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- PDB-8ru5: ATPase family AAA domain containing 2 with crystallization epitop... -

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Basic information

Entry
Database: PDB / ID: 8ru5
TitleATPase family AAA domain containing 2 with crystallization epitope mutations V1022R:Q1027E
ComponentsATPase family AAA domain-containing protein 2
KeywordsSIGNALING PROTEIN / Crystal Epitopes / Bromodomain
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) / ATPase, AAA-type, core / Bromodomain / bromo domain / 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 / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATPase family AAA domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsFairhead, M. / Strain-Damerell, C. / Ye, M. / Mackinnon, S.R. / Pinkas, D. / MacLean, E.M. / Koekemoer, L. / Damerell, D. / Krojer, T. / Arrowsmith, C.H. ...Fairhead, M. / Strain-Damerell, C. / Ye, M. / Mackinnon, S.R. / Pinkas, D. / MacLean, E.M. / Koekemoer, L. / Damerell, D. / Krojer, T. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Yue, W. / Burgess-Brown, N. / Marsden, B. / von Delft, F. / Structural Genomics Consortium (SGC)
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: A fast, parallel method for efficiently exploring crystallization behaviour of large numbers of protein variants
Authors: Fairhead, M. / Strain-Damerell, C. / Ye, M. / Mackinnon, S.R. / Pinkas, D. / MacLean, E.M. / Damerell, D. / Krojer, T. / Yue, W. / Burgess-Brown, N. / Marsden, B. / von Delft, F.
History
DepositionJan 30, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release

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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)15,6373
Polymers15,5131
Non-polymers1242
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint5 kcal/mol
Surface area7670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.400, 47.760, 80.290
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.37 Å3/Da / Density % sol: 48.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% PEG6000 10% ethylene glycol 0.1M tris pH 7.5 0.1M calcium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91739 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91739 Å / Relative weight: 1
ReflectionResolution: 1.36→41.05 Å / Num. obs: 31956 / % possible obs: 98.6 % / Redundancy: 6.4 % / CC1/2: 0.999 / Net I/σ(I): 19.1
Reflection shellResolution: 1.36→1.4 Å / Num. unique obs: 2196 / CC1/2: 0.519

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
xia2data reduction
xia2data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.36→41.047 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.963 / Cross valid method: FREE R-VALUE / ESU R: 0.065 / ESU R Free: 0.062
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.2214 1573 4.93 %
Rwork0.2109 30335 -
all0.211 --
obs-31908 98.251 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 29.255 Å2
Baniso -1Baniso -2Baniso -3
1-1.625 Å20 Å20 Å2
2---0.565 Å2-0 Å2
3----1.061 Å2
Refinement stepCycle: LAST / Resolution: 1.36→41.047 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1043 0 8 132 1183
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0121118
X-RAY DIFFRACTIONr_angle_refined_deg1.5461.861519
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7575139
X-RAY DIFFRACTIONr_dihedral_angle_2_deg1.141515
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.24110187
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.9711059
X-RAY DIFFRACTIONr_chiral_restr0.0840.2171
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02857
X-RAY DIFFRACTIONr_nbd_refined0.2150.2529
X-RAY DIFFRACTIONr_nbtor_refined0.3210.2792
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2810.286
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1690.219
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2550.210
X-RAY DIFFRACTIONr_mcbond_it1.3882.641544
X-RAY DIFFRACTIONr_mcangle_it2.264.735687
X-RAY DIFFRACTIONr_scbond_it2.3992.989574
X-RAY DIFFRACTIONr_scangle_it3.9795.337832
X-RAY DIFFRACTIONr_lrange_it5.73932.6861788
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.36-1.3950.3351070.33720870.33723580.9230.90893.0450.324
1.395-1.4330.3621210.33120760.33323060.9020.91795.27320.311
1.433-1.4750.3211120.320660.30122280.9210.93597.75580.273
1.475-1.520.26990.24320360.24421650.9510.95698.61430.211
1.52-1.570.257840.23720250.23821200.9540.96199.48110.205
1.57-1.6250.2171110.22719300.22720490.9660.96699.60960.198
1.625-1.6860.2341050.22418540.22519870.9650.96698.59080.195
1.686-1.7550.2331020.21418080.21519180.9630.9799.58290.188
1.755-1.8330.268950.21617440.21918500.9530.96999.40540.194
1.833-1.9220.251850.22216570.22317510.960.96899.4860.204
1.922-2.0260.263750.21115730.21316640.950.97199.03850.199
2.026-2.1490.217820.2114910.21115870.9720.97599.11780.206
2.149-2.2970.208670.20214120.20214940.980.97598.9960.199
2.297-2.480.237720.19113040.19313970.9710.97698.49680.198
2.48-2.7160.158510.21312450.21113050.9830.97199.31030.223
2.716-3.0340.246510.20711240.20811800.9630.97499.57630.23
3.034-3.5010.238550.29840.20210490.960.97499.04670.229
3.501-4.280.151460.1748470.1739100.9870.98198.13190.208
4.28-6.020.247380.2056550.2077170.9690.97596.65270.266
6.02-41.0470.177150.2514170.2484410.9780.96497.95920.321

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