HEADER TRANSCRIPTION 26-JAN-10 3LJW TITLE CRYSTAL STRUCTURE OF THE SECOND BROMODOMAIN OF HUMAN POLYBROMO COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN POLYBROMO-1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: BROMODOMAIN 2 (UNP RESIDUES 174-293); COMPND 5 SYNONYM: HPB1, POLYBROMO-1D, BRG1-ASSOCIATED FACTOR 180, BAF180; 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: PB1, PBRM1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX 4T1 KEYWDS ALPHA HELIX, ALTERNATIVE SPLICING, BROMODOMAIN, CHROMATIN REGULATOR, KEYWDS 2 DNA-BINDING, NUCLEUS, PHOSPHOPROTEIN, TRANSCRIPTION, TRANSCRIPTION KEYWDS 3 REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR Z.CHARLOP-POWERS,M.M.ZHOU,L.ZENG,Q.ZHANG REVDAT 3 06-SEP-23 3LJW 1 REMARK LINK REVDAT 2 15-APR-20 3LJW 1 REMARK REVDAT 1 19-MAY-10 3LJW 0 JRNL AUTH Z.CHARLOP-POWERS,L.ZENG,Q.ZHANG,M.M.ZHOU JRNL TITL STRUCTURAL INSIGHTS INTO SELECTIVE HISTONE H3 RECOGNITION BY JRNL TITL 2 THE HUMAN POLYBROMO BROMODOMAIN 2. JRNL REF CELL RES. V. 20 529 2010 JRNL REFN ISSN 1001-0602 JRNL PMID 20368734 JRNL DOI 10.1038/CR.2010.43 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.5_2) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.34 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.070 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 3 NUMBER OF REFLECTIONS : 53142 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.610 REMARK 3 FREE R VALUE TEST SET COUNT : 1920 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 28.3446 - 3.2332 0.91 4959 184 0.1571 0.1757 REMARK 3 2 3.2332 - 2.5668 0.95 5192 196 0.1683 0.1775 REMARK 3 3 2.5668 - 2.2425 0.95 5165 195 0.1695 0.1826 REMARK 3 4 2.2425 - 2.0376 0.96 5233 202 0.1697 0.2228 REMARK 3 5 2.0376 - 1.8915 0.96 5203 191 0.1816 0.1997 REMARK 3 6 1.8915 - 1.7800 0.93 5075 190 0.1785 0.2165 REMARK 3 7 1.7800 - 1.6909 0.95 5151 187 0.1786 0.2230 REMARK 3 8 1.6909 - 1.6173 0.94 5128 197 0.1859 0.2051 REMARK 3 9 1.6173 - 1.5551 0.94 5141 191 0.1854 0.2090 REMARK 3 10 1.5551 - 1.5014 0.92 4975 187 0.1966 0.2185 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.38 REMARK 3 B_SOL : 48.31 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.38 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 : 0.006 1907 REMARK 3 ANGLE : 0.927 2575 REMARK 3 CHIRALITY : 0.058 291 REMARK 3 PLANARITY : 0.005 329 REMARK 3 DIHEDRAL : 13.029 707 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 3LJW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-JAN-10. REMARK 100 THE DEPOSITION ID IS D_1000057367. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JUN-09 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97854 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 130 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 59763 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.455 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 5.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06900 REMARK 200 FOR THE DATA SET : 35.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.51 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.57 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.21500 REMARK 200 FOR SHELL : 6.170 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: 3G0J REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 35% PEG 4000, 10 MM SODIUM ACETATE, PH REMARK 280 5.