HEADER TRANSCRIPTION 14-NOV-11 4A7J
TITLE SYMMETRIC DIMETHYLATION OF H3 ARGININE 2 IS A NOVEL HISTONE MARK THAT
TITLE 2 SUPPORTS EUCHROMATIN MAINTENANCE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: WD REPEAT-CONTAINING PROTEIN 5;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: RESIDUES 21-334;
COMPND 5 SYNONYM: BMP2-INDUCED 3-KB GENE PROTEIN;
COMPND 6 ENGINEERED: YES;
COMPND 7 MOL_ID: 2;
COMPND 8 MOLECULE: HISTONE H3.1T;
COMPND 9 CHAIN: B;
COMPND 10 FRAGMENT: HISTONE TAIL, RESIDUES 1-16;
COMPND 11 SYNONYM: H3/T, H3T, H3/G;
COMPND 12 ENGINEERED: YES;
COMPND 13 OTHER_DETAILS: SYMMETRICALLY DIMETHYLATED ARGININE 2
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21;
SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA;
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PGEX;
SOURCE 11 MOL_ID: 2;
SOURCE 12 SYNTHETIC: YES;
SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 14 ORGANISM_COMMON: HUMAN;
SOURCE 15 ORGANISM_TAXID: 9606
KEYWDS TRANSCRIPTION, HISTONE METHYLATION
EXPDTA X-RAY DIFFRACTION
AUTHOR V.MIGLIORI,J.MULLER,S.PHALKE,D.LOW,M.BEZZI,W.CHUENMOK,J.GUNARATNE,
AUTHOR 2 P.CAPASSO,C.BASSI,V.CECATIELLO,A.DEMARCO,W.BLACKSTOCK,V.KUZNETSOV,
AUTHOR 3 B.AMATI,M.MAPELLI,E.GUCCIONE
REVDAT 3 20-DEC-23 4A7J 1 LINK
REVDAT 2 15-FEB-12 4A7J 1 JRNL
REVDAT 1 11-JAN-12 4A7J 0
JRNL AUTH V.MIGLIORI,J.MULLER,S.PHALKE,D.LOW,M.BEZZI,W.CHUENMOK,
JRNL AUTH 2 S.K.SAHU,J.GUNARATNE,P.CAPASSO,C.BASSI,V.CECATIELLO,
JRNL AUTH 3 A.DEMARCO,W.BLACKSTOCK,V.KUZNETSOV,B.AMATI,M.MAPELLI,
JRNL AUTH 4 E.GUCCIONE
JRNL TITL SYMMETRIC DIMETHYLATION OF H3R2 IS A NEWLY IDENTIFIED
JRNL TITL 2 HISTONE MARK THAT SUPPORTS EUCHROMATIN MAINTENANCE
JRNL REF NAT.STRUCT.MOL.BIOL. V. 19 136 2012
JRNL REFN ISSN 1545-9993
JRNL PMID 22231400
JRNL DOI 10.1038/NSMB.2209
REMARK 2
REMARK 2 RESOLUTION. 1.90 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CNS 1.2
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 : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.31
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1249102.870
REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.3
REMARK 3 NUMBER OF REFLECTIONS : 22754
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING SET) : 0.184
REMARK 3 FREE R VALUE : 0.222
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900
REMARK 3 FREE R VALUE TEST SET COUNT : 1109
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 6
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.90
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3373
REMARK 3 BIN R VALUE (WORKING SET) : 0.2020
REMARK 3 BIN FREE R VALUE : 0.2570
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.80
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 171
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.020
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2401
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 0
REMARK 3 SOLVENT ATOMS : 244
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 5.20
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.40
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 1.94000
REMARK 3 B22 (A**2) : 0.95000
REMARK 3 B33 (A**2) : -2.89000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 1.33000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.19
REMARK 3 ESD FROM SIGMAA (A) : 0.10
REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00
REMARK 3
REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.24
REMARK 3 ESD FROM C-V SIGMAA (A) : 0.18
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.016
REMARK 3 BOND ANGLES (DEGREES) : 1.800
REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.60
REMARK 3 IMPROPER ANGLES (DEGREES) : 1.080
REMARK 3
REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
REMARK 3 MAIN-CHAIN BOND (A**2) : 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 : FLAT MODEL
REMARK 3 KSOL : 0.35
REMARK 3 BSOL : 35.05
REMARK 3
REMARK 3 NCS MODEL : NONE
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 : 2MR_080229.PARAM
REMARK 3 PARAMETER FILE 3 : WATER.PARAM
REMARK 3 PARAMETER FILE 4 : NULL
REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP
REMARK 3 TOPOLOGY FILE 2 : 2MR_080229.TOP
REMARK 3 TOPOLOGY FILE 3 : WATER.TOP
REMARK 3 TOPOLOGY FILE 4 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED
REMARK 4
REMARK 4 4A7J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-NOV-11.
