PDB Short entry for 3DM1 HEADER TRANSCRIPTION 30-JUN-08 3DM1 TITLE CRYSTAL STRUCTURE OF THE COMPLEX OF HUMAN CHROMOBOX HOMOLOG 3 (CBX3) TITLE 2 WITH PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHROMOBOX PROTEIN HOMOLOG 3; COMPND 3 CHAIN: A, C, E, G; COMPND 4 FRAGMENT: CHROMO 1 DOMAIN: RESIDUES 29-86; COMPND 5 SYNONYM: HETEROCHROMATIN PROTEIN 1 HOMOLOG GAMMA, HP1 GAMMA, MODIFIER COMPND 6 2 PROTEIN, HECH; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-9 SPECIFIC 3; COMPND 10 CHAIN: B, D, F, H; COMPND 11 FRAGMENT: UNP RESIDUES 179-190; COMPND 12 SYNONYM: HISTONE H3-K9 METHYLTRANSFERASE 3, H3-K9-HMTASE 3, COMPND 13 EUCHROMATIC HISTONE-LYSINE N-METHYLTRANSFERASE 2, HLA-B-ASSOCIATED COMPND 14 TRANSCRIPT 8, PROTEIN G9A, LYSINE N-METHYLTRANSFERASE 1C; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 GENE: CBX3; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 OTHER_DETAILS: SYNTHETIC PEPTIDE WITH THE SEQUENCE MATCHING THE SOURCE 13 RESIDUES 179-190 OF THE HUMAN HISTONE H3-K9 METHYLTRANSFERASE 3, SOURCE 14 EHMT2_HUMAN, UNP ENTRY Q96KQ7 KEYWDS CHROMOBOX HOMOLOG 3, STRUCTURAL GENOMICS, STRUCTURAL GENOMICS KEYWDS 2 CONSORTIUM, SGC, CHROMATIN REGULATOR, NUCLEUS, PHOSPHOPROTEIN, KEYWDS 3 REPRESSOR, TRANSCRIPTION, TRANSCRIPTION REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR M.F.AMAYA,M.RAVICHANDRAN,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 25-OCT-17 3DM1 1 REMARK REVDAT 3 23-JAN-13 3DM1 1 JRNL VERSN REVDAT 2 24-FEB-09 3DM1 1 VERSN REVDAT 1 19-AUG-08 3DM1 0 JRNL AUTH J.RUAN,H.OUYANG,M.F.AMAYA,M.RAVICHANDRAN,P.LOPPNAU,J.MIN, JRNL AUTH 2 J.ZANG JRNL TITL STRUCTURAL BASIS OF THE CHROMODOMAIN OF CBX3 BOUND TO JRNL TITL 2 METHYLATED PEPTIDES FROM HISTONE H1 AND G9A. JRNL REF PLOS ONE V. 7 35376 2012 JRNL REFN ESSN 1932-6203 JRNL PMID 22514736 JRNL DOI 10.1371/JOURNAL.PONE.0035376 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.10 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 17856 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) : 0.222 REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 908 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.47 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1218 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.62 REMARK 3 BIN R VALUE (WORKING SET) : 0.2700 REMARK 3 BIN FREE R VALUE SET COUNT : 76 REMARK 3 BIN FREE R VALUE : 0.4140 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2010 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 91 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.53 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.12000 REMARK 3 B22 (A**2) : 0.12000 REMARK 3 B33 (A**2) : -0.18000 REMARK 3 B12 (A**2) : 0.06000 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): 0.267 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.231 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.164 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.890 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.935 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.922 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2062 ; 0.021 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2792 ; 1.826 ; 1.953 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 238 ; 6.515 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 112 ;31.057 ;24.643 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 342 ;14.956 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;14.559 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 302 ; 0.118 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1562 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 766 ; 0.206 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1357 ; 0.312 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 111 ; 0.278 ; 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): 30 ; 0.180 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 13 ; 0.286 ; 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): 1251 ; 1.215 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1952 ; 2.072 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 941 ; 2.784 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 839 ; 4.211 ; 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 3DM1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-JUL-08. REMARK 100 THE DEPOSITION ID IS D_1000048206. