HEADER NUCLEAR PROTEIN 30-MAR-21 7M98 TITLE ATAD2 BROMODOMAIN COMPLEXED WITH HISTONE H4K5AC (RES 1-10) LIGAND COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATPASE FAMILY AAA DOMAIN-CONTAINING PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: AAA NUCLEAR COREGULATOR CANCER-ASSOCIATED PROTEIN,ANCCA; COMPND 5 EC: 3.6.1.-; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: HISTONE H4; COMPND 10 CHAIN: B; COMPND 11 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: ATAD2, L16, PRO2000; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX-6P1; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 GENE: H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, SOURCE 15 H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, SOURCE 16 HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, HIST1H4H, SOURCE 17 H4C9, H4/M, H4FM, HIST1H4I, H4C11, H4/E, H4FE, HIST1H4J, H4C12, SOURCE 18 H4/D, H4FD, HIST1H4K, H4C13, H4/K, H4FK, HIST1H4L, H4C14, H4/N, SOURCE 19 H4F2, H4FN, HIST2H4, HIST2H4A, H4C15, H4/O, H4FO, HIST2H4B, H4-16, SOURCE 20 HIST4H4; SOURCE 21 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 22 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 23 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 24 EXPRESSION_SYSTEM_PLASMID: PGEX-6P1 KEYWDS BROMODOMAIN, EPIGENETICS, NUCLEAR PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.L.MALONE,M.PHILLIPS,J.C.NIX,K.C.GLASS REVDAT 3 15-NOV-23 7M98 1 REMARK REVDAT 2 18-OCT-23 7M98 1 REMARK REVDAT 1 22-SEP-21 7M98 0 JRNL AUTH C.M.EVANS,M.PHILLIPS,K.L.MALONE,M.TONELLI,G.CORNILESCU, JRNL AUTH 2 C.CORNILESCU,S.J.HOLTON,M.GORJANACZ,L.WANG,S.CARLSON, JRNL AUTH 3 J.C.GAY,J.C.NIX,B.DEMELER,J.L.MARKLEY,K.C.GLASS JRNL TITL COORDINATION OF DI-ACETYLATED HISTONE LIGANDS BY THE ATAD2 JRNL TITL 2 BROMODOMAIN. JRNL REF INT J MOL SCI V. 22 2021 JRNL REFN ESSN 1422-0067 JRNL PMID 34502039 JRNL DOI 10.3390/IJMS22179128 REMARK 2 REMARK 2 RESOLUTION. 1.60 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.54 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 31784 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 1612 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 44.5400 - 3.6600 1.00 2760 156 0.1682 0.1983 REMARK 3 2 3.6600 - 2.9100 1.00 2589 129 0.1778 0.2170 REMARK 3 3 2.9100 - 2.5400 1.00 2521 145 0.1918 0.1936 REMARK 3 4 2.5400 - 2.3100 1.00 2541 125 0.1892 0.2112 REMARK 3 5 2.3100 - 2.1400 1.00 2472 138 0.2044 0.2181 REMARK 3 6 2.1400 - 2.0200 1.00 2511 139 0.1899 0.2272 REMARK 3 7 2.0200 - 1.9100 1.00 2477 141 0.2478 0.2751 REMARK 3 8 1.9100 - 1.8300 1.00 2483 137 0.3039 0.3236 REMARK 3 9 1.8300 - 1.7600 1.00 2457 127 0.2410 0.2626 REMARK 3 10 1.7600 - 1.7000 1.00 2506 122 0.2438 0.2696 REMARK 3 11 1.7000 - 1.6500 1.00 2426 142 0.2830 0.2791 REMARK 3 12 1.6500 - 1.6000 0.98 2429 111 0.3167 0.3423 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) : 0.195 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.003 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.92 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.75 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 : 0.014 1227 REMARK 3 ANGLE : 1.250 1659 REMARK 3 CHIRALITY : 0.076 181 REMARK 3 PLANARITY : 0.009 222 REMARK 3 DIHEDRAL : 22.227 503 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 7M98 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-MAR-21. REMARK 100 THE DEPOSITION ID IS D_1000254853. