HEADER GENE REGULATION 21-SEP-20 7K6R TITLE CRYSTAL STRUCTURE OF THE BROMODOMAIN (BD) OF HUMAN BROMODOMAIN AND PHD TITLE 2 FINGER-CONTAINING TRANSCRIPTION FACTOR (BPTF) BOUND TO GSK4027 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOSOME-REMODELING FACTOR SUBUNIT BPTF; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BROMODOMAIN AND PHD FINGER-CONTAINING TRANSCRIPTION FACTOR, COMPND 5 FETAL ALZ-50 CLONE 1 PROTEIN,FETAL ALZHEIMER ANTIGEN; 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: BPTF, FAC1, FALZ; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS BRD, PHD, GENE REGULATION, FAC1, FALZ, NUCLEOSOME-REMODELING FACTOR KEYWDS 2 SUBUNIT EXPDTA X-RAY DIFFRACTION AUTHOR A.CHAN,E.SCHONBRUNN REVDAT 2 18-OCT-23 7K6R 1 REMARK REVDAT 1 09-DEC-20 7K6R 0 JRNL AUTH P.D.YCAS,H.ZAHID,A.CHAN,N.M.OLSON,J.A.JOHNSON,S.K.TALLURI, JRNL AUTH 2 E.SCHONBRUNN,W.C.K.POMERANTZ JRNL TITL NEW INHIBITORS FOR THE BPTF BROMODOMAIN ENABLED BY JRNL TITL 2 STRUCTURAL BIOLOGY AND BIOPHYSICAL ASSAY DEVELOPMENT. JRNL REF ORG.BIOMOL.CHEM. V. 18 5174 2020 JRNL REFN ESSN 1477-0539 JRNL PMID 32588860 JRNL DOI 10.1039/D0OB00506A REMARK 2 REMARK 2 RESOLUTION. 1.60 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.28 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.010 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 3 NUMBER OF REFLECTIONS : 17235 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.410 REMARK 3 FREE R VALUE TEST SET COUNT : 1104 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 37.2800 - 3.2000 0.95 2032 140 0.1425 0.1623 REMARK 3 2 3.2000 - 2.5400 0.94 2027 138 0.1579 0.1906 REMARK 3 3 2.5400 - 2.2200 0.94 2012 138 0.1652 0.2096 REMARK 3 4 2.2200 - 2.0200 0.95 2036 139 0.1639 0.2086 REMARK 3 5 2.0200 - 1.8700 0.94 2017 138 0.1817 0.2422 REMARK 3 6 1.8700 - 1.7600 0.94 2029 139 0.1877 0.2397 REMARK 3 7 1.7600 - 1.6700 0.93 1975 135 0.1873 0.2358 REMARK 3 8 1.6700 - 1.6000 0.93 2003 137 0.1898 0.2129 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.030 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.55 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.50 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 2916 THROUGH 2929 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.3909 -14.6386 -27.4187 REMARK 3 T TENSOR REMARK 3 T11: 0.1693 T22: 0.2227 REMARK 3 T33: 0.1247 T12: -0.0149 REMARK 3 T13: 0.0047 T23: -0.0177 REMARK 3 L TENSOR REMARK 3 L11: 7.0925 L22: 5.3392 REMARK 3 L33: 5.1714 L12: -0.8688 REMARK 3 L13: 1.2898 L23: 1.8384 REMARK 3 S TENSOR REMARK 3 S11: -0.0391 S12: 0.3998 S13: 0.1936 REMARK 3 S21: -0.4374 S22: 0.0502 S23: -0.3977 REMARK 3 S31: -0.2056 S32: 0.6963 S33: -0.0340 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 2930 THROUGH 2963 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.0707 -9.7737 -6.0053 REMARK 3 T TENSOR REMARK 3 T11: 0.1290 T22: 0.1389 REMARK 3 T33: 0.1308 T12: -0.0304 REMARK 3 T13: 0.0132 T23: 0.0489 REMARK 3 L TENSOR REMARK 3 L11: 1.4072 L22: 3.4368 REMARK 3 L33: 3.3352 L12: -0.5060 REMARK 3 L13: -0.1299 L23: 2.1771 REMARK 3 S TENSOR REMARK 3 S11: 0.0512 S12: -0.1119 S13: -0.0594 REMARK 3 S21: 0.2045 S22: -0.0804 S23: 0.0363 REMARK 3 S31: 0.1522 S32: -0.1064 S33: 0.0108 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 2964 THROUGH 3011 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.6037 -4.7739 -12.3256 REMARK 3 T TENSOR REMARK 3 T11: 0.1023 T22: 0.1413 REMARK 3 T33: 0.1579 T12: 0.0007 REMARK 3 T13: -0.0111 T23: 0.0194 REMARK 3 L TENSOR REMARK 3 L11: 1.0332 L22: 3.7627 REMARK 3 L33: 2.2299 L12: -0.3570 REMARK 3 L13: 0.2255 L23: 1.3741 REMARK 3 S TENSOR REMARK 3 S11: -0.0496 S12: 0.0044 S13: 0.0510 REMARK 3 S21: -0.0239 S22: 0.0204 S23: 0.1354 REMARK 3 S31: -0.1298 S32: -0.0129 S33: 0.0405 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 3012 THROUGH 3037 ) REMARK 3 ORIGIN FOR THE GROUP (A): 