HEADER NUCLEAR PROTEIN 07-APR-23 8SDX TITLE ATAD2B BROMODOMAIN IN COMPLEX WITH HISTONE H4 ACETYLATED AT LYSINE 5 TITLE 2 WITH SERINE 1 MUTATION TO CYSTEINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATPASE FAMILY AAA DOMAIN-CONTAINING PROTEIN 2B; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: BROMODOMAIN (UNP RESIDUES 953-1085); COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: HISTONE H4S1CK5AC; COMPND 8 CHAIN: C, D; 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 8SDX 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. 2.69 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) : 2.69 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.52 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 12555 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.226 REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.170 REMARK 3 FREE R VALUE TEST SET COUNT : 649 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 33.5200 - 4.6000 0.99 2456 145 0.1757 0.1983 REMARK 3 2 4.6000 - 3.6500 0.99 2450 131 0.2051 0.2412 REMARK 3 3 3.6500 - 3.1900 0.99 2442 120 0.2686 0.3630 REMARK 3 4 3.1900 - 2.9000 0.99 2438 146 0.2956 0.3550 REMARK 3 5 2.9000 - 2.6900 0.86 2120 107 0.3637 0.4048 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) : 0.466 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.863 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 64.12 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 : 0.011 2347 REMARK 3 ANGLE : 1.409 3155 REMARK 3 CHIRALITY : 0.073 358 REMARK 3 PLANARITY : 0.009 410 REMARK 3 DIHEDRAL : 24.625 930 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 8SDX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-APR-23. REMARK 100 THE DEPOSITION ID IS D_1000273619. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-APR-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 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) : 1.072 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 : 12940 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.690 REMARK 200 RESOLUTION RANGE LOW (A) : 33.520 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.12440 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.6300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.69 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.78 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.62600 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 (%): 64.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM SULFATE, 0.1 M TRIS PH REMARK 280 8.5, 25% W/V PEG 3350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 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 39.81450 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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: 1020 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 REMARK 350 BIOMOLECULE: 2 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: 790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8800 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D 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 950 REMARK 465 LYS C 8 REMARK 465 GLY C 9 REMARK 465 LEU C 10 REMARK 465 GLY C 11 REMARK 465 LYS C 12 REMARK 465 GLY C 13 REMARK 465 GLY C 14 REMARK 465 ALA C 15 REMARK 465 LYS D 8 REMARK 465 GLY D 9 REMARK 465 LEU D 10 REMARK 465 GLY D 11 REMARK 465 LYS D 12 REMARK 465 GLY D 13 REMARK 465 GLY D 14 REMARK 465 ALA D 15 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 ASP A 954 -72.89 -69.22 REMARK 500 ILE A 989 58.19 -114.43 REMARK 500 GLU A 990 -61.86 -128.42 REMARK 500 GLU A1001 75.34 -154.94 REMARK 500 ASP A1040 55.40 -114.22 REMARK 500 LYS A1084 -91.16 -133.92 REMARK 500 LYS B1041 -52.08 -135.30 REMARK 500 ILE B1083 47.94 -70.80 REMARK 500 LYS B1084 -41.54 -158.57 REMARK 500 ALY C 5 -73.82 -78.53 REMARK 500 REMARK 500 REMARK: NULL DBREF 8SDX A 953 1085 UNP Q9ULI0 ATD2B_HUMAN 953 1085 DBREF 8SDX B 953 1085 UNP Q9ULI0 ATD2B_HUMAN 953 1085 DBREF 8SDX C 1 15 PDB 8SDX 8SDX 1 15 DBREF 8SDX D 1 15 PDB 8SDX 8SDX 1 15 SEQADV 8SDX GLY A 950 UNP Q9ULI0 EXPRESSION TAG SEQADV 8SDX PRO A 951 UNP Q9ULI0 EXPRESSION TAG SEQADV 8SDX LEU A 952 UNP Q9ULI0 EXPRESSION TAG SEQADV 8SDX GLY B 950 UNP Q9ULI0 EXPRESSION TAG SEQADV 8SDX PRO B 951 UNP Q9ULI0 EXPRESSION TAG SEQADV 8SDX LEU B 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 136 GLY PRO LEU GLU ASP GLN GLU GLU ASN THR LEU ARG GLU SEQRES 2 B 136 LEU ARG LEU PHE LEU ARG ASP VAL THR LYS ARG LEU ALA SEQRES 3 B 136 THR ASP LYS ARG PHE ASN ILE PHE SER LYS PRO VAL ASP SEQRES 4 B 136 ILE GLU GLU VAL SER ASP TYR LEU GLU VAL ILE LYS GLU SEQRES 5 B 136 PRO MET ASP LEU SER THR VAL ILE THR LYS ILE ASP LYS SEQRES 6 B 136 HIS ASN TYR LEU THR ALA LYS ASP PHE LEU LYS ASP ILE SEQRES 7 B 136 ASP LEU ILE CYS SER ASN ALA LEU GLU TYR ASN PRO ASP SEQRES 8 B 136 LYS ASP PRO GLY ASP LYS ILE ILE ARG HIS ARG ALA CYS SEQRES 9 B 136 THR LEU LYS ASP THR ALA HIS ALA ILE ILE ALA ALA GLU SEQRES 10 B 136 LEU ASP PRO GLU PHE ASN LYS LEU CYS GLU GLU ILE LYS SEQRES 11 B 136 GLU ALA ARG ILE LYS ARG SEQRES 1 C 15 CYS GLY ARG GLY ALY GLY GLY LYS GLY LEU GLY LYS GLY SEQRES 2 C 15 GLY ALA SEQRES 1 D 15 CYS GLY ARG GLY ALY GLY GLY LYS GLY LEU GLY LYS GLY SEQRES 2 D 15 GLY ALA HET ALY C 5 12 HET ALY D 5 12 HET SO4 B1101 5 HETNAM ALY N(6)-ACETYLLYSINE HETNAM SO4 SULFATE ION FORMUL 3 ALY 2(C8 H16 N2 O3) FORMUL 5 SO4 O4 S 2- FORMUL 6 HOH *26(H2 O) HELIX 1 AA1 PRO A 951 ASP A 977 1 27 HELIX 2 AA2 LYS A 978 SER A 984 5 7 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 ILE A 1083 1 16 HELIX 8 AA8 GLU B 953 THR B 976 1 24 HELIX 9 AA9 ASP B 977 SER B 984 5 8 HELIX 10 AB1 ASP B 994 ILE B 999 1 6 HELIX 11 AB2 ASP B 1004 LYS B 1014 1 11 HELIX 12 AB3 THR B 1019 ASN B 1038 1 20 HELIX 13 AB4 ASP B 1042 LEU B 1067 1 26 HELIX 14 AB5 ASP B 1068 ILE B 1083 1 16 LINK C GLY C 4 N ALY C 5 1555 1555 1.34 LINK C ALY C 5 N GLY C 6 1555 1555 1.34 LINK C GLY D 4 N ALY D 5 1555 1555 1.31 LINK C ALY D 5 N GLY D 6 1555 1555 1.31 CRYST1 47.687 79.629 64.348 90.00 105.14 90.00 P 1 21 1 4 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 0.020970 0.000000 0.005674 0.00000 SCALE2 0.000000 0.012558 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016099 0.00000