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,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 16.88367 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 33.76733 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: MONOMERIC 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 THR A 174 REMARK 465 GLU A 175 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 210 CG CD CE NZ REMARK 470 LYS A 214 CG CD CE NZ REMARK 470 LYS A 225 CG CD CE NZ REMARK 470 GLN A 235 CG CD OE1 NE2 REMARK 470 GLN A 238 CG CD OE1 NE2 REMARK 470 GLU A 288 CG CD OE1 OE2 REMARK 470 MET A 292 CG SD CE REMARK 470 GLN B 238 CG CD OE1 NE2 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 997 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 347 O REMARK 620 2 HOH B 635 O 78.6 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 999 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 998 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 997 DBREF 3LJW A 174 293 UNP Q86U86 PB1_HUMAN 174 293 DBREF 3LJW B 174 293 UNP Q86U86 PB1_HUMAN 174 293 SEQRES 1 A 120 THR GLU GLY SER SER PRO ALA TYR LEU LYS GLU ILE LEU SEQRES 2 A 120 GLU GLN LEU LEU GLU ALA ILE VAL VAL ALA THR ASN PRO SEQRES 3 A 120 SER GLY ARG LEU ILE SER GLU LEU PHE GLN LYS LEU PRO SEQRES 4 A 120 SER LYS VAL GLN TYR PRO ASP TYR TYR ALA ILE ILE LYS SEQRES 5 A 120 GLU PRO ILE ASP LEU LYS THR ILE ALA GLN ARG ILE GLN SEQRES 6 A 120 ASN GLY SER TYR LYS SER ILE HIS ALA MET ALA LYS ASP SEQRES 7 A 120 ILE ASP LEU LEU ALA LYS ASN ALA LYS THR TYR ASN GLU SEQRES 8 A 120 PRO GLY SER GLN VAL PHE LYS ASP ALA ASN SER ILE LYS SEQRES 9 A 120 LYS ILE PHE TYR MET LYS LYS ALA GLU ILE GLU HIS HIS SEQRES 10 A 120 GLU MET ALA SEQRES 1 B 120 THR GLU GLY SER SER PRO ALA TYR LEU LYS GLU ILE LEU SEQRES 2 B 120 GLU GLN LEU LEU GLU ALA ILE VAL VAL ALA THR ASN PRO SEQRES 3 B 120 SER GLY ARG LEU ILE SER GLU LEU PHE GLN LYS LEU PRO SEQRES 4 B 120 SER LYS VAL GLN TYR PRO ASP TYR TYR ALA ILE ILE LYS SEQRES 5 B 120 GLU PRO ILE ASP LEU LYS THR ILE ALA GLN ARG ILE GLN SEQRES 6 B 120 ASN GLY SER TYR LYS SER ILE HIS ALA MET ALA LYS ASP SEQRES 7 B 120 ILE ASP LEU LEU ALA LYS ASN ALA LYS THR TYR ASN GLU SEQRES 8 B 120 PRO GLY SER GLN VAL PHE LYS ASP ALA ASN SER ILE LYS SEQRES 9 B 120 LYS ILE PHE TYR MET LYS LYS ALA GLU ILE GLU HIS HIS SEQRES 10 B 120 GLU MET ALA HET ACT A 999 4 HET ACT B 998 4 HET NA B 997 1 HETNAM ACT ACETATE ION HETNAM NA SODIUM ION FORMUL 3 ACT 2(C2 H3 O2 1-) FORMUL 5 NA NA 1+ FORMUL 6 HOH *688(H2 O) HELIX 1 1 SER A 178 ALA A 196 1 19 HELIX 2 2 SER A 205 GLN A 209 5 5 HELIX 3 3 TYR A 217 ILE A 224 1 8 HELIX 4 4 ASP A 229 GLY A 240 1 12 HELIX 5 5 SER A 244 ASN A 263 1 20 HELIX 6 6 SER A 267 MET A 292 1 26 HELIX 7 7 SER B 178 ALA B 196 1 19 HELIX 8 8 SER B 205 GLN B 209 5 5 HELIX 9 9 TYR B 217 ILE B 224 1 8 HELIX 10 10 ASP B 229 GLY B 240 1 12 HELIX 11 11 SER B 244 ASN B 263 1 20 HELIX 12 12 SER B 267 MET B 292 1 26 LINK O HOH B 347 NA NA B 997 1555 1555 3.20 LINK O HOH B 635 NA NA B 997 1555 1555 3.05 SITE 1 AC1 5 HOH A 116 SER A 244 ILE A 245 HIS A 246 SITE 2 AC1 5 HOH A 353 SITE 1 AC2 5 HOH B 105 SER B 244 ILE B 245 HIS B 246 SITE 2 AC2 5 HOH B 333 SITE 1 AC3 1 HOH B 635 CRYST1 78.964 78.964 50.651 90.00 90.00 120.00 P 31 6 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 0.012664 0.007312 0.000000 0.00000 SCALE2 0.000000 0.014623 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019743 0.00000