PDB Short entry for 2B2U HEADER PEPTIDE BINDING PROTEIN 19-SEP-05 2B2U TITLE TANDEM CHROMODOMAINS OF HUMAN CHD1 COMPLEXED WITH HISTONE H3 TAIL TITLE 2 CONTAINING TRIMETHYLLYSINE 4 AND DIMETHYLARGININE 2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN 1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 268-443; COMPND 5 SYNONYM: CHD-1; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: CHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN 1; COMPND 9 CHAIN: C; COMPND 10 FRAGMENT: RESIDUES 268-373; COMPND 11 SYNONYM: CHD-1; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: HISTONE H3; COMPND 15 CHAIN: D; COMPND 16 FRAGMENT: RESIDUES 1-15; COMPND 17 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: CHD1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET11A; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: CHD1; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 17 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PET11A; SOURCE 21 MOL_ID: 3; SOURCE 22 SYNTHETIC: YES; SOURCE 23 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN HOMO SAPIENS SOURCE 24 (HUMANS). KEYWDS CHD, CHROMODOMAIN, THREE STRANDED ANTIPARALLEL BETA SHEET, ALPHA KEYWDS 2 HELIX LINKER, HISTONE H3, ASYMMETRIC DIMETHYLARGININE, KEYWDS 3 TRIMETHYLLYSINE, PEPTIDE BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.F.FLANAGAN IV,L.-Z.MI,M.CHRUSZCZ,M.CYMBOROWSKI,K.L.CLINES,Y.KIM, AUTHOR 2 W.MINOR,F.RASTINEJAD,S.KHORASANIZADEH REVDAT 7 15-NOV-23 2B2U 1 REMARK REVDAT 6 23-AUG-23 2B2U 1 REMARK REVDAT 5 13-APR-22 2B2U 1 AUTHOR JRNL SEQADV SEQRES REVDAT 5 2 1 LINK REVDAT 4 11-OCT-17 2B2U 1 REMARK REVDAT 3 06-NOV-13 2B2U 1 HETATM VERSN REVDAT 2 24-FEB-09 2B2U 1 VERSN REVDAT 1 27-DEC-05 2B2U 0 JRNL AUTH J.F.FLANAGAN,L.Z.MI,M.CHRUSZCZ,M.CYMBOROWSKI,K.L.CLINES, JRNL AUTH 2 Y.KIM,W.MINOR,F.RASTINEJAD,S.KHORASANIZADEH JRNL TITL DOUBLE CHROMODOMAINS COOPERATE TO RECOGNIZE THE METHYLATED JRNL TITL 2 HISTONE H3 TAIL. JRNL REF NATURE V. 438 1181 2005 JRNL REFN ISSN 0028-0836 JRNL PMID 16372014 JRNL DOI 10.1038/NATURE04290 REMARK 2 REMARK 2 RESOLUTION. 2.95 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) : 2.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 203.00 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.4 REMARK 3 NUMBER OF REFLECTIONS : 11120 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.238 REMARK 3 FREE R VALUE : 0.290 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.600 REMARK 3 FREE R VALUE TEST SET COUNT : 796 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3568 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.87 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 9.71100 REMARK 3 B22 (A**2) : -6.18200 REMARK 3 B33 (A**2) : -3.52900 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -7.07500 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.860 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 10.00 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 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2B2U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-OCT-05. REMARK 100 THE DEPOSITION ID IS D_1000034606. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-APR-05 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID 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 : DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11356 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.950 REMARK 200 RESOLUTION RANGE LOW (A) : 32.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.5 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.11100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 70.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.37800 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.110 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2B2T REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4% PEG3350, 0.05M HEPES, PH 8.0, 10MM REMARK 280 BTP, 12.5MM NACL, 5MM TCEP, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 283K, PH 8.00 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 55.99200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.37650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 55.99200 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 27.37650 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 4 CHAIN(S). ACCORDING TO AUTHORS, THE REMARK 300 BIOLOGICAL UNIT IS UNKNOWN. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 MET A 1 REMARK 465 LYS A 2 REMARK 465 LYS A 3 REMARK 465 HIS A 4 REMARK 465 HIS A 5 REMARK 465 HIS A 6 REMARK 465 HIS A 7 REMARK 465 HIS A 8 REMARK 465 HIS A 9 REMARK 465 GLU A 10 REMARK 465 GLU A 11 REMARK 465 GLU A 12 REMARK 465 LYS A 51 REMARK 465 ASN A 52 REMARK 465 MET B 1 REMARK 465 LYS B 2 REMARK 465 LYS B 3 REMARK 465 HIS B 4 REMARK 465 HIS B 5 REMARK 465 HIS B 6 REMARK 465 HIS B 7 REMARK 465 HIS B 8 REMARK 465 HIS B 9 REMARK 465 GLU B 10 REMARK 465 ASN B 52 REMARK 465 SER B 144 REMARK 465 ALA B 145 REMARK 465 LYS B 186 REMARK 465 LYS B 187 REMARK 465 MET C 1 REMARK 465 LYS C 2 REMARK 465 LYS C 3 REMARK 465 HIS C 4 REMARK 465 HIS C 5 REMARK 465 HIS C 6 REMARK 465 HIS C 7 REMARK 465 HIS C 8 REMARK 465 HIS C 9 REMARK 465 GLU C 10 REMARK 465 GLU C 11 REMARK 465 GLU C 12 REMARK 465 GLU C 100 REMARK 465 THR C 101 REMARK 465 LYS C 102 REMARK 465 ARG C 103 REMARK 465 TRP C 104 REMARK 465 LEU C 105 REMARK 465 LYS C 106 REMARK 465 ASN C 107 REMARK 465 ALA C 108 REMARK 465 SER C 109 REMARK 465 PRO C 110 REMARK 465 GLU C 111 REMARK 465 ASP C 112 REMARK 465 VAL C 113 REMARK 465 GLU C 114 REMARK 465 TYR C 115 