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- PDB-4tte: Crystal structure of ATAD2A bromodomain complexed with methyl 3-a... -

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Basic information

Entry
Database: PDB / ID: 4tte
TitleCrystal structure of ATAD2A bromodomain complexed with methyl 3-amino-5-(3,5-dimethyl-1,2-oxazol-4-yl)benzoate
ComponentsATPase family AAA domain-containing protein 2
KeywordsGENE REGULATION / ATAD2 bromodomain 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. / Bromodomain-like / Histone Acetyltransferase; Chain A / ATPase family associated with various cellular activities (AAA) / 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. / Bromodomain-like / Histone Acetyltransferase; Chain A / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / 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-36Z / ATPase family AAA domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPoncet-Montange, G. / Zhan, Y. / Bardenhagen, J. / Petrocchi, A. / Leo, E. / Shi, X. / Lee, G. / Leonard, P. / Geck Do, M. / Cardozo, M. ...Poncet-Montange, G. / Zhan, Y. / Bardenhagen, J. / Petrocchi, A. / Leo, E. / Shi, X. / Lee, G. / Leonard, P. / Geck Do, M. / Cardozo, M. / Palmer, W. / Andersen, J. / Jones, P. / Ladbury, J.
CitationJournal: Biochem.J. / Year: 2015
Title: Observed bromodomain flexibility reveals histone peptide- and small molecule ligand-compatible forms of ATAD2.
Authors: Poncet-Montange, G. / Zhan, Y. / Bardenhagen, J.P. / Petrocchi, A. / Leo, E. / Shi, X. / Lee, G.R. / Leonard, P.G. / Geck Do, M.K. / Cardozo, M.G. / Andersen, J.N. / Palmer, W.S. / Jones, P. / Ladbury, J.E.
History
DepositionJun 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Derived calculations
Revision 1.2Mar 4, 2015Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list / refine_hist
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)15,9235
Polymers15,4541
Non-polymers4704
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.310, 79.310, 137.381
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 1 types, 1 molecules A

#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: bromodomain (UNP residues 981-1108)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATAD2, L16, PRO2000 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6PL18, EC: 3.6.1.3

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Non-polymers , 5 types, 257 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-36Z / methyl 3-amino-5-(3,5-dimethyl-1,2-oxazol-4-yl)benzoate


Mass: 246.262 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H14N2O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 4.04 Å3/Da / Density % sol: 69.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 2.1-2.4M Ammonium Sulfate, 0.1M Bis-Tris pH5.5, 10% Glycerol
PH range: 5.2-5.7

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 1.8→48.57 Å / Num. obs: 24459 / % possible obs: 100 % / Redundancy: 21.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.018 / Net I/σ(I): 25 / Num. measured all: 519476 / Scaling rejects: 45
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.8-1.84130.982.51837014110.8040.28100
9-48.5716.40.02650.6431626310.00798.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
Aimless0.1.27data scaling
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DAI

3dai


Resolution: 1.8→68.68 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.925 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.197 1244 5.1 %RANDOM
Rwork0.1833 23152 --
obs0.184 24396 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 86.71 Å2 / Biso mean: 30.077 Å2 / Biso min: 13.7 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 1.8→68.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1084 0 30 253 1367
Biso mean--41 44.15 -
Num. residues----130
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191184
X-RAY DIFFRACTIONr_bond_other_d0.0010.021135
X-RAY DIFFRACTIONr_angle_refined_deg1.4822.0031613
X-RAY DIFFRACTIONr_angle_other_deg0.8443.0042619
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3295145
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.52123.63666
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.29615222
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3341514
X-RAY DIFFRACTIONr_chiral_restr0.0890.2179
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211329
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02269
X-RAY DIFFRACTIONr_mcbond_it1.9542.666535
X-RAY DIFFRACTIONr_mcbond_other1.9462.658534
X-RAY DIFFRACTIONr_mcangle_it2.9753.979671
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 87 -
Rwork0.298 1664 -
all-1751 -
obs--100 %

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