HEADER GENE REGULATION 15-JUL-20 6ZS4 TITLE CRYSTAL STRUCTURE OF THE FIFTH BROMODOMAIN OF HUMAN PROTEIN POLYBROMO- TITLE 2 1 IN COMPLEX WITH TERT-BUTYL 4-[3-AMINO-6-(2-HYDROXYPHENYL)PYRIDAZIN- TITLE 3 4-YL]PIPERAZINE-1-CARBOXYLATE 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BROMODOMAIN, COMPLEX, SMALL MOLECULE, STRUCTURAL GENOMICS CONSORTIUM, KEYWDS 2 SGC, TRANSCRIPTION, GENE REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR F.PREUSS,A.C.JOERGER,A.KRAEMER,M.WANIOR,S.KNAPP,STRUCTURAL GENOMICS AUTHOR 2 CONSORTIUM (SGC) REVDAT 3 31-JAN-24 6ZS4 1 REMARK REVDAT 2 05-MAY-21 6ZS4 1 JRNL REVDAT 1 07-OCT-20 6ZS4 0 JRNL AUTH M.WANIOR,F.PREUSS,X.NI,A.KRAMER,S.MATHEA,T.GOBEL, JRNL AUTH 2 D.HEIDENREICH,S.SIMONYI,A.S.KAHNT,A.C.JOERGER,S.KNAPP JRNL TITL PAN-SMARCA/PB1 BROMODOMAIN INHIBITORS AND THEIR ROLE IN JRNL TITL 2 REGULATING ADIPOGENESIS. JRNL REF J.MED.CHEM. V. 63 14680 2020 JRNL REFN ISSN 0022-2623 JRNL PMID 33216538 JRNL DOI 10.1021/ACS.JMEDCHEM.0C01242 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_2155 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.40 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.337 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 9276 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.797 REMARK 3 FREE R VALUE TEST SET COUNT : 445 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 36.3871 - 2.8842 0.99 3025 137 0.1700 0.2088 REMARK 3 2 2.8842 - 2.2894 0.99 2924 140 0.2119 0.2355 REMARK 3 3 2.2894 - 2.0000 0.98 2882 168 0.2094 0.2807 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.246 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.330 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.44 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.28 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 : 0.007 938 REMARK 3 ANGLE : 0.779 1270 REMARK 3 CHIRALITY : 0.042 139 REMARK 3 PLANARITY : 0.006 177 REMARK 3 DIHEDRAL : 13.324 592 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 6ZS4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-JUL-20. REMARK 100 THE DEPOSITION ID IS D_1292108287. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-MAY-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91842 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9289 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 36.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.09800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.36000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.000 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: 5FH7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 5000 MME, 0.2 M (NH4)2SO4, 0.1 REMARK 280 M MES PH 5.8, VAPOR DIFFUSION, SITTING DROP, 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 63.13500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 14.87000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 63.13500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 14.87000 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 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 SER A 643 REMARK 465 MET A 644 REMARK 465 SER A 645 REMARK 465 GLY A 646 REMARK 465 ILE A 647 REMARK 465 SER A 648 REMARK 465 PRO A 649 REMARK 465 LYS A 650 REMARK 465 LYS A 651 REMARK 465 SER A 652 REMARK 465 LYS A 653 REMARK 465 TYR A 654 REMARK 465 GLY A 765 REMARK 465 ASP A 766 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 MET A 655 CG SD CE REMARK 470 GLN A 659 CG CD OE1 NE2 REMARK 470 GLN A 660 CG CD OE1 NE2 REMARK 470 LYS A 661 CG CD CE NZ REMARK 470 LYS A 702 CG CD CE NZ REMARK 470 LYS A 708 CD CE NZ REMARK 470 LYS A 717 CG CD CE NZ REMARK 470 GLN A 719 CG CD OE1 NE2 REMARK 470 ARG A 761 CG CD NE CZ NH1 NH2 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 716 15.29 53.88 REMARK 500 LYS A 717 2.81 -66.02 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue QP8 A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 802 DBREF 6ZS4 A 645 766 UNP Q86U86 PB1_HUMAN 645 766 SEQADV 6ZS4 SER A 643 UNP Q86U86 EXPRESSION TAG SEQADV 6ZS4 MET A 644 UNP Q86U86 EXPRESSION TAG SEQRES 1 A 124 SER MET SER GLY ILE SER PRO LYS LYS SER LYS TYR MET SEQRES 2 A 124 THR PRO MET GLN GLN LYS LEU ASN GLU VAL TYR GLU ALA SEQRES 3 A 124 VAL LYS ASN TYR THR ASP LYS ARG GLY ARG ARG LEU SER SEQRES 4 A 124 ALA ILE PHE LEU ARG LEU PRO SER ARG SER GLU LEU PRO SEQRES 5 A 124 ASP TYR TYR LEU THR ILE LYS LYS PRO MET ASP MET GLU SEQRES 6 A 124 LYS ILE ARG SER HIS MET MET ALA ASN LYS TYR GLN ASP SEQRES 7 A 124 ILE ASP SER MET VAL GLU ASP PHE VAL MET MET PHE ASN SEQRES 8 A 124 ASN ALA CYS THR TYR ASN GLU PRO GLU SER LEU ILE TYR SEQRES 9 A 124 LYS ASP ALA LEU VAL LEU HIS LYS VAL LEU LEU GLU THR SEQRES 10 A 124 ARG ARG ASP LEU GLU GLY ASP HET QP8 A 801 27 HET EDO A 802 4 HETNAM QP8 TERT-BUTYL 4-[3-AMINO-6-(2-HYDROXYPHENYL)PYRIDAZIN-4- HETNAM 2 QP8 YL]PIPERAZINE-1-CARBOXYLATE HETNAM EDO 1,2-ETHANEDIOL HETSYN QP8 ~{TERT}-BUTYL 4-[3-AZANYL-6-(2-HYDROXYPHENYL)PYRIDAZIN- HETSYN 2 QP8 4-YL]PIPERAZINE-1-CARBOXYLATE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 QP8 C19 H25 N5 O3 FORMUL 3 EDO C2 H6 O2 FORMUL 4 HOH *82(H2 O) HELIX 1 AA1 THR A 656 TYR A 672 1 17 HELIX 2 AA2 ARG A 679 LEU A 685 5 7 HELIX 3 AA3 LEU A 693 ILE A 700 1 8 HELIX 4 AA4 ASP A 705 ALA A 715 1 11 HELIX 5 AA5 ASP A 720 ASN A 739 1 20 HELIX 6 AA6 SER A 743 LEU A 763 1 21 SITE 1 AC1 10 ILE A 683 PHE A 684 LEU A 693 TYR A 696 SITE 2 AC1 10 MET A 704 ALA A 735 TYR A 738 ASN A 739 SITE 3 AC1 10 ILE A 745 LYS A 747 SITE 1 AC2 3 LYS A 675 ARG A 676 LYS A 701 CRYST1 126.270 29.740 36.610 90.00 96.41 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 0.007920 0.000000 0.000890 0.00000 SCALE2 0.000000 0.033625 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027487 0.00000