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- PDB-5f3a: Crystal structure of the bromodomain of human ATAD2 in complex wi... -

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Basic information

Entry
Database: PDB / ID: 5f3a
TitleCrystal structure of the bromodomain of human ATAD2 in complex with Compound A14
ComponentsATPase family AAA domain-containing protein 2
KeywordsTRANSFERASE / HYDROLASE INHIBITOR 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
Chem-5U9 / ATPase family AAA domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.599 Å
AuthorsDong, J. / Caflisch, A.
CitationJournal: To Be Published
Title: Crystal structure of the bromodomain of human ATAD2 in complex with Compound A14
Authors: Dong, J. / Caflisch, A.
History
DepositionDec 2, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)15,7763
Polymers15,4541
Non-polymers3222
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-6 kcal/mol
Surface area7920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.938, 79.938, 137.533
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-1334-

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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-5U9 / ~{N}-(4-ethanoyl-1,3-thiazol-2-yl)azetidin-1-ium-3-carboxamide


Mass: 226.275 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12N3O2S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 4.1 Å3/Da / Density % sol: 70.03 %
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: 1.599→69.228 Å / Num. all: 34993 / Num. obs: 34993 / % possible obs: 99.6 % / Redundancy: 19.1 % / Rpim(I) all: 0.011 / Rrim(I) all: 0.048 / Rsym value: 0.047 / Net I/av σ(I): 8.195 / Net I/σ(I): 35.8 / Num. measured all: 667289
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.6-1.6918.80.6631.29169048700.1550.6635.197.5
1.69-1.7919.60.4011.99346147730.0920.4018.6100
1.79-1.9118.40.2313.38251544730.0550.23113.5100
1.91-2.0620.20.1275.98489841930.0290.12723.6100
2.06-2.2619.70.0749.87622438660.0170.07437.8100
2.26-2.5318.70.05313.16633635380.0130.05349100
2.53-2.92200.04315.56272731420.010.04364.1100
2.92-3.5717.90.03616.44806226910.0090.03676.399.9
3.57-5.0618.80.03118.14038121520.0070.03190.8100
5.06-48.78816.20.03213.62099512950.0080.03281.499.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.42 Å48.79 Å
Translation6.42 Å48.79 Å

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHASER2.5.7phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DAI

3dai


Resolution: 1.599→48.788 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.21 1780 5.1 %
Rwork0.1791 33149 -
obs0.1807 34929 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.67 Å2 / Biso mean: 35.8647 Å2 / Biso min: 14.62 Å2
Refinement stepCycle: final / Resolution: 1.599→48.788 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1064 0 20 93 1177
Biso mean--54.17 37.14 -
Num. residues----130
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081113
X-RAY DIFFRACTIONf_angle_d0.7771510
X-RAY DIFFRACTIONf_chiral_restr0.048170
X-RAY DIFFRACTIONf_plane_restr0.004199
X-RAY DIFFRACTIONf_dihedral_angle_d19.163433
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5988-1.6420.25681300.20962359248995
1.642-1.69030.19841310.172125162647100
1.6903-1.74490.2181280.16625202648100
1.7449-1.80730.21951460.169225012647100
1.8073-1.87960.23621180.171925222640100
1.8796-1.96520.21851340.174725272661100
1.9652-2.06880.21571510.183725162667100
2.0688-2.19840.18131440.171825372681100
2.1984-2.36810.16161310.16325582689100
2.3681-2.60640.1921390.174525702709100
2.6064-2.98350.21341350.191725842719100
2.9835-3.75870.2141490.187326292778100
3.7587-48.81040.22681440.176928102954100

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