REMARK 465 THR D 6 REMARK 465 ALA D 7 REMARK 465 ARG D 8 REMARK 465 LYS D 9 REMARK 465 SER D 10 REMARK 465 THR D 11 REMARK 465 GLY D 12 REMARK 465 GLY D 13 REMARK 465 LYS D 14 REMARK 465 ALA D 15 REMARK 465 TYR D 16 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 GLU B 11 CG CD OE1 OE2 REMARK 470 PHE B 13 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS B 51 CG CD CE NZ REMARK 470 GLN B 142 CG CD OE1 NE2 REMARK 470 ARG B 185 CG CD NE CZ NH1 NH2 REMARK 470 PHE C 13 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS C 51 CG CD CE NZ REMARK 470 LYS C 53 CG CD CE NZ REMARK 470 ASP C 98 CG OD1 OD2 REMARK 470 GLN C 99 CG CD OE1 NE2 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 GLU B 181 CB PHE B 183 1.89 REMARK 500 NH2 ARG C 26 O ALA C 47 1.90 REMARK 500 O LEU B 170 N SER B 172 2.04 REMARK 500 O GLY B 168 N LEU B 170 2.13 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 ALA A 47 CB - CA - C ANGL. DEV. = -12.5 DEGREES REMARK 500 ALA A 47 N - CA - C ANGL. DEV. = 18.9 DEGREES REMARK 500 ALA B 47 CB - CA - C ANGL. DEV. = -12.9 DEGREES REMARK 500 ALA B 47 N - CA - C ANGL. DEV. = 18.3 DEGREES REMARK 500 ASN B 84 CB - CA - C ANGL. DEV. = -24.7 DEGREES REMARK 500 VAL B 85 N - CA - CB ANGL. DEV. = -14.9 DEGREES REMARK 500 PRO B 159 C - N - CA ANGL. DEV. = 9.7 DEGREES REMARK 500 PHE C 13 N - CA - C ANGL. DEV. = 18.3 DEGREES REMARK 500 GLU C 14 N - CA - C ANGL. DEV. = 23.0 DEGREES REMARK 500 LYS C 53 N - CA - C ANGL. DEV. = -17.4 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 THR A 33 -9.41 -51.10 REMARK 500 PHE A 49 -93.85 -68.91 REMARK 500 GLU A 54 129.79 -11.80 REMARK 500 SER A 109 163.04 -48.62 REMARK 500 GLN A 119 0.49 -56.45 REMARK 500 ARG A 135 133.46 -177.90 REMARK 500 ALA A 138 152.72 166.96 REMARK 500 SER A 144 175.18 -51.56 REMARK 500 ARG A 185 18.12 -68.07 REMARK 500 LYS A 186 76.42 -109.35 REMARK 500 PHE B 13 122.37 158.61 REMARK 500 ALA B 41 -75.87 -58.60 REMARK 500 ASP B 42 -98.56 -82.73 REMARK 500 PRO B 45 -17.86 -47.56 REMARK 500 PHE B 49 132.16 0.75 REMARK 500 GLU B 54 152.25 163.97 REMARK 500 THR B 79 -37.10 -32.96 REMARK 500 GLN B 82 6.08 -58.89 REMARK 500 MET B 88 -0.86 -59.38 REMARK 500 TYR B 130 -29.81 -34.85 REMARK 500 ARG B 135 125.60 -170.02 REMARK 500 ALA B 169 -62.27 52.14 REMARK 500 LEU B 170 -100.59 -68.01 REMARK 500 ILE B 171 -56.39 7.10 REMARK 500 GLU B 181 -101.67 -68.04 REMARK 500 TYR B 182 -135.93 25.80 REMARK 500 PHE B 183 22.63 82.99 REMARK 500 GLU C 14 68.66 67.44 REMARK 500 ARG C 18 141.47 -179.45 REMARK 500 THR C 33 4.62 -66.79 REMARK 500 GLU C 50 136.29 167.32 REMARK 500 LYS C 51 82.13 -56.69 REMARK 500 ASN C 52 -4.16 -176.42 REMARK 500 GLU C 54 67.74 -103.13 REMARK 500 ASN C 84 45.40 75.62 REMARK 500 LYS C 95 26.06 -67.02 REMARK 500 DA2 D 2 99.91 101.82 REMARK 500 THR D 3 -165.53 -116.