REMARK 100 THE DEPOSITION ID IS D_1290050225.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 28-JAN-08
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 7.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : ESRF
REMARK 200 BEAMLINE : ID14-1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.937
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC CCD
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23998
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900
REMARK 200 RESOLUTION RANGE LOW (A) : 30.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0
REMARK 200 DATA REDUNDANCY : 3.600
REMARK 200 R MERGE (I) : 0.01000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.6000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97
REMARK 200 COMPLETENESS FOR SHELL (%) : 90.0
REMARK 200 DATA REDUNDANCY IN SHELL : 2.60
REMARK 200 R MERGE FOR SHELL (I) : 0.03000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.400
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: PDB ENTRY 2H13
REMARK 200
REMARK 200 REMARK: NONE
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 41.00
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH 7.5; 60 MM AMMONIUM
REMARK 280 SULPHATE; 30% PEG 3350
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,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 23.40000
REMARK 290 SMTRY3 2 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: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 1120 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 11880 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.7 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 GLY A 17
REMARK 465 PRO A 18
REMARK 465 LEU A 19
REMARK 465 GLY A 20
REMARK 465 SER A 21
REMARK 465 SER A 22
REMARK 465 ALA A 23
REMARK 465 THR A 24
REMARK 465 GLN A 25
REMARK 465 SER A 26
REMARK 465 LYS A 27
REMARK 465 PRO A 28
REMARK 465 THR A 29
REMARK 465 PRO A 30
REMARK 465 VAL A 31
REMARK 465 MET B 0
REMARK 465 ARG B 8
REMARK 465 LYS B 9
REMARK 465 SER B 10
REMARK 465 THR B 11
REMARK 465 GLY B 12
REMARK 465 GLY B 13
REMARK 465 LYS B 14
REMARK 465 ALA B 15
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 ALA B 7 CA C O CB
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 HOH A 2165 O HOH A 2167 0.00
REMARK 500 O HOH A 2048 O HOH A 2049 0.01
REMARK 500 O HOH A 2164 O HOH A 2166 0.09
REMARK 500 O HOH A 2020 O HOH A 2022 0.10
REMARK 500 O HOH A 2056 O HOH A 2057 0.25
REMARK 500 O HOH A 2140 O HOH A 2141 0.26
REMARK 500 O HOH A 2008 O HOH A 2010 0.27
REMARK 500 O HOH A 2123 O HOH A 2126 0.27
REMARK 500 O HOH A 2112 O HOH A 2113 0.31
REMARK 500 O HOH A 2226 O HOH A 2227 0.32
REMARK 500 O HOH A 2125 O HOH A 2127 0.45
REMARK 500 NZ LYS A 331 O HOH A 2053 0.47
REMARK 500 CB ALA A 65 O HOH A 2041 0.48
REMARK 500 O HOH A 2238 O HOH A 2239 0.49
REMARK 500 O GLY A 127 O HOH A 2110 0.56
REMARK 500 O ALA A 65 O HOH A 2042 1.09
REMARK 500 CA ALA A 65 O HOH A 2041 1.74
REMARK 500 C GLY A 127 O HOH A 2110 1.84
REMARK 500 CE LYS A 331 O HOH A 2053 1.94
REMARK 500 C ALA A 65 O HOH A 2042 2.02
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15
REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A
REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375
REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE
REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.
