465 GLY F 2 REMARK 465 ARG F 3 REMARK 465 GLY F 4 REMARK 465 LYS F 5 REMARK 465 GLY F 6 REMARK 465 GLY F 7 REMARK 465 LYS F 8 REMARK 465 GLY F 9 REMARK 465 LEU F 10 REMARK 465 GLY F 11 REMARK 465 LYS F 12 REMARK 465 GLY F 13 REMARK 465 GLY F 14 REMARK 465 ALA F 15 REMARK 465 LYS F 16 REMARK 465 ARG F 17 REMARK 465 HIS F 18 REMARK 465 ARG F 19 REMARK 465 LYS F 20 REMARK 465 VAL F 21 REMARK 465 LEU F 22 REMARK 465 ARG F 23 REMARK 465 ASP F 24 REMARK 465 GLY F 102 REMARK 465 GLY G -3 REMARK 465 SER G -2 REMARK 465 HIS G -1 REMARK 465 MET G 0 REMARK 465 SER G 1 REMARK 465 GLY G 2 REMARK 465 ARG G 3 REMARK 465 GLY G 4 REMARK 465 LYS G 5 REMARK 465 GLN G 6 REMARK 465 GLY G 7 REMARK 465 GLY G 8 REMARK 465 LYS G 9 REMARK 465 ALA G 10 REMARK 465 ARG G 11 REMARK 465 ALA G 12 REMARK 465 LYS G 13 REMARK 465 ASN G 110 REMARK 465 ILE G 111 REMARK 465 GLN G 112 REMARK 465 ALA G 113 REMARK 465 VAL G 114 REMARK 465 LEU G 115 REMARK 465 LEU G 116 REMARK 465 PRO G 117 REMARK 465 LYS G 118 REMARK 465 LYS G 119 REMARK 465 THR G 120 REMARK 465 GLU G 121 REMARK 465 SER G 122 REMARK 465 HIS G 123 REMARK 465 HIS G 124 REMARK 465 LYS G 125 REMARK 465 ALA G 126 REMARK 465 LYS G 127 REMARK 465 GLY G 128 REMARK 465 LYS G 129 REMARK 465 GLY H -3 REMARK 465 SER H -2 REMARK 465 HIS H -1 REMARK 465 MET H 0 REMARK 465 PRO H 1 REMARK 465 GLU H 2 REMARK 465 PRO H 3 REMARK 465 SER H 4 REMARK 465 ARG H 5 REMARK 465 SER H 6 REMARK 465 THR H 7 REMARK 465 PRO H 8 REMARK 465 ALA H 9 REMARK 465 PRO H 10 REMARK 465 LYS H 11 REMARK 465 LYS H 12 REMARK 465 GLY H 13 REMARK 465 SER H 14 REMARK 465 LYS H 15 REMARK 465 LYS H 16 REMARK 465 ALA H 17 REMARK 465 ILE H 18 REMARK 465 THR H 19 REMARK 465 LYS H 20 REMARK 465 ALA H 21 REMARK 465 GLN H 22 REMARK 465 LYS H 23 REMARK 465 LYS H 24 REMARK 465 ASP H 25 REMARK 465 GLY H 26 REMARK 465 LYS H 27 REMARK 465 LYS H 28 REMARK 465 ARG H 29 REMARK 465 LYS H 30 REMARK 465 ARG H 31 REMARK 465 LYS H 125 REMARK 465 DA I -72 REMARK 465 DT I -71 REMARK 465 DC I -70 REMARK 465 DA I -69 REMARK 465 DG I -68 REMARK 465 DA I -67 REMARK 465 DA I -66 REMARK 465 DT I -65 REMARK 465 DT I 62 REMARK 465 DA I 63 REMARK 465 DT I 64 REMARK 465 DA I 65 REMARK 465 DC I 66 REMARK 465 DA I 67 REMARK 465 DT I 68 REMARK 465 DC I 69 REMARK 465 DG I 70 REMARK 465 DA I 71 REMARK 465 DT I 72 REMARK 465 DA J -72 REMARK 465 DT J -71 REMARK 465 DC J -70 REMARK 465 DG J -69 REMARK 465 DA J -68 REMARK 465 DT J -67 REMARK 465 DG J -66 REMARK 465 DT J -65 REMARK 465 DA J -64 REMARK 465 DT J -63 REMARK 465 DA J -62 REMARK 465 DA J 65 REMARK 465 DT J 66 REMARK 465 DT J 67 REMARK 465 DC J 68 REMARK 465 DT J 69 REMARK 465 DG J 70 REMARK 465 DA J 71 REMARK 465 DT J 72 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 PRO C 109 O REMARK 470 PRO G 109 O