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JUN-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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+ DW REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.28268 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17856 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 10.52 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 24.6300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.80 REMARK 200 R MERGE FOR SHELL (I) : 0.83600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.380 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXD REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5 MICROLITER OF THE PROTEIN SOLUTION REMARK 280 MIXED WITH WITH 1.5 MICROLITER OF THE RESERVOIR SOLUTION REMARK 280 CONTAINING 40% PEG 550 MME, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 73.52533 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 36.76267 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 36.76267 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 73.52533 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4, 5 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: 1160 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.4 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 350 REMARK 350 BIOMOLECULE: 2 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: 1040 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.6 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 3 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: 1100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4280 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.7 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F 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 350 REMARK 350 BIOMOLECULE: 4 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: 4350 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: G, H 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 350 REMARK 350 BIOMOLECULE: 5 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12970 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -62.1 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H 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 LYS A 81 REMARK 465 ALA A 82 REMARK 465 GLY A 83 REMARK 465 LYS A 84 REMARK 465 GLU A 85 REMARK 465 LYS A 86 REMARK 465 MET B 167 REMARK 465 SER B 168 REMARK 465 LYS B 169 REMARK 465 PRO B 170 REMARK 465 LYS C 81 REMARK 465 ALA C 82 REMARK 465 GLY C 83 REMARK 465 LYS C 84 REMARK 465 GLU C 85 REMARK 465 LYS C 86 REMARK 465 LYS D 159 REMARK 465 PRO D 170 REMARK 465 ALA E 82 REMARK 465 GLY E 83 REMARK 465 LYS E 84 REMARK 465 GLU E 85 REMARK 465 LYS E 86 REMARK 465 SER F 168 REMARK 465 LYS F 169 REMARK 465 PRO F 170 REMARK 465 ALA G 82 REMARK 465 GLY G 83 REMARK 465 LYS G 84 REMARK 465 GLU G 85 REMARK 465 LYS G 86 REMARK 465 THR H 166 REMARK 465 MET H 167 REMARK 465 SER H 168 REMARK 465 LYS H 169 REMARK 465 PRO H 170 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 ASN A 42 CG OD1 ND2 REMARK 470 LYS A 44 CG CD CE NZ REMARK 470 ARG B 164 CG CD NE CZ NH1 NH2 REMARK 470 ARG D 164 CG CD NE CZ NH1 NH2 REMARK 470 LYS D 169 CG CD CE NZ REMARK 470 VAL E 41 CG1 CG2 REMARK 470 ASN E 42 CG OD1 ND2 REMARK 470 LYS E 44 CG CD CE NZ REMARK 470 LYS E 50 CD CE NZ REMARK 470 LYS E 52 CE NZ REMARK 470 LYS E 81 CE NZ REMARK 470 LYS F 159 CG CD CE NZ REMARK 470 VAL F 160 CG1 CG2 REMARK 470 ARG F 164 CG CD NE CZ NH1 NH2 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 C 108 O HOH G 99 1.77 REMARK 500 O HOH G 87 O HOH G 99 1.90 REMARK 500 O GLN A 80 O HOH A 103 2.01 REMARK 500 NH2 ARG C 38 OD1 ASN C 78 2.15 REMARK 500 N GLU A 29 O HOH A 109 2.19 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 110 O HOH C 107 4565 2.00 REMARK 500 O HOH A 105 O HOH C 106 4565 2.18 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 MET F 167 CG MET F 167 SD -0.276 