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-DEC-20 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : NULL 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 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 : 32508 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.590 REMARK 200 RESOLUTION RANGE LOW (A) : 44.540 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.13100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.8700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.59 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.62 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.66120 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.750 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: 4TT2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0 M SODIUM PHOSPHATE MONOBASIC REMARK 280 MONOHYDRATE/POTASSIUM PHOSPHATE DIBASIC, PH 6.6, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 2 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,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z+1/2 REMARK 290 7555 Y,X,-Z+1/4 REMARK 290 8555 -Y,-X,-Z+3/4 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 80.17500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 120.26250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 40.08750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 80.17500 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 40.08750 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 120.26250 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 890 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8870 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 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 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 961 REMARK 465 PRO A 962 REMARK 465 LEU A 963 REMARK 465 GLY A 964 REMARK 465 SER A 965 REMARK 465 GLU A 966 REMARK 465 PRO A 967 REMARK 465 ARG A 968 REMARK 465 SER A 969 REMARK 465 LEU A 970 REMARK 465 THR A 971 REMARK 465 ALA A 972 REMARK 465 GLU A 973 REMARK 465 GLU A 974 REMARK 465 VAL A 975 REMARK 465 LYS A 976 REMARK 465 ARG A 977 REMARK 465 ARG A 1111 REMARK 465 GLY A 1112 REMARK 465 LYS B 8 REMARK 465 GLY B 9 REMARK 465 LEU B 10 REMARK 465 GLY B 11 REMARK 465 LYS B 12 REMARK 465 GLY B 13 REMARK 465 GLY B 14 REMARK 465 ALA B 15 DBREF 7M98 A 966 1112 UNP Q6PL18 ATAD2_HUMAN 966 1112 DBREF 7M98 B 1 15 UNP P62805 H4_HUMAN 2 16 SEQADV 7M98 GLY A 961 UNP Q6PL18 EXPRESSION TAG SEQADV 7M98 PRO A 962 UNP Q6PL18 EXPRESSION TAG SEQADV 7M98 LEU A 963 UNP Q6PL18 EXPRESSION TAG SEQADV 7M98 GLY A 964 UNP Q6PL18 EXPRESSION TAG SEQADV 7M98 SER A 965 UNP Q6PL18 EXPRESSION TAG SEQADV 7M98 ALA A 1101 UNP Q6PL18 CYS 1101 ENGINEERED MUTATION SEQRES 1 A 152 GLY PRO LEU GLY SER GLU PRO ARG SER LEU THR ALA GLU SEQRES 2 A 152 GLU VAL LYS ARG LEU GLU GLU GLN GLU GLU ASP THR PHE SEQRES 3 A 152 ARG GLU LEU ARG ILE PHE LEU ARG ASN VAL THR HIS ARG SEQRES 4 A 152 LEU ALA ILE ASP LYS ARG PHE ARG VAL PHE THR LYS PRO SEQRES 5 A 152 VAL ASP PRO ASP GLU VAL PRO ASP TYR VAL THR VAL ILE SEQRES 6 A 152 LYS GLN PRO MET ASP LEU SER SER VAL ILE SER LYS ILE SEQRES 7 A 152 ASP LEU HIS LYS TYR LEU THR VAL LYS ASP TYR LEU ARG SEQRES 8 A 152 ASP ILE ASP LEU ILE CYS SER ASN ALA LEU GLU TYR ASN SEQRES 9 A 152 PRO ASP ARG ASP PRO GLY ASP ARG LEU ILE ARG HIS ARG SEQRES 10 A 152 ALA CYS ALA LEU ARG ASP THR ALA TYR ALA ILE ILE LYS SEQRES 11 A 152 GLU GLU LEU ASP GLU ASP PHE GLU GLN LEU ALA GLU GLU SEQRES 12 A 152 ILE GLN GLU SER ARG LYS LYS ARG GLY SEQRES 1 B 15 SER GLY ARG GLY ALY GLY GLY LYS GLY LEU GLY LYS GLY SEQRES 2 B 15 GLY ALA MODRES 7M98 ALY B 5 LYS MODIFIED RESIDUE HET ALY B 5 12 HETNAM ALY N(6)-ACETYLLYSINE FORMUL 2 ALY C8 H16 N2 O3 FORMUL 3 HOH *203(H2 O) HELIX 1 AA1 GLU A 979 ASP A 1003 1 25 HELIX 2 AA2 LYS A 1004 THR A 1010 5 7 HELIX 3 AA3 ASP A 1020 ILE A 1025 1 6 HELIX 4 AA4 ASP A 1030 LEU A 1040 1 11 HELIX 5 AA5 THR A 1045 ASN A 1064 1 20 HELIX 6 AA6 ASP A 1068 LEU A 1093 1 26 HELIX 7 AA7 ASP A 1094 LYS A 1109 1 16 LINK C GLY B 4 N ALY B 5 1555 1555 1.32 LINK C ALY B 5 N GLY B 6 1555 1555 1.32 CRYST1 53.560 53.560 160.350 90.00 90.00 90.00 P 43 2 2 8 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 0.018671 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018671 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006236 0.00000