REMARK 470 SER H 124 O REMARK 470 DC I -64 P OP1 OP2 REMARK 470 DT J -61 P OP1 OP2 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 ALA F 33 CD2 LEU F 37 1.45 REMARK 500 O HIS H 109 OG SER H 112 2.16 REMARK 500 OG1 THR H 90 OE1 GLU H 93 2.17 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 DT I -28 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT I -16 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DG I -7 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT I -6 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DA I 16 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DC I 22 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DA I 24 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DG I 25 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DA J -53 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 DG J -36 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DG J -6 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DA J 16 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT J 22 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG J 23 O4' - C1' - N9 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 ASP B 24 34.23 39.03 REMARK 500 THR B 96 137.05 -39.87 REMARK 500 LYS E 115 -3.92 70.57 REMARK 500 GLN F 27 -3.88 -59.46 REMARK 500 GLN G 104 25.91 49.87 REMARK 500 HIS H 49 70.42 -116.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-30631 RELATED DB: EMDB REMARK 900 THE MOUSE NUCLEOSOME STRUCTURE CONTAINING H3MM18 REMARK 900 RELATED ID: EMD-31882 RELATED DB: EMDB REMARK 900 THE MOUSE NUCLEOSOME STRUCTURE CONTAINING H3MM18 AIDED BY PL2-6 SCFV REMARK 900 RELATED ID: 7VBM RELATED DB: PDB REMARK 900 THE MOUSE NUCLEOSOME STRUCTURE CONTAINING H3MM18 AIDED BY PL2-6 SCFV DBREF 7DBH A -3 135 PDB 7DBH 7DBH -3 135 DBREF 7DBH B 0 102 UNP P62806 H4_MOUSE 1 103 DBREF 7DBH C 0 129 UNP C0HKE1 H2A1B_MOUSE 1 130 DBREF 7DBH D 0 125 UNP Q9D2U9 H2B3A_MOUSE 1 126 DBREF 7DBH E -3 135 PDB 7DBH 7DBH -3 135 DBREF 7DBH F 0 102 UNP P62806 H4_MOUSE 1 103 DBREF 7DBH G 0 129 UNP C0HKE1 H2A1B_MOUSE 1 130 DBREF 7DBH H 0 125 UNP Q9D2U9 H2B3A_MOUSE 1 126 DBREF 7DBH I -72 72 PDB 7DBH 7DBH -72 72 DBREF 7DBH J -72 72 PDB 7DBH 7DBH -72 72 SEQADV 7DBH GLY B -3 UNP P62806 EXPRESSION TAG SEQADV 7DBH SER B -2 UNP P62806 EXPRESSION TAG SEQADV 7DBH HIS B -1 UNP P62806 EXPRESSION TAG SEQADV 7DBH GLY C -3 UNP C0HKE1 EXPRESSION TAG SEQADV 7DBH SER C -2 UNP C0HKE1 EXPRESSION TAG SEQADV 7DBH HIS C -1 UNP C0HKE1 EXPRESSION TAG SEQADV 7DBH GLY D -3 UNP Q9D2U9 EXPRESSION TAG SEQADV 7DBH SER D -2 UNP Q9D2U9 EXPRESSION TAG SEQADV 7DBH HIS D -1 UNP Q9D2U9 EXPRESSION TAG SEQADV 7DBH GLY F -3 UNP P62806 EXPRESSION TAG SEQADV 7DBH SER F -2 UNP P62806 EXPRESSION TAG SEQADV 7DBH HIS F -1 UNP P62806 EXPRESSION TAG