19.8142 -6.6355 -12.2749 REMARK 3 T TENSOR REMARK 3 T11: 0.1101 T22: 0.1417 REMARK 3 T33: 0.1261 T12: -0.0195 REMARK 3 T13: -0.0135 T23: 0.0325 REMARK 3 L TENSOR REMARK 3 L11: 2.3085 L22: 3.5646 REMARK 3 L33: 3.5112 L12: -0.7437 REMARK 3 L13: -0.3903 L23: 2.4133 REMARK 3 S TENSOR REMARK 3 S11: 0.0174 S12: 0.0219 S13: 0.0485 REMARK 3 S21: -0.0164 S22: 0.0582 S23: -0.1882 REMARK 3 S31: -0.0818 S32: 0.1058 S33: -0.1411 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 7K6R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-SEP-20. REMARK 100 THE DEPOSITION ID IS D_1000246732. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUL-19 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 : APS REMARK 200 BEAMLINE : 23-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17236 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 37.280 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.8 REMARK 200 DATA REDUNDANCY : 1.830 REMARK 200 R MERGE (I) : 0.03500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.8400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.5 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : 0.21800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.370 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 3UV2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M LITHIUM SULFATE MONOHYDRATE, REMARK 280 0.1M BIS-TRIS, 25 PERCENT POLYETHYLENE GLYCOL 3,350, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 291K 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 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 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 2915 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 ALA A2961 93.77 -174.48 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A3367 DISTANCE = 6.67 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 9ST A 3101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 3102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 3103 DBREF 7K6R A 2917 3037 UNP Q12830 BPTF_HUMAN 2917 3037 SEQADV 7K6R SER A 2915 UNP Q12830 EXPRESSION TAG SEQADV 7K6R MET A 2916 UNP Q12830 EXPRESSION TAG SEQRES 1 A 123 SER MET SER THR GLU ASP ALA MET THR VAL LEU THR PRO SEQRES 2 A 123 LEU THR GLU LYS ASP TYR GLU GLY LEU LYS ARG VAL LEU SEQRES 3 A 123 ARG SER LEU GLN ALA HIS LYS MET ALA TRP PRO PHE LEU SEQRES 4 A 123 GLU PRO VAL ASP PRO ASN ASP ALA PRO ASP TYR TYR GLY SEQRES 5 A 123 VAL ILE LYS GLU PRO MET ASP LEU ALA THR MET GLU GLU SEQRES 6 A 123 ARG VAL GLN ARG ARG TYR TYR GLU LYS LEU THR GLU PHE SEQRES 7 A 123 VAL ALA ASP MET THR LYS ILE PHE ASP ASN CYS ARG TYR SEQRES 8 A 123 TYR ASN PRO SER ASP SER PRO PHE TYR GLN CYS ALA GLU SEQRES 9 A 123 VAL LEU GLU SER PHE PHE VAL GLN LYS LEU LYS GLY PHE SEQRES 10 A 123 LYS ALA SER ARG SER HIS HET 9ST A3101 23 HET EDO A3102 4 HET EDO A3103 4 HETNAM 9ST 4-BROMO-2-METHYL-5-[[(3~{R},5~{R})-1-METHYL-5-PHENYL- HETNAM 2 9ST PIPERIDIN-3-YL]AMINO]PYRIDAZIN-3-ONE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 9ST C17 H21 BR N4 O FORMUL 3 EDO 2(C2 H6 O2) FORMUL 5 HOH *167(H2 O) HELIX 1 AA1 SER A 2917 THR A 2926 1 10 HELIX 2 AA2 THR A 2929 ALA A 2945 1 17 HELIX 3 AA3 HIS A 2946 LEU A 2953 5 8 HELIX 4 AA4 ASP A 2957 ALA A 2961 5 5 HELIX 5 AA5 ASP A 2963 ILE A 2968 1 6 HELIX 6 AA6 ASP A 2973 ARG A 2983 1 11 HELIX 7 AA7 LYS A 2988 ASN A 3007 1 20 HELIX 8 AA8 SER A 3011 HIS A 3037 1 27 SITE 1 AC1 10 LEU A2925 PRO A2951 PHE A2952 PRO A2955 SITE 2 AC1 10 ASP A2960 TYR A3006 ASN A3007 PHE A3013 SITE 3 AC1 10 HOH A3210 HOH A3247 SITE 1 AC2 6 VAL A2967 LYS A2969 TYR A3005 HOH A3230 SITE 2 AC2 6 HOH A3276 HOH A3282 SITE 1 AC3 3 MET A2922 THR A2926 TRP A2950 CRYST1 27.060 35.520 41.150 114.12 95.93 91.06 P 1 1 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 0.036955 0.000681 0.004524 0.00000 SCALE2 0.000000 0.028158 0.012765 0.00000 SCALE3 0.000000 0.000000 0.026825 0.00000