HEADER TRANSCRIPTION 11-JAN-23 8FTA TITLE CRYSTAL STRUCTURE OF THE SECOND BROMODOMAIN OF HUMAN POLYBROMO-1 (PB1) TITLE 2 IN COMPLEX WITH COMPOUND 16 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN POLYBROMO-1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HPB1,BRG1-ASSOCIATED FACTOR 180,BAF180,POLYBROMO-1D; COMPND 5 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: PBRM1, BAF180, PB1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS PROTEIN POLYBROMO-1, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR R.NUNEZ,B.C.SMITH REVDAT 1 24-JAN-24 8FTA 0 JRNL AUTH R.NUNEZ,B.C.SMITH JRNL TITL CRYSTAL STRUCTURE OF THE SECOND BROMODOMAIN OF HUMAN JRNL TITL 2 POLYBROMO-1 (PB1) IN COMPLEX WITH COMPOUND 16 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.78 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX V1.20.1-4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.78 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.51 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 13228 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.990 REMARK 3 FREE R VALUE TEST SET COUNT : 1322 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 42.5100 - 3.7000 1.00 1353 149 0.1890 0.2002 REMARK 3 2 3.7000 - 2.9400 1.00 1339 149 0.1748 0.2169 REMARK 3 3 2.9400 - 2.5700 1.00 1323 147 0.1722 0.1981 REMARK 3 4 2.5700 - 2.3300 1.00 1312 147 0.1632 0.1936 REMARK 3 5 2.3300 - 2.1700 1.00 1325 147 0.1676 0.2024 REMARK 3 6 2.1700 - 2.0400 1.00 1316 145 0.1705 0.1890 REMARK 3 7 2.0400 - 1.9400 1.00 1312 147 0.1617 0.1968 REMARK 3 8 1.9400 - 1.8500 1.00 1314 145 0.1870 0.2514 REMARK 3 9 1.8500 - 1.7800 0.99 1312 146 0.2386 0.2922 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.193 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.552 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.14 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 : 0.008 970 REMARK 3 ANGLE : 1.043 1309 REMARK 3 CHIRALITY : 0.053 144 REMARK 3 PLANARITY : 0.007 165 REMARK 3 DIHEDRAL : 15.975 385 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 8FTA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JAN-23. REMARK 100 THE DEPOSITION ID IS D_1000271309. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-OCT-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 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 MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 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 : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25465 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.780 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 2.100 REMARK 200 R MERGE (I) : 0.99100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 57.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.78 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : 0.07800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES PH 5.5, 14.4% PEG 8000, 10% REMARK 280 ETHYLENE GLYCOL, 0.01M ZNCL2, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 42.32850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.65250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 42.32850 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 24.65250 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: MONOMERIC 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 482 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 570 LIES ON A SPECIAL POSITION. 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 ZN A 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 184 OE2 REMARK 620 2 GLU A 187 OE1 95.5 REMARK 620 3 HIS A 290 ND1 58.4 70.3 REMARK 620 4 GLU A 291 OXT 50.2 75.9 8.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 303 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 246 ND1 REMARK 620 2 HIS A 289 NE2 145.0 REMARK 620 3 HOH A 518 O 148.3 14.9 REMARK 620 4 HOH A 521 O 129.7 15.9 22.5 REMARK 620 N 1 2 3 DBREF 8FTA A 178 291 UNP Q86U86 PB1_HUMAN 178 291 SEQADV 8FTA SER A 176 UNP Q86U86 EXPRESSION TAG SEQADV 8FTA MET A 177 UNP Q86U86 EXPRESSION TAG SEQRES 1 A 116 SER MET SER PRO ALA TYR LEU LYS GLU ILE LEU GLU GLN SEQRES 2 A 116 LEU LEU GLU ALA ILE VAL VAL ALA THR ASN PRO SER GLY SEQRES 3 A 116 ARG LEU ILE SER GLU LEU PHE GLN LYS LEU PRO SER LYS SEQRES 4 A 116 VAL GLN TYR PRO ASP TYR TYR ALA ILE ILE LYS GLU PRO SEQRES 5 A 116 ILE ASP LEU LYS THR ILE ALA GLN ARG ILE GLN ASN GLY SEQRES 6 A 116 SER TYR LYS SER ILE HIS ALA MET ALA LYS ASP ILE ASP SEQRES 7 A 116 LEU LEU ALA LYS ASN ALA LYS THR TYR ASN GLU PRO GLY SEQRES 8 A 116 SER GLN VAL PHE LYS ASP ALA ASN SER ILE LYS LYS ILE SEQRES 9 A 116 PHE TYR MET LYS LYS ALA GLU ILE GLU HIS HIS GLU HET Y8X A 301 19 HET ZN A 302 1 HET ZN A 303 1 HETNAM Y8X (2S)-5-CHLORO-2-(3-METHYLPHENYL)-2,3-DIHYDROQUINAZOLIN- HETNAM 2 Y8X 4(1H)-ONE HETNAM ZN ZINC ION FORMUL 2 Y8X C15 H13 CL N2 O FORMUL 3 ZN 2(ZN 2+) FORMUL 5 HOH *170(H2 O) HELIX 1 AA1 SER A 178 ALA A 196 1 19 HELIX 2 AA2 SER A 205 GLN A 209 5 5 HELIX 3 AA3 TYR A 217 ILE A 224 1 8 HELIX 4 AA4 ASP A 229 GLY A 240 1 12 HELIX 5 AA5 SER A 244 ASN A 263 1 20 HELIX 6 AA6 SER A 267 HIS A 290 1 24 LINK OE2 GLU A 184 ZN ZN A 302 1555 2555 1.96 LINK OE1 GLU A 187 ZN ZN A 302 1555 2555 1.97 LINK ND1 HIS A 246 ZN ZN A 303 1555 2556 2.18 LINK NE2 HIS A 289 ZN ZN A 303 1555 1555 2.15 LINK ND1 HIS A 290 ZN ZN A 302 1555 1555 2.21 LINK OXT GLU A 291 ZN ZN A 302 1555 1555 2.06 LINK ZN ZN A 303 O HOH A 518 1555 1555 2.17 LINK ZN ZN A 303 O HOH A 521 1555 1555 2.32 CRYST1 84.657 49.305 33.544 90.00 97.75 90.00 C 1 2 1 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 0.011812 0.000000 0.001608 0.00000 SCALE2 0.000000 0.020282 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030086 0.00000