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

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Basic information

Entry
Database: PDB / ID: 5epb
TitleCrystal structure of the bromodomain of human ATAD2 in complex with Compound 49
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-5QW / 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: To Be Published
Title: Crystal structure of the bromodomain of human ATAD2 in complex with Compound 49
Authors: Dong, J. / Caflisch, A.
History
DepositionNov 11, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 23, 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)16,2484
Polymers15,4541
Non-polymers7953
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-11 kcal/mol
Surface area8040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.258, 79.258, 139.121
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-1378-

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, adenosinetriphosphatase
#2: Chemical ChemComp-5QW / ~{N}-[(2~{S})-2-morpholin-4-ylpropyl]-4-oxidanylidene-3,5-dihydro-2~{H}-1,5-benzothiazepine-7-carboxamide


Mass: 349.448 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H23N3O3S
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99987 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 1.5→68.639 Å / Num. all: 41688 / Num. obs: 41688 / % possible obs: 99.2 % / Redundancy: 19 % / Rpim(I) all: 0.009 / Rrim(I) all: 0.038 / Rsym value: 0.036 / Net I/av σ(I): 10.095 / Net I/σ(I): 41.9 / Num. measured all: 790978
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
1.5-1.5819.30.4231.811114557720.0970.4237.196.6
1.58-1.6819.10.2652.910785456340.0610.26511.299.1
1.68-1.7919.20.1654.610279353420.0380.16517.199.5
1.79-1.9419.80.17.59897350070.0230.126.799.7
1.94-2.1218.80.06311.48676146120.0150.06340.699.8
2.12-2.3719.60.04515.48313442410.010.04560.599.9
2.37-2.7418.30.03717.86895537610.0090.0377199.9
2.74-3.3518.80.03120.36057032210.0070.03190.7100
3.35-4.7417.50.02622.54472825540.0060.026103.499.7
4.74-48.85816.90.02318.42606515440.0060.02397.899.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.5 Å48.86 Å
Translation1.5 Å48.86 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: 1.5→48.858 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1857 2107 5.06 %
Rwork0.1671 39537 -
obs0.1681 41644 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.08 Å2 / Biso mean: 30.9246 Å2 / Biso min: 14.85 Å2
Refinement stepCycle: final / Resolution: 1.5→48.858 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1084 0 53 221 1358
Biso mean--44.56 42.35 -
Num. residues----130
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051170
X-RAY DIFFRACTIONf_angle_d0.8211584
X-RAY DIFFRACTIONf_chiral_restr0.046171
X-RAY DIFFRACTIONf_plane_restr0.005207
X-RAY DIFFRACTIONf_dihedral_angle_d18.838725
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 (%)
1.5-1.53490.2281350.17942464259995
1.5349-1.57330.20821290.17152529265897
1.5733-1.61580.20021290.1582586271598
1.6158-1.66340.19011460.15262552269899
1.6634-1.71710.1811520.14582592274499
1.7171-1.77840.17631340.1522608274299
1.7784-1.84960.16971360.15862623275999
1.8496-1.93380.18851380.16272624276299
1.9338-2.03580.19831400.169726242764100
2.0358-2.16330.16531230.164926602783100
2.1633-2.33040.17261470.151926592806100
2.3304-2.56490.18461370.16726752812100
2.5649-2.9360.17631620.170526812843100
2.936-3.69880.19271320.167627572889100
3.6988-48.88370.19011670.176529033070100

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