HEADER GENE REGULATION 16-MAR-21 7M2E TITLE CRYSTAL STRUCTURE OF BPTF BROMODOMAIN IN COMPLEX WITH CB02-092 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOSOME-REMODELING FACTOR SUBUNIT BPTF; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: BPTF BROMODOMAIN (UNIPROT RESIDUES 2917-3037); COMPND 5 SYNONYM: BROMODOMAIN AND PHD FINGER-CONTAINING TRANSCRIPTION FACTOR, COMPND 6 FETAL ALZ-50 CLONE 1 PROTEIN,FETAL ALZHEIMER ANTIGEN; COMPND 7 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BPTF, BROMODOMAIN, BROMODOMAIN INHIBITOR, GENE REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR S.NITHIANANTHAM,M.FISCHER REVDAT 2 18-OCT-23 7M2E 1 REMARK REVDAT 1 16-FEB-22 7M2E 0 JRNL AUTH H.ZAHID,C.R.BUCHHOLZ,M.SINGH,M.F.CICCONE,A.CHAN, JRNL AUTH 2 S.NITHIANANTHAM,K.SHI,H.AIHARA,M.FISCHER,E.SCHONBRUNN, JRNL AUTH 3 C.O.DOS SANTOS,J.W.LANDRY,W.C.K.POMERANTZ JRNL TITL NEW DESIGN RULES FOR DEVELOPING POTENT CELL-ACTIVE JRNL TITL 2 INHIBITORS OF THE NUCLEOSOME REMODELING FACTOR (NURF) VIA JRNL TITL 3 BPTF BROMODOMAIN INHIBITION JRNL REF J.MED.CHEM. V. 64 13902 2021 JRNL REFN ISSN 0022-2623 JRNL DOI 10.1021/ACS.JMEDCHEM.1C01294 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.27 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.4 REMARK 3 NUMBER OF REFLECTIONS : 12318 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.880 REMARK 3 FREE R VALUE TEST SET COUNT : 601 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 33.2700 - 2.7800 0.99 3220 180 0.1617 0.1910 REMARK 3 2 2.7800 - 2.2100 0.95 3061 166 0.1794 0.2261 REMARK 3 3 2.2100 - 1.9300 0.89 2891 142 0.1621 0.2890 REMARK 3 4 1.9300 - 1.7500 0.78 2545 113 0.1798 0.2539 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.010 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.42 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 : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ( CHAIN A AND RESID 2917:2944 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.182 22.832 8.450 REMARK 3 T TENSOR REMARK 3 T11: 0.1751 T22: 0.1804 REMARK 3 T33: 0.1791 T12: -0.0070 REMARK 3 T13: -0.0159 T23: -0.0113 REMARK 3 L TENSOR REMARK 3 L11: 0.6161 L22: 1.9310 REMARK 3 L33: 1.4896 L12: -0.4478 REMARK 3 L13: -0.9324 L23: 0.7441 REMARK 3 S TENSOR REMARK 3 S11: -0.0204 S12: -0.0611 S13: 0.1460 REMARK 3 S21: 0.0565 S22: 0.1312 S23: -0.2038 REMARK 3 S31: 0.0159 S32: 0.2681 S33: -0.0929 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN A AND RESID 2945:2973 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.704 2.157 4.223 REMARK 3 T TENSOR REMARK 3 T11: 0.1802 T22: 0.1580 REMARK 3 T33: 0.2022 T12: -0.0109 REMARK 3 T13: 0.0160 T23: -0.0087 REMARK 3 L TENSOR REMARK 3 L11: 1.8940 L22: 1.0397 REMARK 3 L33: 1.7515 L12: 0.3205 REMARK 3 L13: -0.7465 L23: -0.2027 REMARK 3 S TENSOR REMARK 3 S11: -0.1122 S12: 0.1265 S13: -0.1886 REMARK 3 S21: 0.0098 S22: 0.0475 S23: 0.0844 REMARK 3 S31: 0.1687 S32: -0.1796 S33: 0.0515 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ( CHAIN A AND RESID 2974:2988 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.604 19.525 5.657 REMARK 3 T TENSOR REMARK 3 T11: 0.1263 T22: 0.1875 REMARK 3 T33: 0.1805 T12: -0.0030 REMARK 3 T13: -0.0134 T23: 0.0165 REMARK 3 L TENSOR REMARK 3 L11: 1.8870 L22: 3.3507 REMARK 3 L33: 1.1903 L12: 0.3810 REMARK 3 L13: 0.0239 L23: 0.3159 REMARK 3 S TENSOR REMARK 3 S11: 0.0266 S12: 0.0814 S13: 0.1793 