[English] 日本語
Yorodumi
- PDB-8ar9: Crystal to structure pipeline for ambient temperature, in situ cr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ar9
TitleCrystal to structure pipeline for ambient temperature, in situ crystallography at beamline VMXi
ComponentsNuclear receptor coactivator 7
KeywordsANTIVIRAL PROTEIN / NCOA7 / oxidative resistance
Function / homology
Function and homology information


negative regulation of cellular response to oxidative stress / nuclear receptor binding / response to oxidative stress / transcription coactivator activity / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
TLDc domain / TLDc domain / TLDc domain profile. / domain in TBC and LysM domain containing proteins / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain
Similarity search - Domain/homology
Nuclear receptor coactivator 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsCampeotto, I. / Foster, T.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust217414/Z/19/Z United Kingdom
Citation
Journal: Iucrj / Year: 2023
Title: Protein-to-structure pipeline for ambient-temperature in situ crystallography at VMXi.
Authors: Mikolajek, H. / Sanchez-Weatherby, J. / Sandy, J. / Gildea, R.J. / Campeotto, I. / Cheruvara, H. / Clarke, J.D. / Foster, T. / Fujii, S. / Paulsen, I.T. / Shah, B.S. / Hough, M.A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
History
DepositionAug 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1May 31, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jul 19, 2023Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _diffrn_source.pdbx_synchrotron_site
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nuclear receptor coactivator 7


Theoretical massNumber of molelcules
Total (without water)20,8141
Polymers20,8141
Non-polymers00
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Monomer in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.986, 54.822, 44.299
Angle α, β, γ (deg.)90.000, 119.520, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

#1: Protein Nuclear receptor coactivator 7 / 140 kDa estrogen receptor-associated protein / Estrogen nuclear receptor coactivator 1


Mass: 20814.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCOA7, ERAP140, ESNA1, Nbla00052, Nbla10993 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8NI08
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M di ammonium hydrogen citrate, 20% w/v PEG 3350

-
Data collection

DiffractionMean temperature: 291 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: VMXi / Wavelength: 0.7749 Å
DetectorType: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: May 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionResolution: 2.36→46.39 Å / Num. obs: 33925 / % possible obs: 92.55 % / Redundancy: 13.9 % / Biso Wilson estimate: 30.77 Å2 / CC1/2: 0.949 / Rmerge(I) obs: 0.483 / Rpim(I) all: 0.13 / Net I/σ(I): 5.7
Reflection shellResolution: 2.36→2.4 Å / Rmerge(I) obs: 2.335 / Num. unique obs: 420 / CC1/2: 0.261 / Rpim(I) all: 0.654

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
xia2.multiplexdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ACJ

4acj


Resolution: 2.36→46.38 Å / SU ML: 0.3178 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.7765
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2579 412 5.18 %
Rwork0.2042 7547 -
obs0.207 7959 91.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.35 Å2
Refinement stepCycle: LAST / Resolution: 2.36→46.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1319 0 0 48 1367
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00231358
X-RAY DIFFRACTIONf_angle_d0.57541838
X-RAY DIFFRACTIONf_chiral_restr0.0397189
X-RAY DIFFRACTIONf_plane_restr0.0027235
X-RAY DIFFRACTIONf_dihedral_angle_d5.7826178
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.36-2.70.32231380.29582481X-RAY DIFFRACTION91.06
2.7-3.40.30721390.23122532X-RAY DIFFRACTION92.58
3.4-46.380.20671350.16052534X-RAY DIFFRACTION90.88
Refinement TLS params.Method: refined / Origin x: 20.2479846217 Å / Origin y: 16.1409668649 Å / Origin z: 9.95326992923 Å
111213212223313233
T0.118199120266 Å20.00554681343266 Å20.0101054520546 Å2-0.133566755166 Å2-0.00304615170221 Å2--0.116782695757 Å2
L1.44393578493 °20.223692634812 °2-0.503393857247 °2-1.82469693104 °2-0.0757113921516 °2--0.593873521293 °2
S-0.0166358530426 Å °0.00396716574257 Å °-0.0371502117665 Å °-0.0038380081278 Å °-0.0356392808344 Å °-0.0332531973425 Å °-0.0169093639736 Å °0.0351089319303 Å °-2.70551867769E-5 Å °
Refinement TLS groupSelection details: (chain A and resseq 21:183)

+
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