HEADER DNA BINDING PROTEIN 17-SEP-25 9YBU TITLE ARID1B ARID BOUND TO COMPOUND A-3 (5-(PHENYLETHYNYL)PYRIDINE-3- TITLE 2 CARBOXYLIC ACID) COMPND MOL_ID: 1; COMPND 2 MOLECULE: AT-RICH INTERACTIVE DOMAIN-CONTAINING PROTEIN 1B; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1124-1242; COMPND 5 SYNONYM: ARID DOMAIN-CONTAINING PROTEIN 1B,BRG1-ASSOCIATED FACTOR COMPND 6 250B,BAF250B,BRG1-BINDING PROTEIN HELD/OSA1,OSA HOMOLOG 2,HOSA2, COMPND 7 P250R; COMPND 8 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: ARID1B, BAF250B, DAN15, KIAA1235, OSA2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ARID, BAF, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.E.CARBONE,M.J.HOLLIDAY REVDAT 1 05-AUG-26 9YBU 0 JRNL AUTH M.J.HOLLIDAY,C.E.CARBONE,V.Y.ZHAO,H.SCHOENHERR JRNL TITL CRYPTIC SMALL MOLECULE BINDING SITES IN THE ARID1B DNA JRNL TITL 2 BINDING DOMAIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.61 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.61 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.43 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 16145 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.070 REMARK 3 FREE R VALUE TEST SET COUNT : 1625 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 36.4300 - 3.6900 0.99 1244 139 0.1566 0.1941 REMARK 3 2 3.6800 - 2.9300 1.00 1213 139 0.1718 0.1896 REMARK 3 3 2.9200 - 2.5600 1.00 1218 134 0.1815 0.1864 REMARK 3 4 2.5500 - 2.3200 1.00 1218 135 0.1850 0.2247 REMARK 3 5 2.3200 - 2.1600 1.00 1202 134 0.1616 0.2077 REMARK 3 6 2.1600 - 2.0300 1.00 1212 137 0.1733 0.2022 REMARK 3 7 2.0300 - 1.9300 1.00 1198 136 0.1645 0.2070 REMARK 3 8 1.9300 - 1.8400 1.00 1202 135 0.2072 0.2561 REMARK 3 9 1.8400 - 1.7700 1.00 1194 130 0.2027 0.2267 REMARK 3 10 1.7700 - 1.7100 1.00 1209 139 0.2082 0.2574 REMARK 3 11 1.7100 - 1.6600 1.00 1194 130 0.2239 0.2423 REMARK 3 12 1.6600 - 1.6100 1.00 1216 137 0.2338 0.2681 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.166 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.138 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.34 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 : 0.006 947 REMARK 3 ANGLE : 0.849 1273 REMARK 3 CHIRALITY : 0.047 131 REMARK 3 PLANARITY : 0.007 163 REMARK 3 DIHEDRAL : 13.266 355 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -22.1880 18.4256 -1.7706 REMARK 3 T TENSOR REMARK 3 T11: 0.1068 T22: 0.1234 REMARK 3 T33: 0.1048 T12: -0.0074 REMARK 3 T13: 0.0031 T23: -0.0077 REMARK 3 L TENSOR REMARK 3 L11: 1.4906 L22: 1.9671 REMARK 3 L33: 1.7306 L12: -0.3928 REMARK 3 L13: 0.6255 L23: -0.5528 REMARK 3 S TENSOR REMARK 3 S11: 0.0474 S12: 0.0546 S13: -0.0722 REMARK 3 S21: -0.0796 S22: 0.0065 S23: 0.0466 REMARK 3 S31: 0.0107 S32: 0.0358 S33: -0.0381 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 9YBU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-SEP-25. REMARK 100 THE DEPOSITION ID IS D_1000298947. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JUL-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.953698 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16160 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.610 REMARK 200 RESOLUTION RANGE LOW (A) : 36.430 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 20.13 REMARK 200 R MERGE (I) : 0.22800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.61 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.67 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 20.29 REMARK 200 R MERGE FOR SHELL (I) : 3.07600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5 M SODIUM CITRATE, PH 6.5, 0.033% REMARK 280 W/V 4-NITROBENZOIC ACID, 0.033% W/V 5-SULFOSALICYLIC