HEADER PROTEIN BINDING 19-JUL-22 8AG2 TITLE CRYSTAL STRUCTURE OF THE BPTF BROMODOMAIN IN COMPLEX WITH BI-7190 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BROMODOMAIN, INHIBITOR, COMPLEX, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR G.BADER,J.BOETTCHER,B.WOLKERSTORFER REVDAT 5 07-FEB-24 8AG2 1 REMARK REVDAT 4 29-MAR-23 8AG2 1 JRNL REVDAT 3 22-MAR-23 8AG2 1 JRNL REVDAT 2 15-MAR-23 8AG2 1 JRNL REVDAT 1 31-AUG-22 8AG2 0 JRNL AUTH P.MARTINELLI,O.SCHAAF,A.MANTOULIDIS,L.J.MARTIN,J.E.FUCHS, JRNL AUTH 2 G.BADER,A.GOLLNER,B.WOLKERSTORFER,C.ROGERS,E.BALIKCI, JRNL AUTH 3 J.J.LIPP,N.MISCHERIKOW,S.DOEBEL,T.GERSTBERGER, JRNL AUTH 4 W.SOMMERGRUBER,K.V.M.HUBER,J.BOTTCHER JRNL TITL DISCOVERY OF A CHEMICAL PROBE TO STUDY IMPLICATIONS OF BPTF JRNL TITL 2 BROMODOMAIN INHIBITION IN CELLULAR AND IN VIVO EXPERIMENTS. JRNL REF CHEMMEDCHEM V. 18 00686 2023 JRNL REFN ESSN 1860-7187 JRNL PMID 36649575 JRNL DOI 10.1002/CMDC.202200686 REMARK 2 REMARK 2 RESOLUTION. 1.03 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.11.7 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.03 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.78 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 80.0 REMARK 3 NUMBER OF REFLECTIONS : 54717 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.155 REMARK 3 R VALUE (WORKING SET) : 0.155 REMARK 3 FREE R VALUE : 0.171 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 2673 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.03 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.06 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 16.22 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : NULL REMARK 3 BIN R VALUE (WORKING + TEST SET) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2418 REMARK 3 BIN FREE R VALUE : 0.2773 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 56 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1000 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 240 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 9.86 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.12060 REMARK 3 B22 (A**2) : 0.22690 REMARK 3 B33 (A**2) : -0.10630 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.04940 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.120 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.030 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.031 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.029 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.029 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.972 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.970 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 2109 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 3811 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 624 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : 322 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 2078 ; 10.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 130 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : 2 ; 1.000 ; HARMONIC REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 2098 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 0.94 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.89 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 12.60 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8AG2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-JUL-22. REMARK 100 THE DEPOSITION ID IS D_1292124213. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAY-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000021 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 : AUTOPROC, XDS JAN 26, 201 REMARK 200 DATA SCALING SOFTWARE : AUTOPROC 1.1.7, AIMLESS, REMARK 200 STARANISO REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54717 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.025 REMARK 200 RESOLUTION RANGE LOW (A) : 38.784 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 79.9 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.08500 REMARK 200 R SYM (I) : 0.08500 REMARK 200 FOR THE DATA SET : 11.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.03 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.09 REMARK 200 COMPLETENESS FOR SHELL (%) : 23.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.56900 REMARK 200 R SYM FOR SHELL (I) : 0.56900 REMARK 200 FOR SHELL : 1.800 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: 3UV2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 32 % PEG1 000 200 MM MAGNESIUM REMARK 280 CHLORIDE 100 MM SODIUM CACODYLATE, PH 8.0, VAPOR DIFFUSION, REMARK 280 SITTING 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 32.89550 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 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 3220 O HOH A 3238 1455 1.53 REMARK 500 O HOH A 3120 O HOH A 3238 1455 2.09 REMARK 500 REMARK 500 REMARK: NULL 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 A2835 79.73 -157.40 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 A3340 DISTANCE = 7.46 ANGSTROMS DBREF 8AG2 A 2791 2911 UNP Q12830 BPTF_HUMAN 2917 3037 SEQRES 1 A 121 SER THR GLU ASP ALA MET THR VAL LEU THR PRO LEU THR SEQRES 2 A 121 GLU LYS ASP TYR GLU GLY LEU LYS ARG VAL LEU ARG SER SEQRES 3 A 121 LEU GLN ALA HIS LYS MET ALA TRP PRO PHE LEU GLU PRO SEQRES 4 A 121 VAL ASP PRO ASN ASP ALA PRO ASP TYR TYR GLY VAL ILE SEQRES 5 A 121 LYS GLU PRO MET ASP LEU ALA THR MET GLU GLU ARG VAL SEQRES 6 A 121 GLN ARG ARG TYR TYR GLU LYS LEU THR GLU PHE VAL ALA SEQRES 7 A 121 ASP MET THR LYS ILE PHE ASP ASN CYS ARG TYR TYR ASN SEQRES 8 A 121 PRO SER ASP SER PRO PHE TYR GLN CYS ALA GLU VAL LEU SEQRES 9 A 121 GLU SER PHE PHE VAL GLN LYS LEU LYS GLY PHE LYS ALA SEQRES 10 A 121 SER ARG SER HIS HET M1I A3001 59 HETNAM M1I 5-[3-METHOXY-4-[1-(4-METHYLPIPERAZIN-1-YL) HETNAM 2 M1I CYCLOPROPYL]PHENYL]-1,3,4-TRIMETHYL-PYRIDIN-2-ONE FORMUL 2 M1I C23 H31 N3 O2 FORMUL 3 HOH *240(H2 O) HELIX 1 AA1 THR A 2803 HIS A 2820 1 18 HELIX 2 AA2 LYS A 2821 LEU A 2827 5 7 HELIX 3 AA3 ASP A 2831 ALA A 2835 5 5 HELIX 4 AA4 ASP A 2837 ILE A 2842 1 6 HELIX 5 AA5 ASP A 2847 ARG A 2857 1 11 HELIX 6 AA6 LYS A 2862 ASN A 2881 1 20 HELIX 7 AA7 SER A 2885 ARG A 2909 1 25 CRYST1 27.241 65.791 39.728 90.00 102.51 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 0.036709 0.000000 0.008145 0.00000 SCALE2 0.000000 0.015200 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025783 0.00000