HEADER HYDROLASE/HYDROLASE INHIBITOR 20-DEC-21 7TAB TITLE G-925 BOUND TO THE SMARCA4 (BRG1) BROMODOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ISOFORM 4 OF TRANSCRIPTION ACTIVATOR BRG1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ATP-DEPENDENT HELICASE SMARCA4,BRG1-ASSOCIATED FACTOR 190A, COMPND 5 BAF190A,MITOTIC GROWTH AND TRANSCRIPTION ACTIVATOR,PROTEIN BRG-1, COMPND 6 PROTEIN BRAHMA HOMOLOG 1,SNF2-BETA,SWI/SNF-RELATED MATRIX-ASSOCIATED COMPND 7 ACTIN-DEPENDENT REGULATOR OF CHROMATIN SUBFAMILY A MEMBER 4; COMPND 8 EC: 3.6.4.-; COMPND 9 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: SMARCA4, BAF190A, BRG1, SNF2B, SNF2L4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BROMODOMAIN BRG1 SMARCA4 INHIBITOR, PROTEIN BINDING, HYDROLASE- KEYWDS 2 HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.TANG,F.POY,A.M.TAYLOR,A.G.COCHRAN,S.F.BELLON REVDAT 3 18-OCT-23 7TAB 1 REMARK REVDAT 2 07-SEP-22 7TAB 1 JRNL REVDAT 1 17-AUG-22 7TAB 0 JRNL AUTH A.M.TAYLOR,C.BAILEY,L.D.BELMONT,R.CAMPBELL,N.CANTONE,A.COTE, JRNL AUTH 2 T.D.CRAWFORD,R.CUMMINGS,K.DEMENT,M.DUPLESSIS,M.FLYNN, JRNL AUTH 3 A.C.GOOD,H.R.HUANG,S.JOSHI,Y.LEBLANC,J.MURRAY, JRNL AUTH 4 C.G.NASVESCHUK,A.NEISS,F.POY,F.A.ROMERO,P.SANDY,Y.TANG, JRNL AUTH 5 V.TSUI,L.ZAWADZKE,R.J.SIMS 3RD,J.E.AUDIA,S.F.BELLON, JRNL AUTH 6 S.R.MAGNUSON,B.K.ALBRECHT,A.G.COCHRAN JRNL TITL GNE-064: A POTENT, SELECTIVE, AND ORALLY BIOAVAILABLE JRNL TITL 2 CHEMICAL PROBE FOR THE BROMODOMAINS OF SMARCA2 AND SMARCA4 JRNL TITL 3 AND THE FIFTH BROMODOMAIN OF PBRM1. JRNL REF J.MED.CHEM. V. 65 11177 2022 JRNL REFN ISSN 0022-2623 JRNL PMID 35930799 JRNL DOI 10.1021/ACS.JMEDCHEM.2C00662 REMARK 2 REMARK 2 RESOLUTION. 1.16 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.16 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.88 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 36670 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) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1943 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.16 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.19 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2252 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 81.59 REMARK 3 BIN R VALUE (WORKING SET) : 0.1670 REMARK 3 BIN FREE R VALUE SET COUNT : 114 REMARK 3 BIN FREE R VALUE : 0.1630 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1012 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 126 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.09 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.20000 REMARK 3 B22 (A**2) : 0.19000 REMARK 3 B33 (A**2) : 0.01000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.03000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.041 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.043 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.022 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.434 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.957 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1063 ; 0.014 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1429 ; 2.041 ; 1.644 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 126 ; 5.254 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 55 ;33.143 ;23.091 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 219 ;13.979 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 7 ;12.363 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 135 ; 0.116 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 785 ; 0.013 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 7TAB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-DEC-21. REMARK 100 THE DEPOSITION ID IS D_1000261920. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-DEC-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.2-8.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98011 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 300 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38722 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.160 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 (%) : 98.4 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.16 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.57000 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: MOLREP REMARK 200 STARTING MODEL: 2GRC REMARK 200 REMARK 200 REMARK: VERY THIN PLATES THAT NONETHELESS DIFFRACT TO EXTREME HIGH REMARK 200 RESOLUTION. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN IN BUFFER: 20 MM HEPES PH 7.5, REMARK 280 150 MM NACL, 0.5 MM TCEP, AT A CONCENTRATION OF 15.55 MG/ML REMARK 280 (1.03 MM) RESERVOIR SOLUTION CONTAINS: JEFFAMINE ED-2001 PH 7.0 REMARK 280 AT 30%, TRIS-HCL PH 8.5 AT 0.1 M, 4% PEG 400, 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 14.29850 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 GLY A 1446 REMARK 465 SER A 1447 REMARK 465 GLU A 1571 REMARK 465 GLY A 1572 REMARK 465 GLU A 1573 REMARK 465 GLU A 1574 REMARK 465 SER A 1575 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A1513 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A1515 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF1 7TAB A 1448 1575 UNP SMCA4-4_HUMAN DBREF2 7TAB A P51532-4 1418 1545 SEQADV 7TAB GLY A 1446 UNP P51532-4 EXPRESSION TAG SEQADV 7TAB SER A 1447 UNP P51532-4 EXPRESSION TAG SEQRES 1 A 130 GLY SER ALA GLU LYS LEU SER PRO ASN PRO PRO ASN LEU SEQRES 2 A 130 THR LYS LYS MET LYS LYS ILE VAL ASP ALA VAL ILE LYS SEQRES 3 A 130 TYR LYS ASP SER SER SER GLY ARG GLN LEU SER GLU VAL SEQRES 4 A 130 PHE ILE GLN LEU PRO SER ARG LYS GLU LEU PRO GLU TYR SEQRES 5 A 130 TYR GLU LEU ILE ARG LYS PRO VAL ASP PHE LYS LYS ILE SEQRES 6 A 130 LYS GLU ARG ILE ARG ASN HIS LYS TYR ARG SER LEU ASN SEQRES 7 A 130 ASP LEU GLU LYS ASP VAL MET LEU LEU CYS GLN ASN ALA SEQRES 8 A 130 GLN THR PHE ASN LEU GLU GLY SER LEU ILE TYR GLU ASP SEQRES 9 A 130 SER ILE VAL LEU GLN SER VAL PHE THR SER VAL ARG GLN SEQRES 10 A 130 LYS ILE GLU LYS GLU ASP ASP SER GLU GLY GLU GLU SER HET GGU A1601 20 HETNAM GGU 2-(6-AMINO-5-PHENYLPYRIDAZIN-3-YL)PHENOL FORMUL 2 GGU C16 H13 N3 O FORMUL 3 HOH *126(H2 O) HELIX 1 AA1 PRO A 1455 TYR A 1472 1 18 HELIX 2 AA2 GLN A 1480 ILE A 1486 5 7 HELIX 3 AA3 LEU A 1494 ILE A 1501 1 8 HELIX 4 AA4 ASP A 1506 ASN A 1516 1 11 HELIX 5 AA5 SER A 1521 ASN A 1540 1 20 HELIX 6 AA6 SER A 1544 ASP A 1569 1 26 CRYST1 30.227 28.597 65.740 90.00 91.31 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 0.033083 0.000000 0.000755 0.00000 SCALE2 0.000000 0.034969 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015215 0.00000