HEADER TRANSCRIPTION/DNA BINDING PROTEIN 30-MAR-09 3GV6 TITLE CRYSTAL STRUCTURE OF HUMAN CHROMOBOX HOMOLOG 6 (CBX6) WITH H3K9 TITLE 2 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHROMOBOX PROTEIN HOMOLOG 6; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 8-65; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: HISTONE H3K9ME3 PEPTIDE; COMPND 8 CHAIN: B; COMPND 9 FRAGMENT: UNP RESIDUES 2-16; COMPND 10 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: CBX6; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: P28A-LIC; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: XENOPUS LAEVIS; SOURCE 14 ORGANISM_COMMON: AFRICAN CLAWED FROG; SOURCE 15 ORGANISM_TAXID: 8355; SOURCE 16 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN XENOPUS LAEVIS KEYWDS CHROMOBOX HOMOLOG, CBX6, H3K9 PEPTIDE, SGC, CHROMATIN REGULATOR, KEYWDS 2 NUCLEUS, PHOSPHOPROTEIN, REPRESSOR, TRANSCRIPTION, TRANSCRIPTION KEYWDS 3 REGULATION, CHROMOSOMAL PROTEIN, DNA-BINDING, NUCLEOSOME CORE, KEYWDS 4 TRANSCRIPTION-DNA BINDING PROTEIN COMPLEX, STRUCTURAL GENOMICS, KEYWDS 5 STRUCTURAL GENOMICS CONSORTIUM EXPDTA X-RAY DIFFRACTION AUTHOR A.DONG,M.F.AMAYA,Z.LI,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 3 06-SEP-23 3GV6 1 LINK REVDAT 2 06-APR-11 3GV6 1 JRNL SOURCE REVDAT 1 21-APR-09 3GV6 0 JRNL AUTH L.KAUSTOV,H.OUYANG,M.AMAYA,A.LEMAK,N.NADY,S.DUAN,G.A.WASNEY, JRNL AUTH 2 Z.LI,M.VEDADI,M.SCHAPIRA,J.MIN,C.H.ARROWSMITH JRNL TITL RECOGNITION AND SPECIFICITY DETERMINANTS OF THE HUMAN CBX JRNL TITL 2 CHROMODOMAINS. JRNL REF J.BIOL.CHEM. V. 286 521 2011 JRNL REFN ISSN 0021-9258 JRNL PMID 21047797 JRNL DOI 10.1074/JBC.M110.191411 REMARK 2 REMARK 2 RESOLUTION. 1.76 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) : 1.76 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.85 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 5870 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) : 0.214 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.900 REMARK 3 FREE R VALUE TEST SET COUNT : 437 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) : 1.76 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.81 REMARK 3 REFLECTION IN BIN (WORKING SET) : 353 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.17 REMARK 3 BIN R VALUE (WORKING SET) : 0.4080 REMARK 3 BIN FREE R VALUE SET COUNT : 27 REMARK 3 BIN FREE R VALUE : 0.3070 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 521 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 49 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.22 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.86000 REMARK 3 B22 (A**2) : -0.69000 REMARK 3 B33 (A**2) : 2.55000 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): 0.153 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.151 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.100 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.142 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.940 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 537 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 723 ; 1.390 ; 1.947 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 62 ; 5.914 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 27 ;29.611 ;21.481 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 97 ;14.161 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;13.723 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 76 ; 0.116 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 400 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 231 ; 0.187 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 358 ; 0.303 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 36 ; 0.158 ; 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): 38 ; 0.223 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 12 ; 0.136 ; 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): 327 ; 0.879 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 500 ; 1.418 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 254 ; 1.939 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 223 ; 2.999 ; 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 3GV6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-MAR-09. REMARK 100 THE DEPOSITION ID IS D_1000052346. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-MAR-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E+ SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : VERIMAX HR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6339 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.760 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : 0.08000 REMARK 200 FOR THE DATA SET : 10.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.76 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.82 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 0.47300 REMARK 200 R SYM FOR SHELL (I) : 0.47300 REMARK 200 FOR SHELL : 1.660 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 3DM1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 29.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 14% PEG 3350, 0.2M MGCL2, 0.1M HEPES, REMARK 280 PH7.5 , VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 297K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 14.03750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 26.68800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.22700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 26.68800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 14.03750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.22700 REMARK 290 SMTRY3 4 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: 1260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4280 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 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 ARG A 64 REMARK 465 GLU A 65 REMARK 465 ALA B 1 REMARK 465 ARG B 2 REMARK 465 THR B 3 REMARK 465 LYS B 4 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 GLU A 8 CG CD OE1 OE2 REMARK 470 LYS A 18 CD CE NZ REMARK 470 ILE A 37 CD1 REMARK 470 SER A 51 OG REMARK 470 LYS A 60 CG CD CE NZ DBREF 3GV6 A 8 65 UNP O95503 CBX6_HUMAN 8 65 DBREF 3GV6 B 1 15 UNP Q92133 Q92133_XENLA 1 15 SEQRES 1 A 58 GLU ARG VAL PHE ALA ALA GLU SER ILE ILE LYS ARG ARG SEQRES 2 A 58 ILE ARG LYS GLY ARG ILE GLU TYR LEU VAL LYS TRP LYS SEQRES 3 A 58 GLY TRP ALA ILE LYS TYR SER THR TRP GLU PRO GLU GLU SEQRES 4 A 58 ASN ILE LEU ASP SER ARG LEU ILE ALA ALA PHE GLU GLN SEQRES 5 A 58 LYS GLU ARG GLU ARG GLU SEQRES 1 B 15 ALA ARG THR LYS GLN THR ALA ARG M3L SER THR GLY GLY SEQRES 2 B 15 LYS ALA MODRES 3GV6 M3L B 9 LYS N-TRIMETHYLLYSINE HET M3L B 9 12 HETNAM M3L N-TRIMETHYLLYSINE FORMUL 2 M3L C9 H21 N2 O2 1+ FORMUL 3 HOH *49(H2 O) HELIX 1 1 ALA A 36 SER A 40 5 5 HELIX 2 2 GLU A 46 ILE A 48 5 3 HELIX 3 3 ASP A 50 GLU A 63 1 14 SHEET 1 A 4 THR A 41 PRO A 44 0 SHEET 2 A 4 ARG A 25 TRP A 32 -1 N VAL A 30 O THR A 41 SHEET 3 A 4 ARG A 9 ARG A 22 -1 N ARG A 20 O GLU A 27 SHEET 4 A 4 THR B 6 M3L B 9 -1 O M3L B 9 N ARG A 9 LINK C ARG B 8 N M3L B 9 1555 1555 1.33 LINK C M3L B 9 N SER B 10 1555 1555 1.32 CRYST1 28.075 40.454 53.376 90.00 90.00 90.00 P 21 21 21 4 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 0.035619 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024719 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018735 0.00000