[English] 日本語
Yorodumi
- PDB-5eid: AKR2A ankyrin repeat domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5eid
TitleAKR2A ankyrin repeat domain
ComponentsAnkyrin repeat domain-containing protein 2
KeywordsPROTEIN TRANSPORT / AKR2A / ankyrin repeat domain / cytosolic targeting factor
Function / homology
Function and homology information


chloroplast targeting sequence binding / protein targeting to chloroplast / chloroplast outer membrane / glycolipid binding / nucleus / cytoplasm
Similarity search - Function
STI1/HOP, DP domain / STI1/HOP, DP domain / Ankyrin repeat-containing domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Ankyrin repeat-containing domain superfamily ...STI1/HOP, DP domain / STI1/HOP, DP domain / Ankyrin repeat-containing domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Ankyrin repeat-containing domain superfamily / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Ankyrin repeat domain-containing protein 2A
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsPu, H. / Li, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation31300634 China
CitationJournal: To Be Published
Title: structure of AKR2A ankyrin repeat domain at 2.0 angstroms resolution
Authors: Pu, H. / Li, H.
History
DepositionOct 29, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ankyrin repeat domain-containing protein 2


Theoretical massNumber of molelcules
Total (without water)17,8151
Polymers17,8151
Non-polymers00
Water61334
1
A: Ankyrin repeat domain-containing protein 2

A: Ankyrin repeat domain-containing protein 2


Theoretical massNumber of molelcules
Total (without water)35,6302
Polymers35,6302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-x+1/2,y+1/2,-z1
Unit cell
Length a, b, c (Å)124.141, 39.193, 28.499
Angle α, β, γ (deg.)90.000, 96.290, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Ankyrin repeat domain-containing protein 2 / AtAKR2


Mass: 17814.779 Da / Num. of mol.: 1 / Fragment: UNP residues 211-342
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AKR2, AFT, At4g35450, F15J1.20 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9SAR5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 1.93 Å3/Da / Density % sol: 36.41 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.06 M Ammonium sulfate, 0.05 M Sodium acetate trihydrate, 33% Polyethylene glycol 4000, 10% Glycerol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 9423 / % possible obs: 97 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.4
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.514 / % possible all: 97.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.15data extraction
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HQD

4hqd


Resolution: 2→37.354 Å / FOM work R set: 0.7972 / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2349 430 4.73 %
Rwork0.1872 8664 -
obs0.1895 9094 96.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 65.06 Å2 / Biso mean: 30.91 Å2 / Biso min: 16.24 Å2
Refinement stepCycle: final / Resolution: 2→37.354 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms889 0 0 34 923
Biso mean---35.53 -
Num. residues----123
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007904
X-RAY DIFFRACTIONf_angle_d1.0631226
X-RAY DIFFRACTIONf_chiral_restr0.065147
X-RAY DIFFRACTIONf_plane_restr0.006162
X-RAY DIFFRACTIONf_dihedral_angle_d13.736322
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.28940.27311520.21272882X-RAY DIFFRACTION98
2.2894-2.88430.26711410.20672899X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 20.4142 Å / Origin y: -11.3217 Å / Origin z: 3.919 Å
111213212223313233
T0.2994 Å2-0.0125 Å20.0122 Å2-0.1245 Å20.0054 Å2--0.1466 Å2
L1.4565 °2-0.0565 °20.0669 °2-0.5988 °20.332 °2--0.8239 °2
S0.037 Å °-0.083 Å °0.063 Å °0.0056 Å °-0.0145 Å °0.0498 Å °0.0111 Å °-0.0932 Å °-0.0243 Å °
Refinement TLS groupSelection details: all

+
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