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 TYR B 182 PHE B 183 139.79 REMARK 500 M3L D 4 GLN D 5 -124.93 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1KNA RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF CHROMO DOMAIN OF HP1 COMPLEXED WITH HISTONE H3 REMARK 900 TAIL CONTAINING DIMETHYLLYSINE 9 REMARK 900 RELATED ID: 1KNE RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF CHROMO DOMAIN OF HP1 COMPLEXED WITH HISTONE H3 REMARK 900 TAIL CONTAINING TRIMETHYLLYSINE 9 REMARK 900 RELATED ID: 1Q3L RELATED DB: PDB REMARK 900 CHROMODOMAIN OF HP1 COMPLEXED WITH HISTONE H3 TAIL CONTAINING REMARK 900 MONOMETHYLLYSINE 9 REMARK 900 RELATED ID: 1PDQ RELATED DB: PDB REMARK 900 POLYCOMB CHROMODOMAIN COMPLEXED WITH THE HISTONE H3 TAIL CONTAINING REMARK 900 TRIMETHYLLYSINE 27 REMARK 900 RELATED ID: 2B2T RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE TANDEM CHROMODOMAINS OF HUMAN CHD1 REMARK 900 COMPLEXED WITH HISTONE H3 TAIL CONTAINING TRIMETHYLLYSINE 4 AND REMARK 900 PHOSPHOTHREONINE 3 REMARK 900 RELATED ID: 2B2V RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE ANALYSIS OF HUMAN CHD1 CHROMODOMAINS 1 AND 2 REMARK 900 BOUND TO HISTONE H3 RESI 1-15 MEK4 REMARK 900 RELATED ID: 2B2W RELATED DB: PDB REMARK 900 TANDEM CHROMODOMAINS OF HUMAN CHD1 COMPLEXED WITH HISTONE H3 TAIL REMARK 900 CONTAINING TRIMETHYLLYSINE 4 REMARK 900 RELATED ID: 2B2Y RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE TANDEM CHROMODOMAINS OF HUMAN CHD1 REMARK 999 REMARK 999 SEQUENCE REMARK 999 C-TERMINAL TYROSINE AT POSITION 16 IN CHAIN D DOES NOT REMARK 999 EXIST IN HISTONE 3 NATURALLY DBREF 2B2U A 10 185 UNP O14646 CHD1_HUMAN 268 443 DBREF 2B2U B 10 185 UNP O14646 CHD1_HUMAN 268 443 DBREF 2B2U C 10 115 UNP O14646 CHD1_HUMAN 268 373 DBREF 2B2U D 1 15 UNP P68431 H31_HUMAN 1 15 SEQADV 2B2U MET A 1 UNP O14646 CLONING ARTIFACT SEQADV 2B2U LYS A 2 UNP O14646 CLONING ARTIFACT SEQADV 2B2U LYS A 3 UNP O14646 CLONING ARTIFACT SEQADV 2B2U HIS A 4 UNP O14646 EXPRESSION TAG SEQADV 2B2U HIS A 5 UNP O14646 EXPRESSION TAG SEQADV 2B2U HIS A 6 UNP O14646 EXPRESSION TAG SEQADV 2B2U HIS A 7 UNP O14646 EXPRESSION TAG SEQADV 2B2U HIS A 8 UNP O14646 EXPRESSION TAG SEQADV 2B2U HIS A 9 UNP O14646 EXPRESSION TAG SEQADV 2B2U LYS A 186 UNP O14646 CLONING ARTIFACT SEQADV 2B2U LYS A 187 UNP O14646 CLONING ARTIFACT SEQADV 2B2U MET B 1 UNP O14646 CLONING ARTIFACT SEQADV 2B2U LYS B 2 UNP O14646 CLONING ARTIFACT SEQADV 2B2U LYS B 3 UNP O14646 CLONING ARTIFACT SEQADV 2B2U HIS B 4 UNP O14646 EXPRESSION TAG SEQADV 2B2U HIS B 5 UNP O14646 EXPRESSION TAG SEQADV 2B2U HIS B 6 UNP O14646 EXPRESSION TAG SEQADV 2B2U HIS B 7 UNP O14646 EXPRESSION TAG SEQADV 2B2U HIS B 8 UNP O14646 EXPRESSION TAG SEQADV 2B2U HIS B 9 UNP O14646 EXPRESSION TAG SEQADV 2B2U