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- PDB-5qxr: PanDDA analysis group deposition -- Crystal Structure of ATAD2 in... -

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Basic information

Entry
Database: PDB / ID: 5qxr
TitlePanDDA analysis group deposition -- Crystal Structure of ATAD2 in complex with DF849
ComponentsATPase family AAA domain-containing protein 2
KeywordsHYDROLASE/HYDROLASE INHIBITOR / SGC - Diamond I04-1 fragment screening / PanDDA / XChemExplorer / HYDROLASE-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-RHY / ATPase family AAA domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.66 Å
AuthorsSnee, M. / Talon, R. / Fowley, D. / Collins, P. / Nelson, A. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Von-Delft, F.
CitationJournal: To Be Published
Title: PanDDA analysis group deposition - Bromodomain of human ATAD2 fragment screening
Authors: Snee, M. / Talon, R. / Fowley, D. / Collins, P. / Nelson, A. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Von-Delft, F.
History
DepositionFeb 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)16,1247
Polymers15,5131
Non-polymers6126
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.810, 80.810, 140.090
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-1203-

SO4

21A-1399-

HOH

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Components

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


Mass: 15512.562 Da / Num. of mol.: 1
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-RHY / 1-[(4aS,7aS,9S)-3,4,7,7a,8,9-hexahydro-4a,9-epoxypyrrolo[3',4':4,5]cyclohepta[1,2-d]imidazol-6(5H)-yl]ethan-1-one


Mass: 233.266 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H15N3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.2 Å3/Da / Density % sol: 70.7 % / Mosaicity: 0 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 1.6M Ammonium Sulfate, 0.1M bis-tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.66→49.51 Å / Num. obs: 32740 / % possible obs: 100 % / Redundancy: 18.6 % / CC1/2: 1 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.031 / Rrim(I) all: 0.137 / Net I/σ(I): 18.6 / Num. measured all: 609926 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.66-1.717.22.324065123620.5120.5732.3911.4100
7.42-49.5116.80.021781046610.0050.02189.199.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0238refinement
Aimless0.5.23data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3DAI

3dai


Resolution: 1.66→49.56 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.9 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1916 1630 5 %RANDOM
Rwork0.1693 ---
obs0.1704 31048 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 107.51 Å2 / Biso mean: 29.315 Å2 / Biso min: 14.87 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20.07 Å2-0 Å2
2--0.15 Å20 Å2
3----0.48 Å2
Refinement stepCycle: final / Resolution: 1.66→49.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1084 0 39 224 1347
Biso mean--38.35 40.38 -
Num. residues----130
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0152343
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171482
X-RAY DIFFRACTIONr_angle_refined_deg1.7051.7062353
X-RAY DIFFRACTIONr_angle_other_deg1.4381.6313493
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5925229
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.3721.982111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.65615301
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7381519
X-RAY DIFFRACTIONr_chiral_restr0.0960.2215
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022103
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02375
X-RAY DIFFRACTIONr_mcbond_it1.8572.5411083
X-RAY DIFFRACTIONr_mcbond_other1.92.511012
X-RAY DIFFRACTIONr_mcangle_it3.1123.691047
LS refinement shellResolution: 1.66→1.703 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 123 -
Rwork0.295 2234 -
all-2357 -
obs--99.79 %

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