REMARK 500
REMARK 500 DISTANCE CUTOFF:
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE
REMARK 500 O HOH A 2055 O HOH A 2078 2555 0.13
REMARK 500 O HOH A 2128 O HOH B 2004 2546 0.19
REMARK 500 O HOH A 2037 O HOH A 2154 2555 0.25
REMARK 500 O HOH A 2138 O HOH B 2003 2546 0.25
REMARK 500 O HOH A 2119 O HOH A 2225 2545 0.29
REMARK 500 O HOH A 2118 O HOH A 2237 2545 0.31
REMARK 500 O HOH A 2021 O HOH A 2129 2556 0.33
REMARK 500 O HOH A 2032 O HOH A 2155 2555 0.36
REMARK 500 O HOH A 2133 O HOH A 2228 2545 0.47
REMARK 500 O HOH A 2124 O HOH A 2231 2546 0.63
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS
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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3)
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 RES CSSEQI ATM2 DEVIATION
REMARK 500 ALA A 65 N ALA A 65 CA -0.120
REMARK 500 ALA A 65 CA ALA A 65 CB 0.452
REMARK 500 GLY A 77 CA GLY A 77 C 0.147
REMARK 500 LYS A 78 N LYS A 78 CA 0.130
REMARK 500 GLY A 127 C GLY A 127 O 0.166
REMARK 500 LYS A 331 CE LYS A 331 NZ 0.183
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 65 N - CA - CB ANGL. DEV. = -10.2 DEGREES
REMARK 500 GLY A 77 O - C - N ANGL. DEV. = 14.1 DEGREES
REMARK 500 GLY A 127 CA - C - N ANGL. DEV. = 13.4 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 ASN A 34 58.94 -141.91
REMARK 500 LEU A 234 47.66 -77.78
REMARK 500 LYS A 325 14.84 59.54
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2H13 RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF WDR5/HISTONE H3 COMPLEX
REMARK 900 RELATED ID: 2H6Q RELATED DB: PDB
REMARK 900 HISTONE H3 RECOGNITION AND PRESENTATION BY THE WDR5 MODULEOF THE
REMARK 900 MLL1 COMPLEX
REMARK 900 RELATED ID: 2G99 RELATED DB: PDB
REMARK 900 STRUCTURAL BASIS FOR THE SPECIFIC RECOGNITION OF METHYLATEDHISTONE
REMARK 900 H3 LYSINE 4 BY THE WD-40 PROTEIN WDR5
REMARK 900 RELATED ID: 2CO0 RELATED DB: PDB
REMARK 900 WDR5 AND UNMODIFIED HISTONE H3 COMPLEX AT 2.25 ANGSTROM
REMARK 900 RELATED ID: 2H6K RELATED DB: PDB
REMARK 900 HISTONE H3 RECOGNITION AND PRESENTATION BY THE WDR5 MODULEOF THE
REMARK 900 MLL1 COMPLEX
REMARK 900 RELATED ID: 2CNX RELATED DB: PDB
REMARK 900 WDR5 AND HISTONE H3 LYSINE 4 DIMETHYL COMPLEX AT 2. 1 ANGSTROM
REMARK 900 RELATED ID: 2YBP RELATED DB: PDB
REMARK 900 JMJD2A COMPLEXED WITH R-2-HYDROXYGLUTARATE AND HISTONE H3K36ME3
REMARK 900 PEPTIDE (30-41)
REMARK 900 RELATED ID: 2YBS RELATED DB: PDB