LYS B 186 UNP O14646 CLONING ARTIFACT SEQADV 2B2U LYS B 187 UNP O14646 CLONING ARTIFACT SEQADV 2B2U MET C 1 UNP O14646 CLONING ARTIFACT SEQADV 2B2U LYS C 2 UNP O14646 CLONING ARTIFACT SEQADV 2B2U LYS C 3 UNP O14646 CLONING ARTIFACT SEQADV 2B2U HIS C 4 UNP O14646 EXPRESSION TAG SEQADV 2B2U HIS C 5 UNP O14646 EXPRESSION TAG SEQADV 2B2U HIS C 6 UNP O14646 EXPRESSION TAG SEQADV 2B2U HIS C 7 UNP O14646 EXPRESSION TAG SEQADV 2B2U HIS C 8 UNP O14646 EXPRESSION TAG SEQADV 2B2U HIS C 9 UNP O14646 EXPRESSION TAG SEQADV 2B2U DA2 D 2 UNP P68431 ARG 2 MODIFIED RESIDUE SEQADV 2B2U M3L D 4 UNP P68431 LYS 4 MODIFIED RESIDUE SEQADV 2B2U TYR D 16 UNP P68431 SEE REMARK 999 SEQRES 1 A 187 MET LYS LYS HIS HIS HIS HIS HIS HIS GLU GLU GLU PHE SEQRES 2 A 187 GLU THR ILE GLU ARG PHE MET ASP CYS ARG ILE GLY ARG SEQRES 3 A 187 LYS GLY ALA THR GLY ALA THR THR THR ILE TYR ALA VAL SEQRES 4 A 187 GLU ALA ASP GLY ASP PRO ASN ALA GLY PHE GLU LYS ASN SEQRES 5 A 187 LYS GLU PRO GLY GLU ILE GLN TYR LEU ILE LYS TRP LYS SEQRES 6 A 187 GLY TRP SER HIS ILE HIS ASN THR TRP GLU THR GLU GLU SEQRES 7 A 187 THR LEU LYS GLN GLN ASN VAL ARG GLY MET LYS LYS LEU SEQRES 8 A 187 ASP ASN TYR LYS LYS LYS ASP GLN GLU THR LYS ARG TRP SEQRES 9 A 187 LEU LYS ASN ALA SER PRO GLU ASP VAL GLU TYR TYR ASN SEQRES 10 A 187 CYS GLN GLN GLU LEU THR ASP ASP LEU HIS LYS GLN TYR SEQRES 11 A 187 GLN ILE VAL GLY ARG ILE ILE ALA HIS SER ASN GLN LYS SEQRES 12 A 187 SER ALA ALA GLY TYR PRO ASP TYR TYR CYS LYS TRP GLN SEQRES 13 A 187 GLY LEU PRO TYR SER GLU CYS SER TRP GLU ASP GLY ALA SEQRES 14 A 187 LEU ILE SER LYS LYS PHE GLN ALA CYS ILE ASP GLU TYR SEQRES 15 A 187 PHE SER ARG LYS LYS SEQRES 1 B 187 MET LYS LYS HIS HIS HIS HIS HIS HIS GLU GLU GLU PHE SEQRES 2 B 187 GLU THR ILE GLU ARG PHE MET ASP CYS ARG ILE GLY ARG SEQRES 3 B 187 LYS GLY ALA THR GLY ALA THR THR THR ILE TYR ALA VAL SEQRES 4 B 187 GLU ALA ASP GLY ASP PRO ASN ALA GLY PHE GLU LYS ASN SEQRES 5 B 187 LYS GLU PRO GLY GLU ILE GLN TYR LEU ILE LYS TRP LYS SEQRES 6 B 187 GLY TRP SER HIS ILE HIS ASN THR TRP GLU THR GLU GLU SEQRES 7 B 187 THR LEU LYS GLN GLN ASN VAL ARG GLY MET LYS LYS LEU SEQRES 8 B 187 ASP ASN TYR LYS LYS LYS ASP GLN GLU THR LYS ARG TRP SEQRES 9 B 187 LEU LYS ASN ALA SER PRO GLU ASP VAL GLU TYR TYR ASN SEQRES 10 B 187 CYS GLN GLN GLU LEU THR ASP ASP LEU HIS LYS GLN TYR SEQRES 11 B 187 GLN ILE VAL GLY ARG ILE ILE ALA HIS SER ASN GLN LYS SEQRES 12 B 187 SER ALA ALA GLY TYR PRO ASP TYR TYR CYS LYS TRP GLN SEQRES 13 B 187 GLY LEU PRO TYR SER GLU CYS SER TRP GLU ASP GLY ALA SEQRES 14 B 187 LEU ILE SER LYS LYS PHE GLN ALA CYS ILE ASP GLU TYR SEQRES 15 B 187 PHE SER ARG LYS LYS SEQRES 1 C 115 MET LYS LYS HIS HIS HIS HIS HIS HIS GLU GLU GLU PHE SEQRES 2 C 115 GLU THR ILE GLU ARG PHE MET ASP CYS ARG ILE GLY ARG SEQRES 3 C 115 LYS GLY