HEADER PROTEIN BINDING 14-MAR-18 6CPS TITLE CRYSTAL STRUCTURE OF THE BROMODOMAIN OF HUMAN ATAD2 WITH A DISULFIDE TITLE 2 BRIDGE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATPASE FAMILY AAA DOMAIN-CONTAINING PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: BROMODOMAIN (UNP RESIDUES 981-1108); COMPND 5 SYNONYM: ATAD2, AAA NUCLEAR COREGULATOR CANCER-ASSOCIATED PROTEIN, COMPND 6 ANCCA; COMPND 7 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(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTATM 2 (DE3) PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PDEST15 KEYWDS DISULFIDE BRIDGE, BROMODOMAIN, EPIGENETICS, CHROMATIN READER DOMAIN, KEYWDS 2 PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR K.C.GLASS,B.E.ECKENROTH,S.CARLSON REVDAT 4 04-OCT-23 6CPS 1 REMARK REVDAT 3 01-JAN-20 6CPS 1 REMARK REVDAT 2 30-JAN-19 6CPS 1 JRNL REVDAT 1 19-DEC-18 6CPS 0 JRNL AUTH J.C.GAY,B.E.ECKENROTH,C.M.EVANS,C.LANGINI,S.CARLSON, JRNL AUTH 2 J.T.LLOYD,A.CAFLISCH,K.C.GLASS JRNL TITL DISULFIDE BRIDGE FORMATION INFLUENCES LIGAND RECOGNITION BY JRNL TITL 2 THE ATAD2 BROMODOMAIN. JRNL REF PROTEINS V. 87 157 2019 JRNL REFN ESSN 1097-0134 JRNL PMID 30520161 JRNL DOI 10.1002/PROT.25636 REMARK 2 REMARK 2 RESOLUTION. 1.93 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.93 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 36485 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.180 REMARK 3 FREE R VALUE TEST SET COUNT : 1891 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 39.6900 - 4.6500 0.99 2499 119 0.1885 0.1808 REMARK 3 2 4.6500 - 3.6900 1.00 2504 130 0.1421 0.1813 REMARK 3 3 3.6900 - 3.2200 1.00 2511 134 0.1502 0.1602 REMARK 3 4 3.2200 - 2.9300 1.00 2470 133 0.1782 0.1954 REMARK 3 5 2.9300 - 2.7200 1.00 2524 120 0.1766 0.2828 REMARK 3 6 2.7200 - 2.5600 1.00 2478 141 0.1790 0.2449 REMARK 3 7 2.5600 - 2.4300 1.00 2509 145 0.1818 0.1903 REMARK 3 8 2.4300 - 2.3300 1.00 2456 151 0.1838 0.2256 REMARK 3 9 2.3300 - 2.2400 1.00 2517 125 0.1795 0.2470 REMARK 3 10 2.2400 - 2.1600 1.00 2477 134 0.1849 0.2091 REMARK 3 11 2.1600 - 2.0900 1.00 2460 145 0.2144 0.2663 REMARK 3 12 2.0900 - 2.0300 0.99 2488 135 0.2248 0.2679 REMARK 3 13 2.0300 - 1.9800 0.99 2448 150 0.2609 0.2749 REMARK 3 14 1.9800 - 1.9300 0.90 2253 129 0.4024 0.3683 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.211 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.084 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.11 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.81 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 : 0.007 1159 REMARK 3 ANGLE : 1.004 1583 REMARK 3 CHIRALITY : 0.047 177 REMARK 3 PLANARITY : 0.004 205 REMARK 3 DIHEDRAL : 22.809 470 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 6CPS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-MAR-18. REMARK 100 THE DEPOSITION ID IS D_1000233051. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-APR-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : BRUKER D8 QUEST REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : HELIOS MX REMARK 200 REMARK 200 DETECTOR TYPE : CMOS REMARK 200 DETECTOR MANUFACTURER : BRUKER PHOTON II REMARK 200 INTENSITY-INTEGRATION SOFTWARE : PROTEUM2 REMARK 200 DATA SCALING SOFTWARE : PROTEUM2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36485 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.930 REMARK 200 RESOLUTION RANGE LOW (A) : 39.680 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 16.40 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.93 