SEQADV 7DBH GLY G -3 UNP C0HKE1 EXPRESSION TAG SEQADV 7DBH SER G -2 UNP C0HKE1 EXPRESSION TAG SEQADV 7DBH HIS G -1 UNP C0HKE1 EXPRESSION TAG SEQADV 7DBH GLY H -3 UNP Q9D2U9 EXPRESSION TAG SEQADV 7DBH SER H -2 UNP Q9D2U9 EXPRESSION TAG SEQADV 7DBH HIS H -1 UNP Q9D2U9 EXPRESSION TAG SEQRES 1 A 139 GLY SER HIS MET ALA ARG THR LYS GLN THR ALA ARG LYS SEQRES 2 A 139 SER THR GLY ASP LYS ALA PRO ARG LYS GLN LEU ALA THR SEQRES 3 A 139 LYS ALA ALA ARG LYS SER ALA PRO SER THR GLY GLY VAL SEQRES 4 A 139 LYS LYS PRO HIS CYS TYR ARG PRO GLY THR VAL ALA LEU SEQRES 5 A 139 ARG GLU ILE ARG SER TYR GLN LYS SER SER GLU LEU LEU SEQRES 6 A 139 ILE ARG LYS LEU PRO PHE GLN ARG LEU VAL LEU GLU ILE SEQRES 7 A 139 ALA GLN ASP PHE LYS THR ASP LEU CYS PHE GLN SER ALA SEQRES 8 A 139 ALA ILE GLY ALA LEU GLN GLU ALA SER 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 THR GLN LEU SEQRES 11 A 139 ALA GLY TYR ILE CYS ARG GLU CYS 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 SER ARG SER THR PRO ALA SEQRES 2 D 129 PRO LYS LYS GLY SER LYS LYS ALA ILE THR LYS ALA GLN SEQRES 3 D 129 LYS LYS ASP GLY LYS LYS ARG LYS ARG GLY 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 SER GLU ALA SER ARG LEU ALA HIS TYR ASN LYS ARG SER SEQRES 8 D 129 THR ILE THR SER ARG GLU VAL 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 SER 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 ASP LYS ALA PRO ARG LYS GLN LEU ALA THR SEQRES 3 E 139 LYS ALA ALA ARG LYS SER ALA PRO SER THR GLY GLY VAL SEQRES 4 E 139 LYS LYS PRO HIS CYS TYR ARG PRO GLY THR VAL ALA LEU SEQRES 5 E 139 ARG GLU ILE ARG SER TYR GLN LYS SER SER GLU LEU LEU SEQRES 6 E 139 ILE ARG LYS LEU PRO PHE GLN ARG LEU VAL LEU GLU ILE SEQRES 7 E 139 ALA GLN ASP PHE LYS THR ASP LEU CYS PHE GLN SER ALA SEQRES 8 E 139 ALA ILE GLY ALA LEU GLN GLU ALA SER 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 THR GLN LEU SEQRES 11 E 139 ALA GLY TYR ILE CYS ARG GLU CYS 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 SER ARG SER THR PRO ALA SEQRES 2 H 129 PRO LYS LYS GLY SER LYS LYS ALA ILE THR LYS ALA GLN SEQRES 3 H 129 LYS LYS ASP GLY LYS LYS ARG LYS ARG GLY 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 SER GLU ALA SER ARG LEU ALA HIS TYR ASN LYS ARG SER SEQRES 8 H 129 THR ILE THR SER ARG GLU VAL 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 SER LYS SEQRES 1 I 145 DA DT DC DA DG DA DA DT DC DC DC DG DG SEQRES 2 I 145 DT DG DC DC DG DA DG DG DC DC DG DC DT SEQRES 3 I 145 DC DA DA DT DT DG DG DT DC DG DT DA DG SEQRES 4 I 145 DA DC DA DG DC DT DC DT DA DG DC DA DC SEQRES 5 I 145 DC DG DC DT DT DA DA DA DC DG DC DA DC SEQRES 6 I 145 DG DT DA DC DG DC DG DC DT DG DT DC DC SEQRES 7 I 145 DC DC DC DG DC DG DT DT DT DT DA DA DC SEQRES 8 I 145 DC DG DC DC DA DA DG DG DG DG DA DT DT