ALA THR GLY ALA THR THR THR ILE TYR ALA VAL SEQRES 4 C 115 GLU ALA ASP GLY ASP PRO ASN ALA GLY PHE GLU LYS ASN SEQRES 5 C 115 LYS GLU PRO GLY GLU ILE GLN TYR LEU ILE LYS TRP LYS SEQRES 6 C 115 GLY TRP SER HIS ILE HIS ASN THR TRP GLU THR GLU GLU SEQRES 7 C 115 THR LEU LYS GLN GLN ASN VAL ARG GLY MET LYS LYS LEU SEQRES 8 C 115 ASP ASN TYR LYS LYS LYS ASP GLN GLU THR LYS ARG TRP SEQRES 9 C 115 LEU LYS ASN ALA SER PRO GLU ASP VAL GLU TYR SEQRES 1 D 16 ALA DA2 THR M3L GLN THR ALA ARG LYS SER THR GLY GLY SEQRES 2 D 16 LYS ALA TYR MODRES 2B2U DA2 D 2 ARG NG,NG-DIMETHYL-L-ARGININE MODRES 2B2U M3L D 4 LYS N-TRIMETHYLLYSINE HET DA2 D 2 13 HET M3L D 4 12 HETNAM DA2 NG,NG-DIMETHYL-L-ARGININE HETNAM M3L N-TRIMETHYLLYSINE HETSYN DA2 ADMA FORMUL 4 DA2 C8 H18 N4 O2 FORMUL 4 M3L C9 H21 N2 O2 1+ HELIX 1 1 GLY A 31 THR A 34 5 4 HELIX 2 2 THR A 35 GLY A 43 1 9 HELIX 3 3 SER A 68 ASN A 72 5 5 HELIX 4 4 THR A 76 GLN A 83 1 8 HELIX 5 5 MET A 88 LEU A 105 1 18 HELIX 6 6 SER A 109 TYR A 130 1 22 HELIX 7 7 PRO A 159 CYS A 163 5 5 HELIX 8 8 ASP A 167 ARG A 185 1 19 HELIX 9 9 GLY B 31 THR B 34 5 4 HELIX 10 10 THR B 35 ASP B 42 1 8 HELIX 11 11 SER B 68 ASN B 72 5 5 HELIX 12 12 THR B 76 GLN B 82 1 7 HELIX 13 13 LYS B 89 ALA B 108 1 20 HELIX 14 14 SER B 109 TYR B 130 1 22 HELIX 15 15 PRO B 159 CYS B 163 5 5 HELIX 16 16 ILE B 171 TYR B 182 1 12 HELIX 17 17 GLY C 31 THR C 34 5 4 HELIX 18 18 THR C 35 GLY C 43 1 9 HELIX 19 19 SER C 68 ASN C 72 5 5 HELIX 20 20 THR C 76 ASN C 84 1 9 HELIX 21 21 GLY C 87 LYS C 95 1 9 SHEET 1 A 3 ILE A 16 GLY A 25 0 SHEET 2 A 3 GLU A 57 TRP A 64 -1 O LEU A 61 N ASP A 21 SHEET 3 A 3 THR A 73 GLU A 75 -1 O GLU A 75 N TYR A 60 SHEET 1 B 3 VAL A 133 HIS A 139 0 SHEET 2 B 3 TYR A 151 TRP A 155 -1 O LYS A 154 N ARG A 135 SHEET 3 B 3 SER A 164 GLU A 166 -1 O SER A 164 N CYS A 153 SHEET 1 C 3 ILE B 16 ILE B 24 0 SHEET 2 C 3 ILE B 58 TRP B 64 -1 O LEU B 61 N ASP B 21 SHEET 3 C 3 THR B 73 GLU B 75 -1 O THR B 73 N ILE B 62 SHEET 1 D 3 VAL B 133 HIS B 139 0 SHEET 2 D 3 TYR B 151 TRP B 155 -1 O LYS B 154 N GLY B 134 SHEET 3 D 3 SER B 164 GLU B 166 -1 O GLU B 166 N TYR B 151 SHEET 1 E 3 ILE C 16 PHE C 19 0 SHEET 2 E 3 GLU C 57 TRP C 64 -1 O LYS C 63 N GLU C 17 SHEET 3 E 3 ARG C 23 GLY C 25 -1 N ARG C 23 O GLN C 59 SHEET 1 F 3 ILE C 16 PHE C 19 0 SHEET 2 F 3 GLU C 57 TRP C 64 -1 O LYS C 63 N GLU C 17 SHEET 3 F 3 THR C 73 GLU C 75 -1 O GLU C 75 N TYR C 60 LINK C ALA D 1 N DA2 D 2 1555 1555 1.32 LINK C DA2 D 2 N THR D 3 1555 1555 1.33 LINK C THR D 3 N M3L D 4 1555 1555 1.32 LINK C M3L D 4 N GLN D 5 1555 1555 1.34 CRYST1 111.984 54.753 100.274 90.00 112.32 90.00 C 1 2 1 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 0.008930 0.000000 0.003666 0.00000 SCALE2 0.000000 0.018264 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010780 0.00000