HEADER PROTEIN BINDING 10-APR-18 6D08 TITLE CRYSTAL STRUCTURE OF AN ENGINEERED BUMP-HOLE COMPLEX OF MUTANT HUMAN TITLE 2 CHROMOBOX HOMOLOG 1 (CBX1) WITH H3K9BN PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHROMOBOX PROTEIN HOMOLOG 1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 20-73; COMPND 5 SYNONYM: HP1HSBETA, HETEROCHROMATIN PROTEIN 1 HOMOLOG BETA, HP1 BETA, COMPND 6 HETEROCHROMATIN PROTEIN P25, M31, MODIFIER 1 PROTEIN, P25BETA; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: HISTONE H3.1; COMPND 11 CHAIN: C, D; COMPND 12 FRAGMENT: H3K9BN PEPTIDE (UNP RESIDUES 2-16); COMPND 13 SYNONYM: HISTONE H3/A, HISTONE H3/B, HISTONE H3/C, HISTONE H3/D, COMPND 14 HISTONE H3/F, HISTONE H3/H, HISTONE H3/I, HISTONE H3/J, HISTONE H3/K, COMPND 15 HISTONE H3/L; COMPND 16 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: CBX1, CBX; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606 KEYWDS LYSINE MODIFICATION, CHROMODOMAIN, BUMP-HOLE, EPIGENETICS, PROTEIN KEYWDS 2 BINDING EXPDTA X-RAY DIFFRACTION AUTHOR S.ARORA,W.S.HORNE,K.ISLAM REVDAT 5 15-NOV-23 6D08 1 LINK REVDAT 4 04-OCT-23 6D08 1 REMARK REVDAT 3 01-JAN-20 6D08 1 REMARK REVDAT 2 23-OCT-19 6D08 1 JRNL REVDAT 1 10-APR-19 6D08 0 JRNL AUTH S.ARORA,W.S.HORNE,K.ISLAM JRNL TITL ENGINEERING METHYLLYSINE WRITERS AND READERS FOR JRNL TITL 2 ALLELE-SPECIFIC REGULATION OF PROTEIN-PROTEIN INTERACTIONS. JRNL REF J.AM.CHEM.SOC. V. 141 15466 2019 JRNL REFN ESSN 1520-5126 JRNL PMID 31518125 JRNL DOI 10.1021/JACS.9B05725 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.28 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.2 REMARK 3 NUMBER OF REFLECTIONS : 7130 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.229 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.070 REMARK 3 FREE R VALUE TEST SET COUNT : 718 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 23.2849 - 3.5877 0.95 1353 154 0.2005 0.2081 REMARK 3 2 3.5877 - 2.8493 0.94 1324 154 0.2267 0.2460 REMARK 3 3 2.8493 - 2.4896 0.89 1275 137 0.2791 0.3114 REMARK 3 4 2.4896 - 2.2622 0.87 1225 128 0.2550 0.3535 REMARK 3 5 2.2622 - 2.1002 0.87 1235 145 0.2448 0.3070 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.600 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.002 1044 REMARK 3 ANGLE : 0.445 1394 REMARK 3 CHIRALITY : 0.041 144 REMARK 3 PLANARITY : 0.002 176 REMARK 3 DIHEDRAL : 17.643 621 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6D08 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-APR-18. REMARK 100 THE DEPOSITION ID IS D_1000233819. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-AUG-17 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 SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS HTC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7149 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 25.950 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.4 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.04700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.14200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.800 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 6D07 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M CITRATE, PH 5.0, 3 M AMMONIUM REMARK 280 SULFATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 1660 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4470 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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: 1640 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 THR A 55 REMARK 465 ALA C 1 REMARK 465 ARG C 2 REMARK 465 THR C 11 REMARK 465 GLY C 12 REMARK 465 GLY C 13 REMARK 