HEADER GENE REGULATION 16-NOV-22 8F6G TITLE CRYSTAL STRUCTURE OF BPTF BROMODOMAIN IN COMPLEX WITH BZ2 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; COMPND 8 OTHER_DETAILS: THE FOLLOWING RESIDUES WERE NOT LOCATED. SER A 2915 COMPND 9 MET A 2916 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 1 22-MAY-24 8F6G 0 JRNL AUTH S.NITHIANANTHAM,M.FISCHER JRNL TITL CRYSTAL STRUCTURE OF BPTF BROMODOMAIN IN COMPLEX WITH BZ2 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.43 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 85.6 REMARK 3 NUMBER OF REFLECTIONS : 8537 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.590 REMARK 3 FREE R VALUE TEST SET COUNT : 392 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 33.4300 - 2.8100 0.92 2936 154 0.1741 0.2067 REMARK 3 2 2.8100 - 2.2300 0.89 2807 133 0.2104 0.2516 REMARK 3 3 2.2300 - 1.9500 0.76 2402 105 0.2243 0.2840 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.400 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.004 1074 REMARK 3 ANGLE : 0.716 1458 REMARK 3 CHIRALITY : 0.042 149 REMARK 3 PLANARITY : 0.007 191 REMARK 3 DIHEDRAL : 25.210 409 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 2917 THROUGH 2952 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.2940 17.4354 6.3752 REMARK 3 T TENSOR REMARK 3 T11: 0.1288 T22: 0.1554 REMARK 3 T33: 0.1532 T12: 0.0178 REMARK 3 T13: -0.0313 T23: -0.0049 REMARK 3 L TENSOR REMARK 3 L11: 0.9190 L22: 4.8083 REMARK 3 L33: 1.6489 L12: -0.3044 REMARK 3 L13: -1.1028 L23: 1.6643 REMARK 3 S TENSOR REMARK 3 S11: -0.0687 S12: -0.0541 S13: 0.0744 REMARK 3 S21: -0.0203 S22: 0.2848 S23: -0.3689 REMARK 3 S31: -0.0606 S32: 0.3208 S33: -0.2268 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 2953 THROUGH 2963 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.1758 -3.0212 3.3248 REMARK 3 T TENSOR REMARK 3 T11: 0.1794 T22: 0.2008 REMARK 3 T33: 0.3908 T12: -0.0364 REMARK 3 T13: 0.0024 T23: 0.0021 REMARK 3 L TENSOR REMARK 3 L11: 7.8245 L22: 6.1053 REMARK 3 L33: 2.5955 L12: 1.9916 REMARK 3 L13: 0.5158 L23: 0.7106 REMARK 3 S TENSOR REMARK 3 S11: 0.0180 S12: 0.1324 S13: -1.0344 REMARK 3 S21: 0.0230 S22: 0.4678 S23: 0.5836 REMARK 3 S31: 0.3709 S32: -0.3562 S33: -0.3844 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 2964 THROUGH 3036 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.6194 9.0640 9.1486 REMARK 3 T TENSOR REMARK 3 T11: 0.1375 T22: 0.1713 REMARK 3 T33: 0.1170 T12: 0.0045 REMARK 3 T13: -0.0080 T23: -0.0063 REMARK 3 L TENSOR REMARK 3 L11: 1.4612 L22: 2.6935 REMARK 3 L33: 1.1129 L12: 0.3989 REMARK 3 L13: -0.3608 L23: -0.0157 REMARK 3 S TENSOR REMARK 3 S11: 0.0254 S12: -0.0035 S13: 0.0221 REMARK 3 S21: 0.0036 S22: 0.0192 S23: 0.0624 REMARK 3 S31: 0.0327 S32: 0.0117 S33: -0.0418 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 3037 THROUGH 3037 ) REMARK 3 ORIGIN FOR THE GROUP (A): 27.0695 27.3076 10.4887 REMARK 3 T TENSOR REMARK 3 T11: 0.7849 T22: 0.7935 REMARK 3 T33: 1.0798 T12: -0.4634 REMARK 3 T13: 0.2450 T23: 0.0635 REMARK 3 L TENSOR REMARK 3 L11: 9.9910 L22: 1.9999 REMARK 3 L33: 2.0001 L12: -5.0741 REMARK 3 L13: 8.0136 L23: -2.6322 REMARK 3 S TENSOR REMARK 3 S11: 0.1671 S12: -0.1323 S13: -0.4264 REMARK 3 S21: 0.1852 S22: -0.6039 S23: -0.5206 REMARK 3 S31: -0.5924 S32: 1.1331 S33: 0.4542 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 8F6G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-NOV-22. REMARK 100 THE DEPOSITION ID IS D_1000270085. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-APR-22 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 : M 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 : 9052 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 33.430 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.9 REMARK 200 DATA REDUNDANCY : 2.300 REMARK 200 R MERGE (I) : 0.10500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.98 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : 0.60900 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 1.20 REMARK 200 STARTING MODEL: 7M2E REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0. 2 M 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 33.42950 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 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 A2969 CD CE NZ 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 A3319 DISTANCE = 5.85 ANGSTROMS REMARK 525 HOH A3320 DISTANCE = 6.34 ANGSTROMS DBREF 8F6G A 2917 3037 UNP Q12830 BPTF_HUMAN 2917 3037 SEQADV 8F6G SER A 2915 UNP Q12830 EXPRESSION TAG SEQADV 8F6G 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 XHK A3101 19 HETNAM XHK 6-[4-(2-AMINOETHYL)ANILINO]-5-CHLORO-3-METHYLPYRIMIDIN- HETNAM 2 XHK 4(3H)-ONE FORMUL 2 XHK C13 H15 CL N4 O FORMUL 3 HOH *120(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 2963 ILE A 2968 1 6 HELIX 5 AA5 ASP A 2973 ARG A 2983 1 11 HELIX 6 AA6 LYS A 2988 ASN A 3007 1 20 HELIX 7 AA7 SER A 3011 HIS A 3037 1 27 CRYST1 26.976 66.859 39.564 90.00 104.94 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 0.037070 0.000000 0.009891 0.00000 SCALE2 0.000000 0.014957 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026160 0.00000