REMARK 900 JMJD2A COMPLEXED WITH S-2-HYDROXYGLUTARATE AND HISTONE H3K36ME3
REMARK 900 PEPTIDE (30-41)
REMARK 900 RELATED ID: 2G9A RELATED DB: PDB
REMARK 900 STRUCTURAL BASIS FOR THE SPECIFIC RECOGNITION OF METHYLATEDHISTONE
REMARK 900 H3 LYSINE 4 BY THE WD-40 PROTEIN WDR5
REMARK 900 RELATED ID: 2V1D RELATED DB: PDB
REMARK 900 STRUCTURAL BASIS OF LSD1-COREST SELECTIVITY IN HISTONE H3
REMARK 900 RECOGNITION
REMARK 900 RELATED ID: 2H6N RELATED DB: PDB
REMARK 900 HISTONE H3 RECOGNITION AND PRESENTATION BY THE WDR5 MODULEOF THE
REMARK 900 MLL1 COMPLEX
REMARK 900 RELATED ID: 2GNQ RELATED DB: PDB
REMARK 900 STRUCTURE OF WDR5
REMARK 900 RELATED ID: 2H68 RELATED DB: PDB
REMARK 900 HISTONE H3 RECOGNITION AND PRESENTATION BY THE WDR5 MODULEOF THE
REMARK 900 MLL1 COMPLEX
REMARK 900 RELATED ID: 2H14 RELATED DB: PDB
REMARK 900 CRYSTAL OF WDR5 (APO-FORM)
DBREF 4A7J A 21 334 UNP P61964 WDR5_HUMAN 21 334
DBREF 4A7J B 0 15 UNP Q16695 H31T_HUMAN 1 16
SEQADV 4A7J GLY A 17 UNP P61964 EXPRESSION TAG
SEQADV 4A7J PRO A 18 UNP P61964 EXPRESSION TAG
SEQADV 4A7J LEU A 19 UNP P61964 EXPRESSION TAG
SEQADV 4A7J GLY A 20 UNP P61964 EXPRESSION TAG
SEQRES 1 A 318 GLY PRO LEU GLY SER SER ALA THR GLN SER LYS PRO THR
SEQRES 2 A 318 PRO VAL LYS PRO ASN TYR ALA LEU LYS PHE THR LEU ALA
SEQRES 3 A 318 GLY HIS THR LYS ALA VAL SER SER VAL LYS PHE SER PRO
SEQRES 4 A 318 ASN GLY GLU TRP LEU ALA SER SER SER ALA ASP LYS LEU
SEQRES 5 A 318 ILE LYS ILE TRP GLY ALA TYR ASP GLY LYS PHE GLU LYS
SEQRES 6 A 318 THR ILE SER GLY HIS LYS LEU GLY ILE SER ASP VAL ALA
SEQRES 7 A 318 TRP SER SER ASP SER ASN LEU LEU VAL SER ALA SER ASP
SEQRES 8 A 318 ASP LYS THR LEU LYS ILE TRP ASP VAL SER SER GLY LYS
SEQRES 9 A 318 CYS LEU LYS THR LEU LYS GLY HIS SER ASN TYR VAL PHE
SEQRES 10 A 318 CYS CYS ASN PHE ASN PRO GLN SER ASN LEU ILE VAL SER
SEQRES 11 A 318 GLY SER PHE ASP GLU SER VAL ARG ILE TRP ASP VAL LYS
SEQRES 12 A 318 THR GLY LYS CYS LEU LYS THR LEU PRO ALA HIS SER ASP
SEQRES 13 A 318 PRO VAL SER ALA VAL HIS PHE ASN ARG ASP GLY SER LEU
SEQRES 14 A 318 ILE VAL SER SER SER TYR ASP GLY LEU CYS ARG ILE TRP
SEQRES 15 A 318 ASP THR ALA SER GLY GLN CYS LEU LYS THR LEU ILE ASP
SEQRES 16 A 318 ASP ASP ASN PRO PRO VAL SER PHE VAL LYS PHE SER PRO
SEQRES 17 A 318 ASN GLY LYS TYR ILE LEU ALA ALA THR LEU ASP ASN THR
SEQRES 18 A 318 LEU LYS LEU TRP ASP TYR SER LYS GLY LYS CYS LEU LYS
SEQRES 19 A 318 THR TYR THR GLY HIS LYS ASN GLU LYS TYR CYS ILE PHE
