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- PDB-5f36: Crystal structure of the bromodomain of human ATAD2 in complex wi... -

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Basic information

Entry
Database: PDB / ID: 5f36
TitleCrystal structure of the bromodomain of human ATAD2 in complex with Compound A12
ComponentsATPase family AAA domain-containing protein 2
KeywordsTRANSFERASE / HYDROLASE INHIBITOR Complex
Function / homology
Function and homology information


nucleosome disassembly / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / transcription initiation-coupled chromatin remodeling / nucleosome assembly / histone binding / chromatin binding / positive regulation of DNA-templated transcription / ATP hydrolysis activity / extracellular exosome ...nucleosome disassembly / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / transcription initiation-coupled chromatin remodeling / nucleosome assembly / histone binding / chromatin binding / positive regulation of DNA-templated transcription / ATP hydrolysis activity / extracellular exosome / nucleoplasm / ATP binding / nucleus
Similarity search - Function
ATPase family AAA domain-containing protein ATAD2-like / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / Bromodomain-like / Histone Acetyltransferase; Chain A / ATPase, AAA-type, core / Bromodomain ...ATPase family AAA domain-containing protein ATAD2-like / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / Bromodomain-like / Histone Acetyltransferase; Chain A / ATPase, AAA-type, core / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
Chem-5UE / ATPase family AAA domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsDong, J. / Caflisch, A.
CitationJournal: Acs Med.Chem.Lett. / Year: 2020
Title: Hitting a Moving Target: Simulation and Crystallography Study of ATAD2 Bromodomain Blockers.
Authors: Dolbois, A. / Batiste, L. / Wiedmer, L. / Dong, J. / Brutsch, M. / Huang, D. / Deerain, N.M. / Spiliotopoulos, D. / Cheng-Sanchez, I. / Laul, E. / Nevado, C. / Sledz, P. / Caflisch, A.
History
DepositionDec 2, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATPase family AAA domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7994
Polymers15,4541
Non-polymers3463
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-10 kcal/mol
Surface area8070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.804, 79.804, 137.220
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-1327-

HOH

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Components

#1: Protein ATPase family AAA domain-containing protein 2 / AAA nuclear coregulator cancer-associated protein / ANCCA


Mass: 15453.514 Da / Num. of mol.: 1 / Fragment: UNP residues 981-1108
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATAD2, L16, PRO2000 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6PL18, EC: 3.6.1.3
#2: Chemical ChemComp-5UE / [(2~{R})-1-[(4-ethanoyl-1,3-thiazol-2-yl)amino]-1-oxidanylidene-propan-2-yl]azanium


Mass: 214.265 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H12N3O2S
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.08 Å3/Da / Density % sol: 69.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 2M (NH4)2SO4, 0.1M Bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.5→69.112 Å / Num. all: 42035 / Num. obs: 42035 / % possible obs: 99.7 % / Redundancy: 18.9 % / Biso Wilson estimate: 22.95 Å2 / Rpim(I) all: 0.01 / Rrim(I) all: 0.045 / Rsym value: 0.043 / Net I/av σ(I): 7.866 / Net I/σ(I): 35 / Num. measured all: 793117
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.5-1.5817.70.818110441359060.1980.8184.398.2
1.58-1.6819.10.4681.610945957210.1090.4687.5100
1.68-1.7919.60.2692.810508853740.0620.26912.4100
1.79-1.9418.60.1465.29388250410.0350.14619.9100
1.94-2.1220.10.08199331246440.0180.08134.3100
2.12-2.37190.05213.28087542480.0120.05250.7100
2.37-2.7419.50.041167357537720.0090.04164.1100
2.74-3.3518.80.03516.76047732250.0080.03578.6100
3.35-4.7418.20.03184655625610.0070.0391.4100
4.74-48.69116.50.03114.62548015430.0080.03184.899.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DAI

3dai


Resolution: 1.5→48.691 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1895 2039 4.86 %
Rwork0.169 39925 -
obs0.17 41964 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.21 Å2 / Biso mean: 35.3911 Å2 / Biso min: 16.64 Å2
Refinement stepCycle: final / Resolution: 1.5→48.691 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1077 0 20 101 1198
Biso mean--53.11 42.03 -
Num. residues----130
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091124
X-RAY DIFFRACTIONf_angle_d1.1051523
X-RAY DIFFRACTIONf_chiral_restr0.077170
X-RAY DIFFRACTIONf_plane_restr0.005202
X-RAY DIFFRACTIONf_dihedral_angle_d20.18438
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4997-1.53460.18671370.172507264496
1.5346-1.57290.2271210.157126242745100
1.5729-1.61550.17861380.157425972735100
1.6155-1.6630.14391160.144226552771100
1.663-1.71670.18941250.143526082733100
1.7167-1.77810.18841270.145126362763100
1.7781-1.84930.16271250.15226512776100
1.8493-1.93340.17441390.152226362775100
1.9334-2.03540.16451490.163626382787100
2.0354-2.16290.1861240.171226762800100
2.1629-2.32990.17911280.156526582786100
2.3299-2.56430.19241640.165326692833100
2.5643-2.93530.20641400.186727032843100
2.9353-3.6980.20491550.18227392894100
3.698-48.71690.18421510.168729283079100

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