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- PDB-4tt2: Crystal structure of ATAD2A bromodomain complexed with H4(1-20)K5... -

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Basic information

Entry
Database: PDB / ID: 4tt2
TitleCrystal structure of ATAD2A bromodomain complexed with H4(1-20)K5Ac peptide
Components
  • ATPase family AAA domain-containing protein 2
  • Histone H4K5Ac
KeywordsGENE REGULATION / bromodomain-acetylated histone complex
Function / homology
Function and homology information


Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / histone binding / chromatin binding / positive regulation of DNA-templated transcription / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / 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) / ATPase, AAA-type, core / Bromodomain-like / Histone Acetyltransferase; Chain A / 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) / ATPase, AAA-type, core / Bromodomain-like / Histone Acetyltransferase; Chain A / 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
ATPase family AAA domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 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 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Derived calculations
Revision 1.2Mar 4, 2015Group: Database references
Revision 2.0Nov 22, 2017Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: atom_site_anisotrop / citation ...atom_site_anisotrop / citation / entity_src_gen / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software
Item: _atom_site_anisotrop.pdbx_PDB_model_num / _atom_site_anisotrop.pdbx_label_asym_id ..._atom_site_anisotrop.pdbx_PDB_model_num / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 2.1Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
P: Histone H4K5Ac


Theoretical massNumber of molelcules
Total (without water)16,0572
Polymers16,0572
Non-polymers00
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint-4 kcal/mol
Surface area8270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.550, 77.550, 62.440
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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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: 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
#2: Protein/peptide Histone H4K5Ac


Mass: 603.651 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: H4 histone peptide with an acetyllysine in position 5
Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.92 Å3/Da / Density % sol: 57.85 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M Ammonium Acetate, 100mM Bis-Tris pH5.5, 15-20% (w/v) PEG 10000

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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: Aug 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 2.5→77.55 Å / Num. obs: 7014 / % possible obs: 100 % / Redundancy: 15.2 % / CC1/2: 1 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.031 / Net I/σ(I): 16.2 / Num. measured all: 106865 / Scaling rejects: 46
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
2.5-2.610.91.0422.283327630.820.326100
9.01-77.5512.90.02742.6249319310.00899.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
Blu-Icedata collection
Aimless0.1.27data scaling
iMOSFLMdata reduction
PDB_EXTRACT3.14data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→54.84 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.912 / SU B: 25.007 / SU ML: 0.264 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.472 / ESU R Free: 0.296 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2672 691 9.9 %RANDOM
Rwork0.2197 6293 --
obs0.2244 6984 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 87.33 Å2 / Biso mean: 39.88 Å2 / Biso min: 27.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å2-0 Å2-0 Å2
2--0.63 Å2-0 Å2
3----1.26 Å2
Refinement stepCycle: final / Resolution: 2.5→54.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1125 0 0 29 1154
Biso mean---46.59 -
Num. residues----136
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0191142
X-RAY DIFFRACTIONr_bond_other_d0.0010.021100
X-RAY DIFFRACTIONr_angle_refined_deg0.7751.991538
X-RAY DIFFRACTIONr_angle_other_deg0.67532533
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1625134
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.11623.38762
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.4315212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2311514
X-RAY DIFFRACTIONr_chiral_restr0.0420.2170
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211270
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02256
X-RAY DIFFRACTIONr_mcbond_it1.0173.963542
X-RAY DIFFRACTIONr_mcbond_other1.013.957541
X-RAY DIFFRACTIONr_mcangle_it1.7885.926674
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.422 47 -
Rwork0.402 445 -
all-492 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 4.637 Å / Origin y: 12.895 Å / Origin z: 11.2 Å
111213212223313233
T0.0426 Å2-0.0045 Å20.0216 Å2-0.1705 Å2-0.1118 Å2--0.1064 Å2
L6.7511 °2-3.3717 °2-0.3418 °2-4.5653 °20.0009 °2--0.4644 °2
S0.1154 Å °0.2619 Å °-0.0651 Å °0.0876 Å °-0.1289 Å °0.1567 Å °0.0577 Å °-0.1163 Å °0.0134 Å °

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