HEADER TRANSCRIPTION 10-JUL-09 3I8Z
TITLE CRYSTAL STRUCTURE OF HUMAN CHROMOBOX HOMOLOG 4 (CBX4)
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: E3 SUMO-PROTEIN LIGASE CBX4;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: CHROMO DOMAIN: UNP RESIDUES 8-62;
COMPND 5 SYNONYM: CHROMOBOX PROTEIN HOMOLOG 4, POLYCOMB 2 HOMOLOG, PC2, HPC2;
COMPND 6 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: CBX4;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-V2R-PRARE2;
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID
KEYWDS CHROMOBOX HOMOLOG 4, CBX4, STRUCTURAL GENOMICS, STRUCTURAL GENOMICS
KEYWDS 2 CONSORTIUM, SGC, ALTERNATIVE SPLICING, CHROMATIN REGULATOR,
KEYWDS 3 ISOPEPTIDE BOND, NUCLEUS, PHOSPHOPROTEIN, REPRESSOR, TRANSCRIPTION,
KEYWDS 4 TRANSCRIPTION REGULATION, UBL CONJUGATION, UBL CONJUGATION PATHWAY
EXPDTA X-RAY DIFFRACTION
AUTHOR M.F.AMAYA,L.ZHIHONG,P.LOPPNAU,I.KOZIERADZKI,A.M.EDWARDS,
AUTHOR 2 C.H.ARROWSMITH,J.WEIGELT,C.BOUNTRA,A.BOCHKAREV,J.MIN,H.OUYANG,
AUTHOR 3 STRUCTURAL GENOMICS CONSORTIUM (SGC)
REVDAT 4 06-SEP-23 3I8Z 1 REMARK
REVDAT 3 01-NOV-17 3I8Z 1 REMARK
REVDAT 2 22-SEP-09 3I8Z 1 SOURCE
REVDAT 1 25-AUG-09 3I8Z 0
JRNL AUTH L.ZHIHONG,M.F.AMAYA,P.LOPPNAU,I.KOZIERADZKI,A.M.EDWARDS,
JRNL AUTH 2 C.H.ARROWSMITH,J.WEIGELT,C.BOUNTRA,A.BOCHKAREV,J.MIN,
JRNL AUTH 3 H.OUYANG,STRUCTURAL GENOMICS CONSORTIUM (SGC)
JRNL TITL CRYSTAL STRUCTURE OF HUMAN CHROMOBOX HOMOLOG 4 (CBX4)
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 2
REMARK 2 RESOLUTION. 1.51 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.2.0019
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.51
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6
REMARK 3 NUMBER OF REFLECTIONS : 8902
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING + TEST SET) : 0.229
REMARK 3 R VALUE (WORKING SET) : 0.228
REMARK 3 FREE R VALUE : 0.255
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800
REMARK 3 FREE R VALUE TEST SET COUNT : 425
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 20
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.51
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.55
REMARK 3 REFLECTION IN BIN (WORKING SET) : 622
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.94
REMARK 3 BIN R VALUE (WORKING SET) : 0.2670
REMARK 3 BIN FREE R VALUE SET COUNT : 31
REMARK 3 BIN FREE R VALUE : 0.3120
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 437
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 0
REMARK 3 SOLVENT ATOMS : 59
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.57
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.48000
REMARK 3 B22 (A**2) : -0.48000
REMARK 3 B33 (A**2) : 0.97000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.00000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.096
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.094
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.054
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.375
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.940
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.924
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 449 ; 0.010 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 605 ; 1.227 ; 1.944
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 49 ; 6.123 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 24 ;29.433 ;22.083
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 85 ;15.416 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 6 ;16.367 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 60 ; 0.089 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 342 ; 0.005 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 168 ; 0.218 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 303 ; 0.318 ; 0.200
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 32 ; 0.125 ; 0.200
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 35 ; 0.175 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 10 ; 0.197 ; 0.200
REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 256 ; 0.954 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 406 ; 1.473 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 229 ; 2.380 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 199 ; 3.985 ; 4.500
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 NCS RESTRAINTS STATISTICS
REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : MASK
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.40
REMARK 3 ION PROBE RADIUS : 0.80
REMARK 3 SHRINKAGE RADIUS : 0.80
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING
REMARK 3 POSITIONS
REMARK 4
REMARK 4 3I8Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-JUL-09.
