[English] 日本語
Yorodumi
- PDB-8ru5: ATPase family AAA domain containing 2 with crystallization epitop... -

+
Open data


ID or keywords:

Loading...

-
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 / Bromodomain profile. / bromo domain ...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 / Bromodomain profile. / bromo domain / Bromodomain / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more