HEADER CYTOSOLIC PROTEIN 12-OCT-17 6EPR
TITLE THE ATAD2 BROMODOMAIN IN COMPLEX WITH COMPOUND UZH-DS15
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: 3.6.1.3;
COMPND 6 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: 562
KEYWDS BROMODOMAIN, ATAD2, INHIBITOR, COMPLEX, CYTOSOLIC PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR P.SLEDZ,A.CAFLISCH
REVDAT 2 13-NOV-19 6EPR 1 JRNL
REVDAT 1 31-OCT-18 6EPR 0
JRNL AUTH P.SLEDZ
JRNL TITL HITTING A MOVING TARGET: SIMULATION AND CRYSTALLOGRAPHY
JRNL TITL 2 STUDY OF ATAD2 BROMODOMAIN BLOCKERS
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 2
REMARK 2 RESOLUTION. 2.05 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX (1.11.1_2575: ???)
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) : 2.05
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.89
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 3 NUMBER OF REFLECTIONS : 30857
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.198
REMARK 3 R VALUE (WORKING SET) : 0.196
REMARK 3 FREE R VALUE : 0.232
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980
REMARK 3 FREE R VALUE TEST SET COUNT : 1536
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 48.9023 - 4.5651 1.00 2680 141 0.1683 0.2055
REMARK 3 2 4.5651 - 3.6238 1.00 2654 144 0.1592 0.1673
REMARK 3 3 3.6238 - 3.1659 1.00 2675 139 0.2011 0.2367
REMARK 3 4 3.1659 - 2.8764 1.00 2681 135 0.2227 0.3012
REMARK 3 5 2.8764 - 2.6703 1.00 2655 138 0.2208 0.2628
REMARK 3 6 2.6703 - 2.5129 1.00 2682 136 0.2150 0.2942
REMARK 3 7 2.5129 - 2.3870 1.00 2672 140 0.2252 0.2284
REMARK 3 8 2.3870 - 2.2831 1.00 2654 147 0.2231 0.3083
REMARK 3 9 2.2831 - 2.1952 1.00 2678 138 0.2217 0.3219
REMARK 3 10 2.1952 - 2.1195 1.00 2665 135 0.2484 0.2391
REMARK 3 11 2.1195 - 2.0532 0.99 2625 143 0.2581 0.2536
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) : 0.190
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.540
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 : 0.009 1134
REMARK 3 ANGLE : 1.169 1543
REMARK 3 CHIRALITY : 0.049 172
REMARK 3 PLANARITY : 0.006 202
REMARK 3 DIHEDRAL : 6.638 998
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 6EPR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-OCT-17.
REMARK 100 THE DEPOSITION ID IS D_1200007034.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 09-JUL-17
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 5.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SLS
REMARK 200 BEAMLINE : X06DA
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.000040
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M-F
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : NULL
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30909
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050
REMARK 200 RESOLUTION RANGE LOW (A) : 48.888
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 200 DATA REDUNDANCY : 6.970
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.8900
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6
REMARK 200 DATA REDUNDANCY IN SHELL : 6.53
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.260
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL
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 (%): 70.21
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.13
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 2M AMMONIUM SULFATE, 0.1M BIS-TRIS PH
REMARK 280 5.5, 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 91.89600
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 45.94800
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 68.92200
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 22.97400
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 114.87000
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 91.89600
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 45.94800
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 22.97400
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 68.92200
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 114.87000
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: 180 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 7940 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 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 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 A1361 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 LYS A1004 CD CE NZ
REMARK 470 LYS A1011 CE NZ
REMARK 470 LYS A1026 CG CD CE NZ
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 BQE 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
DBREF 6EPR A 981 1108 UNP Q6PL18 ATAD2_HUMAN 981 1108
SEQADV 6EPR SER A 979 UNP Q6PL18 EXPRESSION TAG
SEQADV 6EPR 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 BQE A1201 34
HET SO4 A1202 5
HETNAM BQE (~{N}~{Z},2~{R})-~{N}-[5-(5-AZANYLPYRIDIN-3-YL)-4-
HETNAM 2 BQE ETHANOYL-3~{H}-1,3-THIAZOL-2-YLIDENE]-1-[2-[4,4-
HETNAM 3 BQE BIS(FLUORANYL)CYCLOHEXYL]ETHYL]PIPERAZINE-2-
HETNAM 4 BQE CARBOXAMIDE
HETNAM SO4 SULFATE ION
FORMUL 2 BQE C23 H30 F2 N6 O2 S
FORMUL 3 SO4 O4 S 2-
FORMUL 4 HOH *81(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 9 VAL A1008 LYS A1011 VAL A1013 TYR A1063
SITE 2 AC1 9 ASN A1064 ASP A1071 ILE A1074 ARG A1077
SITE 3 AC1 9 HOH A1303
SITE 1 AC2 4 ARG A 987 ARG A 990 ARG A 994 ARG A1067
CRYST1 80.087 80.087 137.844 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 0.012486 0.007209 0.000000 0.00000
SCALE2 0.000000 0.014418 0.000000 0.00000
SCALE3 0.000000 0.000000 0.007255 0.00000
(ATOM LINES ARE NOT SHOWN.)
END