REMARK 100 THE DEPOSITION ID IS D_1000054114.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : NULL
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 5.6
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : CHESS
REMARK 200 BEAMLINE : A1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.97800
REMARK 200 MONOCHROMATOR : BENT TRIANGULAR ASYMMETRIC CUT
REMARK 200 SI(111)
REMARK 200 OPTICS : RH-COATED SI MIRROR FOR VERTICAL
REMARK 200 FOCUSING
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8902
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500
REMARK 200 RESOLUTION RANGE LOW (A) : 40.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4
REMARK 200 DATA REDUNDANCY : 6.900
REMARK 200 R MERGE (I) : 0.08200
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.9000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55
REMARK 200 COMPLETENESS FOR SHELL (%) : 86.8
REMARK 200 DATA REDUNDANCY IN SHELL : 4.60
REMARK 200 R MERGE FOR SHELL (I) : 0.22400
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: AMORE
REMARK 200 STARTING MODEL: PDB ENTRY 3H91
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 40.41
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 20% ISOPROPANOL, 20% PEG 4000, 0.1 M
REMARK 280 NA CITRATE PH 5.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE
REMARK 280 298K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2
REMARK 290 3555 -Y,X+1/2,Z+1/4
REMARK 290 4555 Y+1/2,-X,Z+3/4
REMARK 290 5555 X+1/2,Y+1/2,Z+1/2
REMARK 290 6555 -X,-Y,Z
REMARK 290 7555 -Y+1/2,X,Z+3/4
REMARK 290 8555 Y,-X+1/2,Z+1/4
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 29.30300
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 29.30300
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 16.40650
REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 29.30300
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 8.20325
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 29.30300
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 24.60975
REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 29.30300
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 29.30300
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 16.40650
REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 29.30300
REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 24.60975
REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 29.30300
REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 8.20325
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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
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 GLU A 8
REMARK 465 HIS A 9
REMARK 465 VAL A 10
REMARK 465 GLU A 61
REMARK 465 ARG A 62
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3I8Y RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF HUMAN CHROMOBOX HOMOLOG 2 (CBX2)IN COMPLEX
REMARK 900 WITH H3K27(ME)3 PEPTIDE
REMARK 900 RELATED ID: 3I90 RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF HUMAN CHROMOBOX HOMOLOG 6 (CBX6) WITH H3K27
REMARK 900 PEPTIDE
REMARK 900 RELATED ID: 3I91 RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF HUMAN CHROMOBOX HOMOLOG 8 (CBX8) WITH H3K9
REMARK 900 PEPTIDE
DBREF 3I8Z A 8 62 UNP O00257 CBX4_HUMAN 8 62
SEQRES 1 A 55 GLU HIS VAL PHE ALA VAL GLU SER ILE GLU LYS LYS ARG
SEQRES 2 A 55 ILE ARG LYS GLY ARG VAL GLU TYR LEU VAL LYS TRP ARG
SEQRES 3 A 55 GLY TRP SER PRO LYS TYR ASN THR TRP GLU PRO GLU GLU
SEQRES 4 A 55 ASN ILE LEU ASP PRO ARG LEU LEU ILE ALA PHE GLN ASN
SEQRES 5 A 55 ARG GLU ARG
FORMUL 2 HOH *59(H2 O)
HELIX 1 1 SER A 36 ASN A 40 5 5
HELIX 2 2 GLU A 45 LEU A 49 1 5
HELIX 3 3 ASP A 50 LEU A 54 5 5
SHEET 1 A 3 VAL A 13 ARG A 22 0
SHEET 2 A 3 ARG A 25 TRP A 32 -1 O LEU A 29 N GLU A 17
SHEET 3 A 3 THR A 41 PRO A 44 -1 O GLU A 43 N TYR A 28
CRYST1 58.606 58.606 32.813 90.00 90.00 90.00 I 41 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 0.017063 0.000000 0.000000 0.00000
SCALE2 0.000000 0.017063 0.000000 0.00000
SCALE3 0.000000 0.000000 0.030476 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