465 LYS C 14 REMARK 465 ALA C 15 REMARK 465 NH2 C 16 REMARK 465 GLN B 53 REMARK 465 LYS B 54 REMARK 465 THR B 55 REMARK 465 ALA D 1 REMARK 465 ARG D 2 REMARK 465 GLY D 12 REMARK 465 GLY D 13 REMARK 465 LYS D 14 REMARK 465 ALA D 15 REMARK 465 NH2 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 LYS A 54 CG CD CE NZ REMARK 470 THR C 3 OG1 CG2 REMARK 470 SER B 52 OG REMARK 470 THR D 3 N CB OG1 CG2 REMARK 470 THR D 11 OG1 CG2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 D 101 DBREF 6D08 A 2 55 UNP P83916 CBX1_HUMAN 20 73 DBREF 6D08 C 1 15 UNP P68431 H31_HUMAN 2 16 DBREF 6D08 B 2 55 UNP P83916 CBX1_HUMAN 20 73 DBREF 6D08 D 1 15 UNP P68431 H31_HUMAN 2 16 SEQADV 6D08 GLY A 1 UNP P83916 EXPRESSION TAG SEQADV 6D08 PHE A 3 UNP P83916 TYR 21 ENGINEERED MUTATION SEQADV 6D08 GLY A 27 UNP P83916 PHE 45 ENGINEERED MUTATION SEQADV 6D08 NH2 C 16 UNP P68431 AMIDATION SEQADV 6D08 GLY B 1 UNP P83916 EXPRESSION TAG SEQADV 6D08 PHE B 3 UNP P83916 TYR 21 ENGINEERED MUTATION SEQADV 6D08 GLY B 27 UNP P83916 PHE 45 ENGINEERED MUTATION SEQADV 6D08 NH2 D 16 UNP P68431 AMIDATION SEQRES 1 A 55 GLY GLU PHE VAL VAL GLU LYS VAL LEU ASP ARG ARG VAL SEQRES 2 A 55 VAL LYS GLY LYS VAL GLU TYR LEU LEU LYS TRP LYS GLY SEQRES 3 A 55 GLY SER ASP GLU ASP ASN THR TRP GLU PRO GLU GLU ASN SEQRES 4 A 55 LEU ASP CYS PRO ASP LEU ILE ALA GLU PHE LEU GLN SER SEQRES 5 A 55 GLN LYS THR SEQRES 1 C 16 ALA ARG THR LYS GLN THR ALA ARG FQA SER THR GLY GLY SEQRES 2 C 16 LYS ALA NH2 SEQRES 1 B 55 GLY GLU PHE VAL VAL GLU LYS VAL LEU ASP ARG ARG VAL SEQRES 2 B 55 VAL LYS GLY LYS VAL GLU TYR LEU LEU LYS TRP LYS GLY SEQRES 3 B 55 GLY SER ASP GLU ASP ASN THR TRP GLU PRO GLU GLU ASN SEQRES 4 B 55 LEU ASP CYS PRO ASP LEU ILE ALA GLU PHE LEU GLN SER SEQRES 5 B 55 GLN LYS THR SEQRES 1 D 16 ALA ARG THR LYS GLN THR ALA ARG FQA SER THR GLY GLY SEQRES 2 D 16 LYS ALA NH2 MODRES 6D08 FQA C 9 LYS MODIFIED RESIDUE MODRES 6D08 FQA D 9 LYS MODIFIED RESIDUE HET FQA C 9 16 HET FQA D 9 16 HET GOL A 101 6 HET GOL A 102 6 HET SO4 C 101 5 HET GOL B 101 6 HET GOL B 102 6 HET SO4 D 101 5 HETNAM FQA N~6~-BENZYL-L-LYSINE HETNAM GOL GLYCEROL HETNAM SO4 SULFATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 FQA 2(C13 H20 N2 O2) FORMUL 5 GOL 4(C3 H8 O3) FORMUL 7 SO4 2(O4 S 2-) FORMUL 11 HOH *38(H2 O) HELIX 1 AA1 SER A 28 ASN A 32 5 5 HELIX 2 AA2 CYS A 42 LYS A 54 1 13 HELIX 3 AA3 SER B 28 ASN B 32 5 5 HELIX 4 AA4 CYS B 42 SER B 52 1 11 SHEET 1 AA1 5 THR A 33 PRO A 36 0 SHEET 2 AA1 5 LYS A 17 TRP A 24 -1 N LEU A 22 O THR A 33 SHEET 3 AA1 5 GLU A 2 VAL A 14 -1 N ARG A 12 O GLU A 19 SHEET 4 AA1 5 THR C 6 ARG C 8 -1 O ALA C 7 N PHE A 3 SHEET 5 AA1 5 LEU A 40 ASP A 41 -1 N ASP A 41 O THR C 6 SHEET 1 AA2 5 THR B 33 PRO B 36 0 SHEET 2 AA2 5 LYS B 17 TRP B 24 -1 N TYR B 20 O GLU B 35 SHEET 3 AA2 5 GLU B 2 VAL B 14 -1 N LEU B 9 O LEU B 21 SHEET 4 AA2 5 THR D 6 ARG D 8 -1 O ALA D 7 N PHE B 3 SHEET 5 AA2 5 LEU B 40 ASP B 41 -1 N ASP B 41 O THR D 6 LINK C ARG C 8 N FQA C 9 1555 1555 1.33 LINK C FQA C 9 N SER C 10 1555 1555 1.33 LINK C ARG D 8 N FQA D 9 1555 1555 1.33 LINK C FQA D 9 N SER D 10 1555 1555 1.33 SITE 1 AC1 5 ASN A 32 GOL A 102 HOH A 204 LYS B 25 SITE 2 AC1 5 GLY B 26 SITE 1 AC2 2 ARG A 12 GOL A 101 SITE 1 AC3 3 LYS A 54 ARG B 11 ARG C 8 SITE 1 AC4 3 LYS A 25 ARG B 12 GOL B 102 SITE 1 AC5 7 LYS A 25 GLY A 26 GLU B 30 ASN B 32 SITE 2 AC5 7 GOL B 101 HOH B 207 HOH B 213 SITE 1 AC6 3 ARG A 11 ARG D 8 HOH D 201 CRYST1 33.191 34.052 35.267 76.79 89.89 65.10 P 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 0.030128 -0.013983 0.003568 0.00000 SCALE2 0.000000 0.032375 -0.008394 0.00000 SCALE3 0.000000 0.000000 0.029293 0.00000