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 42 74.45 41.49 REMARK 500 ASN E 42 62.36 -158.30 REMARK 500 ASP E 58 67.02 -104.45 REMARK 500 CYS G 69 66.33 -157.87 REMARK 500 REMARK 500 REMARK: NULL DBREF 3DM1 A 29 86 UNP Q13185 CBX3_HUMAN 29 86 DBREF 3DM1 B 159 170 UNP Q96KQ7 EHMT2_HUMAN 179 190 DBREF 3DM1 C 29 86 UNP Q13185 CBX3_HUMAN 29 86 DBREF 3DM1 D 159 170 UNP Q96KQ7 EHMT2_HUMAN 179 190 DBREF 3DM1 E 29 86 UNP Q13185 CBX3_HUMAN 29 86 DBREF 3DM1 F 159 170 UNP Q96KQ7 EHMT2_HUMAN 179 190 DBREF 3DM1 G 29 86 UNP Q13185 CBX3_HUMAN 29 86 DBREF 3DM1 H 159 170 UNP Q96KQ7 EHMT2_HUMAN 179 190 SEQRES 1 A 58 GLU PHE VAL VAL GLU LYS VAL LEU ASP ARG ARG VAL VAL SEQRES 2 A 58 ASN GLY LYS VAL GLU TYR PHE LEU LYS TRP LYS GLY PHE SEQRES 3 A 58 THR ASP ALA ASP ASN THR TRP GLU PRO GLU GLU ASN LEU SEQRES 4 A 58 ASP CYS PRO GLU LEU ILE GLU ALA PHE LEU ASN SER GLN SEQRES 5 A 58 LYS ALA GLY LYS GLU LYS SEQRES 1 B 12 LYS VAL HIS ARG ALA ARG M3L THR MET SER LYS PRO SEQRES 1 C 58 GLU PHE VAL VAL GLU LYS VAL LEU ASP ARG ARG VAL VAL SEQRES 2 C 58 ASN GLY LYS VAL GLU TYR PHE LEU LYS TRP LYS GLY PHE SEQRES 3 C 58 THR ASP ALA ASP ASN THR TRP GLU PRO GLU GLU ASN LEU SEQRES 4 C 58 ASP CYS PRO GLU LEU ILE GLU ALA PHE LEU ASN SER GLN SEQRES 5 C 58 LYS ALA GLY LYS GLU LYS SEQRES 1 D 12 LYS VAL HIS ARG ALA ARG M3L THR MET SER LYS PRO SEQRES 1 E 58 GLU PHE VAL VAL GLU LYS VAL LEU ASP ARG ARG VAL VAL SEQRES 2 E 58 ASN GLY LYS VAL GLU TYR PHE LEU LYS TRP LYS GLY PHE SEQRES 3 E 58 THR ASP ALA ASP ASN THR TRP GLU PRO GLU GLU ASN LEU SEQRES 4 E 58 ASP CYS PRO GLU LEU ILE GLU ALA PHE LEU ASN SER GLN SEQRES 5 E 58 LYS ALA GLY LYS GLU LYS SEQRES 1 F 12 LYS VAL HIS ARG ALA ARG M3L THR MET SER LYS PRO SEQRES 1 G 58 GLU PHE VAL VAL GLU LYS VAL LEU ASP ARG ARG VAL VAL SEQRES 2 G 58 ASN GLY LYS VAL GLU TYR PHE LEU LYS TRP LYS GLY PHE SEQRES 3 G 58 THR ASP ALA ASP ASN THR TRP GLU PRO GLU GLU ASN LEU SEQRES 4 G 58 ASP CYS PRO GLU LEU ILE GLU ALA PHE LEU ASN SER GLN SEQRES 5 G 58 LYS ALA GLY LYS GLU LYS SEQRES 1 H 12 LYS VAL HIS ARG ALA ARG M3L THR MET SER LYS PRO MODRES 3DM1 M3L B 165 LYS N-TRIMETHYLLYSINE MODRES 3DM1 M3L D 165 LYS N-TRIMETHYLLYSINE MODRES 3DM1 M3L F 165 LYS N-TRIMETHYLLYSINE MODRES 3DM1 M3L H 165 LYS N-TRIMETHYLLYSINE HET M3L B 165 12 HET M3L D 165 12 HET M3L F 165 12 HET M3L H 165 12 HETNAM M3L N-TRIMETHYLLYSINE FORMUL 2 M3L 4(C9 H21 N2 O2 1+) FORMUL 9 HOH *91(H2 O) HELIX 1 1 THR A 55 ASN A 59 5 5 HELIX 2 2 GLU A 65 LEU A 67 5 3 HELIX 3 3 CYS A 69 SER A 79 1 11 HELIX 4 4 THR C 55 ASN C 59 5 5 HELIX 5 5 GLU C 65 LEU C 67 5 3 HELIX 6 6 CYS C 69 GLN C 80 1 12 HELIX 7 7 GLU E 65 LEU E 67 5 3 HELIX 8 8 CYS E 69 SER E 79 1 11 HELIX 9 9 THR G 55 ASN G 59 5 5 HELIX 10 10 GLU G 65 LEU G 67 5 3 HELIX 11 11 CYS G 69 SER G 79 1 11 SHEET 1 A 4 THR A 60 PRO A 63 0 SHEET 2 A 4 LYS A 44 TRP A 51 -1 N LEU A 49 O THR A 60 SHEET 3 A 4 PHE A 30 VAL A 41 -1 N LEU A 36 O PHE A 48 SHEET 4 A 4 ARG B 162 ALA B 163 -1 O ALA B 163 N PHE A 30 SHEET 1 B 3 VAL C 32 VAL C 41 0 SHEET 2 B 3 LYS C 44 TRP C 51 -1 O PHE C 48 N LEU C 36 SHEET 3 B 3 THR C 60 PRO C 63 -1 O GLU C 62 N TYR C 47 SHEET 1 C 4 ASN E 59 PRO E 63 0 SHEET 2 C 4 VAL E 45 TRP E 51 -1 N TYR E 47 O GLU E 62 SHEET 3 C 4 PHE E 30 VAL E 40 -1 N GLU E 33 O LYS E 50 SHEET 4 C 4 ARG F 162 ALA F 163 -1 O ALA F 163 N PHE E 30 SHEET 1 D 4 THR G 60 PRO G 63 0 SHEET 2 D 4 VAL G 45 TRP G 51 -1 N TYR G 47 O GLU G 62 SHEET 3 D 4 PHE G 30 VAL G 40 -1 N GLU G 33 O LYS G 50 SHEET 4 D 4 ARG H 162 ALA H 163 -1 O ALA H 163 N PHE G 30 SSBOND 1 CYS A 69 CYS C 69 1555 1555 2.14 SSBOND 2 CYS E 69 CYS G 69 1555 1555 2.13 LINK C ARG B 164 N M3L B 165 1555 1555 1.33 LINK C M3L B 165 N THR B 166 1555 1555 1.33 LINK C ARG D 164 N M3L D 165 1555 1555 1.33 LINK C M3L D 165 N THR D 166 1555 1555 1.34 LINK C ARG F 164 N M3L F 165 1555 1555 1.32 LINK C M3L F 165 N THR F 166 1555 1555 1.33 LINK C ARG H 164 N M3L H 165 1555 1555 1.33 CRYST1 83.671 83.671 110.288 90.00 90.00 120.00 P 32 2 1 24 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 0.011952 0.006900 0.000000 0.00000 SCALE2 0.000000 0.013800 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009067 0.00000