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.320 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: PDB ENTRY 3DAI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES SODIUM, PH 7.5, 1.6 M REMARK 280 LITHIUM SULFATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 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 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-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 92.64000 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 46.32000 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 69.48000 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 23.16000 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 115.80000 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 92.64000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 46.32000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 23.16000 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 69.48000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 115.80000 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: 760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LEU A 980 CG CD1 CD2 REMARK 470 GLN A 981 CG CD OE1 NE2 REMARK 470 GLU A 983 CD OE1 OE2 REMARK 470 LYS A1004 CD CE NZ REMARK 470 ARG A1007 NE CZ NH1 NH2 REMARK 470 LYS A1011 CE NZ REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1537 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH A1538 DISTANCE = 6.36 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 1201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 1202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EPE A 1203 DBREF 6CPS A 981 1108 UNP Q6PL18 ATAD2_HUMAN 981 1108 SEQADV 6CPS GLY A 978 UNP Q6PL18 EXPRESSION TAG SEQADV 6CPS PRO A 979 UNP Q6PL18 EXPRESSION TAG SEQADV 6CPS LEU A 980 UNP Q6PL18 EXPRESSION TAG SEQRES 1 A 131 GLY PRO LEU GLN GLU GLU ASP THR PHE ARG GLU LEU ARG SEQRES 2 A 131 ILE PHE LEU ARG ASN VAL THR HIS ARG LEU ALA ILE ASP SEQRES 3 A 131 LYS ARG PHE ARG VAL PHE THR LYS PRO VAL ASP PRO ASP SEQRES 4 A 131 GLU VAL PRO ASP TYR VAL THR VAL ILE LYS GLN PRO MET SEQRES 5 A 131 ASP LEU SER SER VAL ILE SER LYS ILE ASP LEU HIS LYS SEQRES 6 A 131 TYR LEU THR VAL LYS ASP TYR LEU ARG ASP ILE ASP LEU SEQRES 7 A 131 ILE CYS SER ASN ALA LEU GLU TYR ASN PRO ASP ARG ASP SEQRES 8 A 131 PRO GLY ASP ARG LEU ILE ARG HIS ARG ALA CYS ALA LEU SEQRES 9 A 131 ARG ASP THR ALA TYR ALA ILE ILE LYS GLU GLU LEU ASP SEQRES 10 A 131 GLU ASP PHE GLU GLN LEU CYS GLU GLU ILE GLN GLU SER SEQRES 11 A 131 ARG HET SO4 A1201 5 HET SO4 A1202 5 HET EPE A1203 15 HETNAM SO4 SULFATE ION HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETSYN EPE HEPES FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 EPE C8 H18 N2 O4 S FORMUL 5 HOH *238(H2 O) HELIX 1 AA1 GLY A 978 ILE A 1002 1 25 HELIX 2 AA2 ASP A 1003 THR A 1010 5 8 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 SER A 1107 1 14 SSBOND 1 CYS A 1057 CYS A 1079 1555 1555 2.05 SITE 1 AC1 7 ARG A 987 ARG A 990 ARG A 994 ARG A1067 SITE 2 AC1 7 ARG A1072 HOH A1322 HOH A1422 SITE 1 AC2 9 ARG A 994 ARG A1067 PRO A1069 HOH A1302 SITE 2 AC2 9 HOH A1309 HOH A1313 HOH A1344 HOH A1402 SITE 3 AC2 9 HOH A1412 SITE 1 AC3 10 VAL A1008 LYS A1011 TYR A1021 ASP A1030 SITE 2 AC3 10 ASN A1064 ILE A1074 HOH A1356 HOH A1371 SITE 3 AC3 10 HOH A1393 HOH A1415 CRYST1 79.359 79.359 138.960 90.00 90.00 120.00 P 65 2 2 12 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 0.012601 0.007275 0.000000 0.00000 SCALE2 0.000000 0.014550 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007196 0.00000