SEQRES 9 I 145 DA DC DT DC DC DC DT DA DG DT DC DT DC SEQRES 10 I 145 DC DA DG DG DC DA DC DG DT DG DT DC DA SEQRES 11 I 145 DG DA DT DA DT DA DT DA DC DA DT DC DG SEQRES 12 I 145 DA DT SEQRES 1 J 145 DA DT DC DG DA DT DG DT DA DT DA DT DA SEQRES 2 J 145 DT DC DT DG DA DC DA DC DG DT DG DC DC SEQRES 3 J 145 DT DG DG DA DG DA DC DT DA DG DG DG DA SEQRES 4 J 145 DG DT DA DA DT DC DC DC DC DT DT DG DG SEQRES 5 J 145 DC DG DG DT DT DA DA DA DA DC DG DC DG SEQRES 6 J 145 DG DG DG DG DA DC DA DG DC DG DC DG DT SEQRES 7 J 145 DA DC DG DT DG DC DG DT DT DT DA DA DG SEQRES 8 J 145 DC DG DG DT DG DC DT DA DG DA DG DC DT SEQRES 9 J 145 DG DT DC DT DA DC DG DA DC DC DA DA DT SEQRES 10 J 145 DT DG DA DG DC DG DG DC DC DT DC DG DG SEQRES 11 J 145 DC DA DC DC DG DG DG DA DT DT DC DT DG SEQRES 12 J 145 DA DT HELIX 1 AA1 ARG A 63 ASP A 77 1 15 HELIX 2 AA2 GLN A 85 ALA A 114 1 30 HELIX 3 AA3 MET A 120 CYS A 131 1 12 HELIX 4 AA4 ASP B 24 ILE B 29 5 6 HELIX 5 AA5 THR B 30 GLY B 41 1 12 HELIX 6 AA6 LEU B 49 ALA B 76 1 28 HELIX 7 AA7 THR B 82 GLY B 94 1 13 HELIX 8 AA8 SER C 18 GLY C 22 5 5 HELIX 9 AA9 PRO C 26 GLY C 37 1 12 HELIX 10 AB1 ALA C 45 ASN C 73 1 29 HELIX 11 AB2 ILE C 79 ASP C 90 1 12 HELIX 12 AB3 ASP C 90 LEU C 97 1 8 HELIX 13 AB4 TYR D 37 HIS D 49 1 13 HELIX 14 AB5 SER D 55 ASN D 84 1 30 HELIX 15 AB6 THR D 90 LEU D 102 1 13 HELIX 16 AB7 PRO D 103 SER D 124 1 22 HELIX 17 AB8 ARG E 49 SER E 57 1 9 HELIX 18 AB9 ARG E 63 LYS E 79 1 17 HELIX 19 AC1 GLN E 85 ALA E 114 1 30 HELIX 20 AC2 MET E 120 ARG E 132 1 13 HELIX 21 AC3 ASN F 25 ILE F 29 5 5 HELIX 22 AC4 THR F 30 GLY F 41 1 12 HELIX 23 AC5 SER F 47 ALA F 76 1 30 HELIX 24 AC6 THR F 82 GLN F 93 1 12 HELIX 25 AC7 THR G 16 GLY G 22 1 7 HELIX 26 AC8 PRO G 26 GLY G 37 1 12 HELIX 27 AC9 ALA G 45 ASN G 73 1 29 HELIX 28 AD1 ILE G 79 ASP G 90 1 12 HELIX 29 AD2 ASP G 90 GLY G 98 1 9 HELIX 30 AD3 TYR H 37 HIS H 49 1 13 HELIX 31 AD4 SER H 55 ASN H 84 1 30 HELIX 32 AD5 THR H 90 LEU H 102 1 13 HELIX 33 AD6 PRO H 103 SER H 124 1 22 SHEET 1 AA1 2 CYS A 83 PHE A 84 0 SHEET 2 AA1 2 THR B 80 VAL B 81 1 O VAL B 81 N CYS 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 LEU B 97 TYR B 98 0 SHEET 2 AA3 2 THR G 101 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 88 ILE D 89 1 O ILE D 89 N ARG C 42 SHEET 1 AA5 2 ARG C 77 ILE C 78 0 SHEET 2 AA5 2 GLY D 53 ILE D 54 1 O GLY D 53 N ILE C 78 SHEET 1 AA6 2 THR C 101 ILE C 102 0 SHEET 2 AA6 2 LEU F 97 TYR F 98 1 O TYR F 98 N THR C 101 SHEET 1 AA7 2 CYS E 83 PHE E 84 0 SHEET 2 AA7 2 THR F 80 VAL F 81 1 O VAL F 81 N CYS 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 88 ILE H 89 1 O ILE H 89 N ARG G 42 SHEET 1 AB1 2 ARG G 77 ILE G 78 0 SHEET 2 AB1 2 GLY H 53 ILE H 54 1 O GLY H 53 N ILE G 78 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