REMARK 3 S21: -0.0204 S22: -0.0563 S23: 0.3547 REMARK 3 S31: -0.0073 S32: -0.2840 S33: 0.0189 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: ( CHAIN A AND RESID 2989:3011 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.857 5.397 11.849 REMARK 3 T TENSOR REMARK 3 T11: 0.1766 T22: 0.1633 REMARK 3 T33: 0.1316 T12: 0.0079 REMARK 3 T13: 0.0088 T23: 0.0088 REMARK 3 L TENSOR REMARK 3 L11: 0.5467 L22: 2.3907 REMARK 3 L33: 0.4315 L12: 0.3803 REMARK 3 L13: -0.0169 L23: -0.0355 REMARK 3 S TENSOR REMARK 3 S11: -0.0506 S12: -0.0426 S13: 0.0022 REMARK 3 S21: 0.1080 S22: 0.2041 S23: 0.0366 REMARK 3 S31: 0.0622 S32: 0.0624 S33: -0.1165 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: ( CHAIN A AND RESID 3012:3036 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.737 9.458 7.778 REMARK 3 T TENSOR REMARK 3 T11: 0.0858 T22: 0.1191 REMARK 3 T33: 0.0933 T12: 0.0173 REMARK 3 T13: -0.0131 T23: 0.0034 REMARK 3 L TENSOR REMARK 3 L11: 1.1152 L22: 2.5671 REMARK 3 L33: 0.9043 L12: 0.5740 REMARK 3 L13: -0.0301 L23: 0.3703 REMARK 3 S TENSOR REMARK 3 S11: 0.0108 S12: 0.1000 S13: -0.0267 REMARK 3 S21: 0.1892 S22: 0.0512 S23: -0.2171 REMARK 3 S31: 0.0469 S32: 0.0520 S33: -0.0492 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 7M2E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-MAR-21. REMARK 100 THE DEPOSITION ID IS D_1000255526. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-MAR-21 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 : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12469 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 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 (%) : 91.5 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.14800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 78.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.33200 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: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: PHENIX 1.18 REMARK 200 STARTING MODEL: 3UV2 REMARK 200 REMARK 200 REMARK: THIN NEEDLES REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0. 2M NACL AND 23% PEG 3350, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 33.27300 REMARK 290 SMTRY3 2 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 465 MET A 2916 REMARK 465 HIS A 3037 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 THR A2918 CG2 REMARK 470 LYS A2969 CD CE NZ 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 83.75 -157.75 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 YOV A 3401 DBREF 7M2E A 2917 3037 UNP Q12830 BPTF_HUMAN 2917 3037 SEQADV 7M2E SER A 2915 UNP Q12830 EXPRESSION TAG SEQADV 7M2E 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 YOV A3401 21 HETNAM YOV 4-CHLORO-5-{4-[2-(DIMETHYLAMINO)ETHYL]ANILINO}-2- HETNAM 2 YOV METHYLPYRIDAZIN-3(2H)-ONE FORMUL 2 YOV C15 H19 CL N4 O FORMUL 3 HOH *164(H2 O) HELIX 1 AA1 SER A 2917 THR A 2926 1 10 HELIX 2 AA2 THR A 2929 HIS A 2946 1 18 HELIX 3 AA3 LYS A 2947 LEU A 2953 5 7 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 ARG A 3035 1 25 SITE 1 AC1 8 PRO A2951 PHE A2952 ASP A2957 ASP A2960 SITE 2 AC1 8 TYR A3006 ASN A3007 PHE A3013 HOH A3524 CRYST1 27.006 66.546 39.623 90.00 105.61 90.00 P 1 21 1 2 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 0.037029 0.000000 0.010347 0.00000 SCALE2 0.000000 0.015027 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026205 0.00000