ACID REMARK 280 DIHYDRATE, 0.033% W/V NAPHTHALENE-1,3,6-TRISULFONIC ACID REMARK 280 TRISODIUM SALT HYDRATE, 0.002 M HEPES SODIUM, PH 6.8, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.72333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 15.36167 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 23.04250 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 7.68083 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 38.40417 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 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6980 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 GLU A 1152 REMARK 465 VAL A 1153 REMARK 465 PHE A 1154 REMARK 465 SER A 1155 REMARK 465 THR A 1156 REMARK 465 GLY A 1157 REMARK 465 ASP A 1158 REMARK 465 THR A 1159 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O03 KVD A 1201 O HOH A 1301 1.93 REMARK 500 O HOH A 1316 O HOH A 1368 1.95 REMARK 500 O HOH A 1390 O HOH A 1391 1.98 REMARK 500 O HOH A 1377 O HOH A 1383 2.02 REMARK 500 REMARK 500 REMARK: NULL 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 1301 O HOH A 1339 2564 2.07 REMARK 500 REMARK 500 REMARK: NULL DBREF 9YBU A 1041 1159 UNP Q8NFD5 ARI1B_HUMAN 1124 1242 SEQADV 9YBU GLY A 1040 UNP Q8NFD5 EXPRESSION TAG SEQRES 1 A 120 GLY GLY GLU LYS ILE THR LYS VAL TYR GLU LEU GLY ASN SEQRES 2 A 120 GLU PRO GLU ARG LYS LEU TRP VAL ASP ARG TYR LEU THR SEQRES 3 A 120 PHE MET GLU GLU ARG GLY SER PRO VAL SER SER LEU PRO SEQRES 4 A 120 ALA VAL GLY LYS LYS PRO LEU ASP LEU PHE ARG LEU TYR SEQRES 5 A 120 VAL CYS VAL LYS GLU ILE GLY GLY LEU ALA GLN VAL ASN SEQRES 6 A 120 LYS ASN LYS LYS TRP ARG GLU LEU ALA THR ASN LEU ASN SEQRES 7 A 120 VAL GLY THR SER SER SER ALA ALA SER SER LEU LYS LYS SEQRES 8 A 120 GLN TYR ILE GLN TYR LEU PHE ALA PHE GLU CYS LYS ILE SEQRES 9 A 120 GLU ARG GLY GLU GLU PRO PRO PRO GLU VAL PHE SER THR SEQRES 10 A 120 GLY ASP THR HET KVD A1201 25 HET KVD A1202 25 HETNAM KVD 5-(PHENYLETHYNYL)PYRIDINE-3-CARBOXYLIC ACID FORMUL 2 KVD 2(C14 H9 N O2) FORMUL 4 HOH *93(H2 O) HELIX 1 AA1 LYS A 1043 GLU A 1049 5 7 HELIX 2 AA2 GLU A 1055 ARG A 1070 1 16 HELIX 3 AA3 ASP A 1086 GLY A 1098 1 13 HELIX 4 AA4 GLY A 1099 LYS A 1107 1 9 HELIX 5 AA5 LYS A 1108 LEU A 1116 1 9 HELIX 6 AA6 SER A 1121 LEU A 1136 1 16 HELIX 7 AA7 LEU A 1136 GLY A 1146 1 11 SHEET 1 AA1 2 ALA A1079 VAL A1080 0 SHEET 2 AA1 2 LYS A1083 PRO A1084 -1 O LYS A1083 N VAL A1080 CRYST1 68.671 68.671 46.085 90.00 90.00 120.00 P 65 6 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 0.014562 0.008407 0.000000 0.00000 SCALE2 0.000000 0.016815 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021699 0.00000 CONECT 894 895 899 907 CONECT 895 894 896 911 CONECT 896 895 897 912 CONECT 897 896 898 913 CONECT 898 897 899 914 CONECT 899 894 898 915 CONECT 900 901 909 910 CONECT 901 900 902 905 CONECT 902 901 908 916 CONECT 903 904 908 917 CONECT 904 903 905 906 CONECT 905 901 904 918 CONECT 906 904 907 CONECT 907 894 906 CONECT 908 902 903 CONECT 909 900 CONECT 910 900 CONECT 911 895 CONECT 912 896 CONECT 913 897 CONECT 914 898 CONECT 915 899 CONECT 916 902 CONECT 917 903 CONECT 918 905 CONECT 919 920 924 932 CONECT 920 919 921 936 CONECT 921 920 922 937 CONECT 922 921 923 938 CONECT 923 922 924 939 CONECT 924 919 923 940 CONECT 925 926 934 935 CONECT 926 925 927 930 CONECT 927 926 933 941 CONECT 928 929 933 942 CONECT 929 928 930 931 CONECT 930 926 929 943 CONECT 931 929 932 CONECT 932 919 931 CONECT 933 927 928 CONECT 934 925 CONECT 935 925 CONECT 936 920 CONECT 937 921 CONECT 938 922 CONECT 939 923 CONECT 940 924 CONECT 941 927 CONECT 942 928 CONECT 943 930 MASTER 276 0 2 7 2 0 0 6 1019 1 50 10 END