SEQRES 20 A 318 ALA ASN PHE SER VAL THR GLY GLY LYS TRP ILE VAL SER
SEQRES 21 A 318 GLY SER GLU ASP ASN LEU VAL TYR ILE TRP ASN LEU GLN
SEQRES 22 A 318 THR LYS GLU ILE VAL GLN LYS LEU GLN GLY HIS THR ASP
SEQRES 23 A 318 VAL VAL ILE SER THR ALA CYS HIS PRO THR GLU ASN ILE
SEQRES 24 A 318 ILE ALA SER ALA ALA LEU GLU ASN ASP LYS THR ILE LYS
SEQRES 25 A 318 LEU TRP LYS SER ASP CYS
SEQRES 1 B 16 MET ALA 2MR THR LYS GLN THR ALA ARG LYS SER THR GLY
SEQRES 2 B 16 GLY LYS ALA
MODRES 4A7J 2MR B 2 ARG N3, N4-DIMETHYLARGININE
HET 2MR B 2 13
HETNAM 2MR N3, N4-DIMETHYLARGININE
FORMUL 2 2MR C8 H18 N4 O2
FORMUL 3 HOH *244(H2 O)
SHEET 1 AA 4 ALA A 36 LEU A 41 0
SHEET 2 AA 4 ILE A 327 LYS A 331 -1 O ILE A 327 N LEU A 41
SHEET 3 AA 4 ILE A 315 ALA A 320 -1 O ILE A 316 N TRP A 330
SHEET 4 AA 4 VAL A 304 CYS A 309 -1 N ILE A 305 O ALA A 319
SHEET 1 AB 4 VAL A 48 PHE A 53 0
SHEET 2 AB 4 TRP A 59 SER A 64 -1 O ALA A 61 N LYS A 52
SHEET 3 AB 4 LEU A 68 GLY A 73 -1 O LEU A 68 N SER A 64
SHEET 4 AB 4 PHE A 79 SER A 84 -1 N GLU A 80 O ILE A 71
SHEET 1 AC 4 ILE A 90 TRP A 95 0
SHEET 2 AC 4 LEU A 101 SER A 106 -1 O VAL A 103 N ALA A 94
SHEET 3 AC 4 THR A 110 ASP A 115 -1 O THR A 110 N SER A 106
SHEET 4 AC 4 CYS A 121 LYS A 126 -1 N LEU A 122 O ILE A 113
SHEET 1 AD 4 VAL A 132 PHE A 137 0
SHEET 2 AD 4 LEU A 143 SER A 148 -1 O VAL A 145 N ASN A 136
SHEET 3 AD 4 VAL A 153 ASP A 157 -1 O ARG A 154 N SER A 146
SHEET 4 AD 4 CYS A 163 LEU A 167 -1 N LEU A 164 O ILE A 155
SHEET 1 AE 4 VAL A 174 PHE A 179 0
SHEET 2 AE 4 LEU A 185 SER A 190 -1 O VAL A 187 N HIS A 178
SHEET 3 AE 4 CYS A 195 ASP A 199 -1 O ARG A 196 N SER A 188
SHEET 4 AE 4 CYS A 205 LEU A 209 -1 N LEU A 206 O ILE A 197
SHEET 1 AF 4 VAL A 217 PHE A 222 0
SHEET 2 AF 4 TYR A 228 THR A 233 -1 O LEU A 230 N LYS A 221
SHEET 3 AF 4 THR A 237 ASP A 242 -1 O THR A 237 N THR A 233
SHEET 4 AF 4 LYS A 247 TYR A 252 -1 O LYS A 247 N ASP A 242
SHEET 1 AG 4 ALA A 264 SER A 267 0
SHEET 2 AG 4 TRP A 273 SER A 276 -1 O TRP A 273 N SER A 267
SHEET 3 AG 4 VAL A 283 ASN A 287 -1 O TYR A 284 N SER A 276
SHEET 4 AG 4 ILE A 293 LEU A 297 -1 N VAL A 294 O ILE A 285
LINK C ALA B 1 N 2MR B 2 1555 1555 1.33
LINK C 2MR B 2 N THR B 3 1555 1555 1.33
CRYST1 52.600 46.800 65.000 90.00 104.33 90.00 P 1 21 1 2
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 0.019011 0.000000 0.004857 0.00000
SCALE2 0.000000 0.021368 0.000000 0.00000
SCALE3 0.000000 0.000000 0.015879 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
