HEADER PROTEIN BINDING 06-JUL-20 6ZN6 TITLE PROTEIN POLYBROMO-1 (PB1 BD2) BOUND TO MW278 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN POLYBROMO-1; COMPND 3 CHAIN: A, B; 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 INHIBITOR EPIGENETICS, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR F.PREUSS,S.MATHEA,D.CHATTERJEE,M.WANIOR,A.C.JOERGER,S.KNAPP REVDAT 4 31-JAN-24 6ZN6 1 REMARK REVDAT 3 05-MAY-21 6ZN6 1 REMARK REVDAT 2 10-MAR-21 6ZN6 1 JRNL REVDAT 1 26-AUG-20 6ZN6 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. 2.02 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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) : 2.02 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.60 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.500 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 18157 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.221 REMARK 3 R VALUE (WORKING SET) : 0.218 REMARK 3 FREE R VALUE : 0.278 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.740 REMARK 3 FREE R VALUE TEST SET COUNT : 860 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 36.6000 - 3.6700 1.00 3011 143 0.1623 0.1978 REMARK 3 2 3.6700 - 2.9100 1.00 2871 173 0.2084 0.2643 REMARK 3 3 2.9100 - 2.5400 1.00 2866 133 0.2248 0.3225 REMARK 3 4 2.5400 - 2.3100 1.00 2869 133 0.2325 0.3027 REMARK 3 5 2.3100 - 2.1500 1.00 2840 137 0.2860 0.3623 REMARK 3 6 2.1500 - 2.0200 1.00 2840 141 0.3434 0.4383 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) : 0.381 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.260 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.54 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 1895 REMARK 3 ANGLE : 0.867 2559 REMARK 3 CHIRALITY : 0.043 284 REMARK 3 PLANARITY : 0.006 361 REMARK 3 DIHEDRAL : 11.845 301 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: NULL REMARK 3 ORIGIN FOR THE GROUP (A): 12.4609 13.4160 13.0896 REMARK 3 T TENSOR REMARK 3 T11: 0.1476 T22: 0.1342 REMARK 3 T33: 0.1501 T12: 0.0143 REMARK 3 T13: 0.0188 T23: -0.0136 REMARK 3 L TENSOR REMARK 3 L11: 0.4621 L22: 0.5234 REMARK 3 L33: 0.3934 L12: -0.2918 REMARK 3 L13: 0.3405 L23: -0.3907 REMARK 3 S TENSOR REMARK 3 S11: -0.0086 S12: -0.0097 S13: -0.0356 REMARK 3 S21: 0.0080 S22: 0.0256 S23: 0.0380 REMARK 3 S31: 0.0186 S32: -0.0065 S33: 0.0062 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 6ZN6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-JUL-20. REMARK 100 THE DEPOSITION ID IS D_1292109855. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-NOV-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.99999 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 7.0.078 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18158 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.020 REMARK 200 RESOLUTION RANGE LOW (A) : 36.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.02 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.09 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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 7.0.078 REMARK 200 STARTING MODEL: 3HMF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M NACL 25% (W/V) PEG3350 0.1 M BIS REMARK 280 -TRIS PH 5.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 52.51200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.51200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 35.26250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 36.59650 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 35.26250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 36.59650 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 52.51200 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 35.26250 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 36.59650 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 52.51200 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 35.26250 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 36.59650 REMARK 290 SMTRY3 8 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: 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC 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 SER A 176 REMARK 465 HIS A 290 REMARK 465 GLU A 291 REMARK 465 SER B 176 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 225 CG CD CE NZ REMARK 470 LYS A 250 CE NZ REMARK 470 GLU B 184 CG CD OE1 OE2 REMARK 470 SER B 200 OG REMARK 470 LYS B 210 CE NZ REMARK 470 LYS B 250 CD CE NZ REMARK 470 LYS B 257 CE NZ REMARK 470 HIS B 290 CG ND1 CD2 CE1 NE2 REMARK 470 GLU B 291 CG CD OE1 OE2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue QMT A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue QMT B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 302 DBREF 6ZN6 A 178 291 UNP Q86U86 PB1_HUMAN 178 291 DBREF 6ZN6 B 178 291 UNP Q86U86 PB1_HUMAN 178 291 SEQADV 6ZN6 SER A 176 UNP Q86U86 EXPRESSION TAG SEQADV 6ZN6 MET A 177 UNP Q86U86 EXPRESSION TAG SEQADV 6ZN6 SER B 176 UNP Q86U86 EXPRESSION TAG SEQADV 6ZN6 MET B 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 SEQRES 1 B 116 SER MET SER PRO ALA TYR LEU LYS GLU ILE LEU GLU GLN SEQRES 2 B 116 LEU LEU GLU ALA ILE VAL VAL ALA THR ASN PRO SER GLY SEQRES 3 B 116 ARG LEU ILE SER GLU LEU PHE GLN LYS LEU PRO SER LYS SEQRES 4 B 116 VAL GLN TYR PRO ASP TYR TYR ALA ILE ILE LYS GLU PRO SEQRES 5 B 116 ILE ASP LEU LYS THR ILE ALA GLN ARG ILE GLN ASN GLY SEQRES 6 B 116 SER TYR LYS SER ILE HIS ALA MET ALA LYS ASP ILE ASP SEQRES 7 B 116 LEU LEU ALA LYS ASN ALA LYS THR TYR ASN GLU PRO GLY SEQRES 8 B 116 SER GLN VAL PHE LYS ASP ALA ASN SER ILE LYS LYS ILE SEQRES 9 B 116 PHE TYR MET LYS LYS ALA GLU ILE GLU HIS HIS GLU HET QMT A 301 27 HET QMT B 301 27 HET EDO B 302 4 HETNAM QMT 2-[6-AZANYL-5-[(3~{R})-3-PHENOXYPIPERIDIN-1- HETNAM 2 QMT YL]PYRIDAZIN-3-YL]PHENOL HETNAM EDO 1,2-ETHANEDIOL HETSYN QMT MW278 HETSYN EDO ETHYLENE GLYCOL FORMUL 3 QMT 2(C21 H22 N4 O2) FORMUL 5 EDO C2 H6 O2 FORMUL 6 HOH *107(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 ASN A 239 1 11 HELIX 5 AA5 SER A 244 ASN A 263 1 20 HELIX 6 AA6 SER A 267 GLU A 288 1 22 HELIX 7 AA7 SER B 178 ALA B 196 1 19 HELIX 8 AA8 SER B 205 GLN B 209 5 5 HELIX 9 AA9 TYR B 217 ILE B 224 1 8 HELIX 10 AB1 ASP B 229 ASN B 239 1 11 HELIX 11 AB2 SER B 244 ASN B 263 1 20 HELIX 12 AB3 SER B 267 HIS B 289 1 23 SITE 1 AC1 7 LEU A 207 PHE A 208 TYR A 217 TYR A 220 SITE 2 AC1 7 ILE A 228 ALA A 259 ASN A 263 SITE 1 AC2 11 ARG A 202 GLN A 268 LEU B 207 PHE B 208 SITE 2 AC2 11 TYR B 217 TYR B 220 ILE B 228 ALA B 259 SITE 3 AC2 11 TYR B 262 ASN B 263 VAL B 269 SITE 1 AC3 5 MET B 177 SER B 178 PRO B 179 LEU B 182 SITE 2 AC3 5 LYS B 243 CRYST1 70.525 73.193 105.024 90.00 90.00 90.00 C 2 2 21 16 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 0.014179 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013663 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009522 0.00000