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

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Basic information

Entry
Database: PDB / ID: 5qxz
TitlePanDDA analysis group deposition -- Crystal Structure of ATAD2 in complex with DF853
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


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-RKG / ATPase family AAA domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.64 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)16,2649
Polymers15,5131
Non-polymers7528
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.366, 80.366, 140.157
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-1202-

SO4

21A-1327-

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, EC: 3.6.1.3
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-RKG / methyl (4aS,7aS,9S)-3,4,7,7a,8,9-hexahydro-4a,9-epoxypyrrolo[3',4':4,5]cyclohepta[1,2-d]imidazole-6(5H)-carboxylate


Mass: 249.266 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H15N3O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 0.18 °
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 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.64→28.03 Å / Num. obs: 33725 / % possible obs: 99.7 % / Redundancy: 18.7 % / CC1/2: 1 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.022 / Rrim(I) all: 0.096 / Net I/σ(I): 22.2 / Num. measured all: 631545 / 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
1.64-1.6817.40.8664086823530.8650.2090.8923.196.6
7.32-28.0316.90.033787746610.0080.0346798.4

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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: 1.64→27.92 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.529 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1797 1682 5 %RANDOM
Rwork0.1587 ---
obs0.1597 31977 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 96.21 Å2 / Biso mean: 25.015 Å2 / Biso min: 11.81 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20.08 Å20 Å2
2--0.16 Å20 Å2
3----0.53 Å2
Refinement stepCycle: final / Resolution: 1.64→27.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1084 0 48 223 1355
Biso mean--33.34 37.93 -
Num. residues----130
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0163275
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171917
X-RAY DIFFRACTIONr_angle_refined_deg1.8651.7132953
X-RAY DIFFRACTIONr_angle_other_deg1.3951.6244504
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8475279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.50421.618136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.77515366
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.731524
X-RAY DIFFRACTIONr_chiral_restr0.0920.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022562
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02465
X-RAY DIFFRACTIONr_mcbond_it1.5152.2681502
X-RAY DIFFRACTIONr_mcbond_other1.5282.2311440
X-RAY DIFFRACTIONr_mcangle_it2.8083.1591297
LS refinement shellResolution: 1.636→1.679 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 119 -
Rwork0.232 2250 -
all-2369 -
obs--96.89 %

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