HEADER HYDROLASE/HYDROLASE INHIBITOR 09-JUL-14 4TZ8 TITLE STRUCTURE OF HUMAN ATAD2 BROMODOMAIN BOUND TO FRAGMENT INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATPASE FAMILY AAA DOMAIN-CONTAINING PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 981-1108; COMPND 5 SYNONYM: AAA NUCLEAR COREGULATOR CANCER-ASSOCIATED PROTEIN,ANCCA; COMPND 6 EC: 3.6.1.3; 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) GOLD KEYWDS ATAD2, BROMODOMAIN, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.J.HARNER,B.A.CHAUDER,J.PHAN,S.W.FESIK REVDAT 6 27-SEP-23 4TZ8 1 REMARK REVDAT 5 04-DEC-19 4TZ8 1 REMARK REVDAT 4 22-NOV-17 4TZ8 1 REMARK REVDAT 3 06-SEP-17 4TZ8 1 SOURCE JRNL REMARK REVDAT 2 03-DEC-14 4TZ8 1 JRNL REVDAT 1 29-OCT-14 4TZ8 0 JRNL AUTH M.J.HARNER,B.A.CHAUDER,J.PHAN,S.W.FESIK JRNL TITL FRAGMENT-BASED SCREENING OF THE BROMODOMAIN OF ATAD2. JRNL REF J.MED.CHEM. V. 57 9687 2014 JRNL REFN ISSN 0022-2623 JRNL PMID 25314628 JRNL DOI 10.1021/JM501035J REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.9_1692) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.62 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 14693 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1469 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 34.6204 - 4.6307 0.99 1472 162 0.1862 0.1906 REMARK 3 2 4.6307 - 3.6768 0.99 1358 151 0.1565 0.1905 REMARK 3 3 3.6768 - 3.2124 0.99 1332 149 0.1955 0.2372 REMARK 3 4 3.2124 - 2.9189 1.00 1329 147 0.2122 0.2509 REMARK 3 5 2.9189 - 2.7098 0.99 1299 145 0.2196 0.2545 REMARK 3 6 2.7098 - 2.5501 0.99 1310 145 0.2275 0.2819 REMARK 3 7 2.5501 - 2.4224 0.99 1278 142 0.2252 0.2716 REMARK 3 8 2.4224 - 2.3170 0.99 1295 145 0.2397 0.2756 REMARK 3 9 2.3170 - 2.2278 0.99 1282 143 0.2458 0.3087 REMARK 3 10 2.2278 - 2.1500 0.98 1269 140 0.2597 0.3017 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.090 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 : 0.002 1110 REMARK 3 ANGLE : 0.562 1508 REMARK 3 CHIRALITY : 0.023 169 REMARK 3 PLANARITY : 0.003 196 REMARK 3 DIHEDRAL : 11.390 434 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 4TZ8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JUL-14. REMARK 100 THE DEPOSITION ID IS D_1000202557. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-DEC-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14730 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 34.620 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 23.40 REMARK 200 R MERGE (I) : 0.11300 REMARK 200 R SYM (I) : 0.14500 REMARK 200 FOR THE DATA SET : 13.1900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.19 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.7 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: NULL REMARK 200 STARTING MODEL: PDB ENTRY 3DAI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS, PH 5.5, 2.5 M REMARK 280 (NH4)2SO4, CRYSTALS GENERATED AT 277 K, FRAGMENT SOAKED AT 291 K REMARK 280 OVERNIGHT, VAPOR DIFFUSION, HANGING DROP 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 92.17267 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 46.08633 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 69.12950 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 23.04317 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 115.21583 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 92.17267 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 46.08633 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 23.04317 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 69.12950 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 115.21583 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 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A1306 LIES ON A SPECIAL POSITION. 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 MET A 980 CG SD CE REMARK 470 GLN A 981 CD OE1 NE2 REMARK 470 GLU A 983 CD OE1 OE2 REMARK 470 LYS A1004 CD CE NZ REMARK 470 LYS A1011 CE NZ REMARK 470 GLU A1017 CG CD OE1 OE2 REMARK 470 LYS A1047 CE NZ 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 CL A 1203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 39U A 1204 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4TYL RELATED DB: PDB REMARK 900 RELATED ID: 4TZ2 RELATED DB: PDB DBREF 4TZ8 A 981 1108 UNP Q6PL18 ATAD2_HUMAN 981 1108 SEQADV 4TZ8 SER A 979 UNP Q6PL18 EXPRESSION TAG SEQADV 4TZ8 MET A 980 UNP Q6PL18 EXPRESSION TAG SEQRES 1 A 130 SER MET GLN GLU GLU ASP THR PHE ARG GLU LEU ARG ILE SEQRES 2 A 130 PHE LEU ARG ASN VAL THR HIS ARG LEU ALA ILE ASP LYS SEQRES 3 A 130 ARG PHE ARG VAL PHE THR LYS PRO VAL ASP PRO ASP GLU SEQRES 4 A 130 VAL PRO ASP TYR VAL THR VAL ILE LYS GLN PRO MET ASP SEQRES 5 A 130 LEU SER SER VAL ILE SER LYS ILE ASP LEU HIS LYS TYR SEQRES 6 A 130 LEU THR VAL LYS ASP TYR LEU ARG ASP ILE ASP LEU ILE SEQRES 7 A 130 CYS SER ASN ALA LEU GLU TYR ASN PRO ASP ARG ASP PRO SEQRES 8 A 130 GLY ASP ARG LEU ILE ARG HIS ARG ALA CYS ALA LEU ARG SEQRES 9 A 130 ASP THR ALA TYR ALA ILE ILE LYS GLU GLU LEU ASP GLU SEQRES 10 A 130 ASP PHE GLU GLN LEU CYS GLU GLU ILE GLN GLU SER ARG HET SO4 A1201 5 HET SO4 A1202 5 HET CL A1203 1 HET 39U A1204 14 HETNAM SO4 SULFATE ION HETNAM CL CHLORIDE ION HETNAM 39U 2-AMINO-7,7-DIMETHYL-5,6,7,8-TETRAHYDRO-4H-[1, HETNAM 2 39U 3]THIAZOLO[5,4-C]AZEPIN-4-ONE FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 CL CL 1- FORMUL 5 39U C9 H13 N3 O S FORMUL 6 HOH *135(H2 O) HELIX 1 AA1 SER A 979 ILE A 1002 1 24 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 SITE 1 AC1 7 ARG A 987 ARG A 990 ARG A 994 ARG A1067 SITE 2 AC1 7 ARG A1072 HOH A1321 HOH A1328 SITE 1 AC2 2 ARG A1007 ARG A1077 SITE 1 AC3 1 HOH A1345 SITE 1 AC4 8 VAL A1008 LYS A1011 VAL A1013 ASN A1064 SITE 2 AC4 8 ILE A1074 HOH A1351 HOH A1358 HOH A1399 CRYST1 79.942 79.942 138.259 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 0.012509 0.007222 0.000000 0.00000 SCALE2 0.000000 0.014444 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007233 0.00000