HEADER NUCLEAR PROTEIN 09-OCT-23 8UHL TITLE ATAD2B BROMODOMAIN IN COMPLEX WITH HISTONE H4 ACETYLATED AT LYSINE 12 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATPASE FAMILY AAA DOMAIN-CONTAINING PROTEIN 2B; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: BROMODOMAIN (UNP RESIDUES 953-1085); COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: HISTONE H4; COMPND 8 CHAIN: B, C; 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: ATAD2B, KIAA1240; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_TAXID: 9606 KEYWDS BROMODOMAINS, EPIGENETICS, CHROMATIN READER DOMAIN, PROTEIN BINDING, KEYWDS 2 NUCLEAR PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.PHILLIPS,C.MONTGOMERY,J.C.NIX,K.C.GLASS REVDAT 1 05-JUN-24 8UHL 0 JRNL AUTH M.PHILLIPS,K.L.MALONE,B.W.BOYLE,C.MONTGOMERY,I.A.KRESSY, JRNL AUTH 2 F.M.JOSEPH,K.M.BRIGHT,S.P.BOYSON,S.CHANG,J.C.NIX,N.L.YOUNG, JRNL AUTH 3 V.JEFFERS,S.FRIETZE,K.C.GLASS JRNL TITL IMPACT OF COMBINATORIAL HISTONE MODIFICATIONS ON JRNL TITL 2 ACETYLLYSINE RECOGNITION BY THE ATAD2 AND ATAD2B JRNL TITL 3 BROMODOMAINS. JRNL REF J.MED.CHEM. V. 67 8186 2024 JRNL REFN ISSN 0022-2623 JRNL PMID 38733345 JRNL DOI 10.1021/ACS.JMEDCHEM.4C00210 REMARK 2 REMARK 2 RESOLUTION. 1.92 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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) : 1.92 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.56 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 17341 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.355 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.61 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.69 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 : 0.009 1250 REMARK 3 ANGLE : 1.040 1679 REMARK 3 CHIRALITY : 0.060 189 REMARK 3 PLANARITY : 0.006 219 REMARK 3 DIHEDRAL : 19.404 504 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 8UHL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-OCT-23. REMARK 100 THE DEPOSITION ID IS D_1000278146. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JUL-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 4.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CMOS REMARK 200 DETECTOR MANUFACTURER : RDI CMOS_8M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17341 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.920 REMARK 200 RESOLUTION RANGE LOW (A) : 27.560 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 13.00 REMARK 200 R MERGE (I) : 0.10910 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.2200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.92 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.99 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.8 M AMMONIUM CITRATE TRIBASIC PH 7, REMARK 280 PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 70.32850 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 27.55950 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 27.55950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 35.16425 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 27.55950 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 27.55950 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 105.49275 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 27.55950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 27.55950 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 35.16425 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 27.55950 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 27.55950 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 105.49275 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 70.32850 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 350 REMARK 350 BIOMOLECULE: 2 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: 720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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 950 REMARK 465 GLY B 4 REMARK 465 LYS B 5 REMARK 465 GLY C -11 REMARK 465 LYS C -10 REMARK 465 GLY C -9 REMARK 465 GLY C -8 REMARK 465 LYS C -7 REMARK 465 GLY C -6 REMARK 465 LEU C -5 REMARK 465 GLY C -4 REMARK 465 ALY C -3 REMARK 465 GLY C -2 DBREF 8UHL A 953 1085 UNP Q9ULI0 ATD2B_HUMAN 953 1085 DBREF 8UHL B 4 17 PDB 8UHL 8UHL 4 17 DBREF 8UHL C -11 2 PDB 8UHL 8UHL -11 2 SEQADV 8UHL GLY A 950 UNP Q9ULI0 EXPRESSION TAG SEQADV 8UHL PRO A 951 UNP Q9ULI0 EXPRESSION TAG SEQADV 8UHL LEU A 952 UNP Q9ULI0 EXPRESSION TAG SEQRES 1 A 136 GLY PRO LEU GLU ASP GLN GLU GLU ASN THR LEU ARG GLU SEQRES 2 A 136 LEU ARG LEU PHE LEU ARG ASP VAL THR LYS ARG LEU ALA SEQRES 3 A 136 THR ASP LYS ARG PHE ASN ILE PHE SER LYS PRO VAL ASP SEQRES 4 A 136 ILE GLU GLU VAL SER ASP TYR LEU GLU VAL ILE LYS GLU SEQRES 5 A 136 PRO MET ASP LEU SER THR VAL ILE THR LYS ILE ASP LYS SEQRES 6 A 136 HIS ASN TYR LEU THR ALA LYS ASP PHE LEU LYS ASP ILE SEQRES 7 A 136 ASP LEU ILE CYS SER ASN ALA LEU GLU TYR ASN PRO ASP SEQRES 8 A 136 LYS ASP PRO GLY ASP LYS ILE ILE ARG HIS ARG ALA CYS SEQRES 9 A 136 THR LEU LYS ASP THR ALA HIS ALA ILE ILE ALA ALA GLU SEQRES 10 A 136 LEU ASP PRO GLU PHE ASN LYS LEU CYS GLU GLU ILE LYS SEQRES 11 A 136 GLU ALA ARG ILE LYS ARG SEQRES 1 B 14 GLY LYS GLY GLY LYS GLY LEU GLY ALY GLY GLY ALA LYS SEQRES 2 B 14 ARG SEQRES 1 C 14 GLY LYS GLY GLY LYS GLY LEU GLY ALY GLY GLY ALA LYS SEQRES 2 C 14 ARG HET ALY B 12 12 HETNAM ALY N(6)-ACETYLLYSINE FORMUL 2 ALY C8 H16 N2 O3 FORMUL 4 HOH *100(H2 O) HELIX 1 AA1 PRO A 951 THR A 976 1 26 HELIX 2 AA2 ASP A 977 SER A 984 5 8 HELIX 3 AA3 ASP A 994 ILE A 999 1 6 HELIX 4 AA4 ASP A 1004 LYS A 1014 1 11 HELIX 5 AA5 THR A 1019 ASN A 1038 1 20 HELIX 6 AA6 ASP A 1042 LEU A 1067 1 26 HELIX 7 AA7 ASP A 1068 ARG A 1085 1 18 LINK C GLY B 11 N ALY B 12 1555 1555 1.32 LINK C ALY B 12 N GLY B 13 1555 1555 1.33 CRYST1 55.119 55.119 140.657 90.00 90.00 90.00 P 41 21 2 16 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 0.018143 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018143 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007109 0.00000