[English] 日本語
Yorodumi
- PDB-4pui: BolA domain of SufE1 from Arabidopsis thaliana -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4pui
TitleBolA domain of SufE1 from Arabidopsis thaliana
ComponentsSufE-like protein, chloroplastic
KeywordsPROTEIN BINDING / stress-responsive protein / METAL BINDING PROTEIN / PROTEIN BINDING PROTEIN
Function / homology
Function and homology information


chloroplast stroma / enzyme activator activity / chloroplast / mitochondrion / cytosol
Similarity search - Function
Fe-S metabolism associated domain, SufE-like / Fe-S metabolism associated domain / BolA-like / BolA protein / BolA-like superfamily / BolA-like protein / GMP Synthetase; Chain A, domain 3 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
SufE-like protein 1, chloroplastic/mitochondrial
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.698 Å
AuthorsRoret, T. / Didierjean, C.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structural and Spectroscopic Insights into BolA-Glutaredoxin Complexes.
Authors: Roret, T. / Tsan, P. / Couturier, J. / Zhang, B. / Johnson, M.K. / Rouhier, N. / Didierjean, C.
History
DepositionMar 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SufE-like protein, chloroplastic
B: SufE-like protein, chloroplastic


Theoretical massNumber of molelcules
Total (without water)21,2782
Polymers21,2782
Non-polymers00
Water2,972165
1
A: SufE-like protein, chloroplastic


Theoretical massNumber of molelcules
Total (without water)10,6391
Polymers10,6391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SufE-like protein, chloroplastic


Theoretical massNumber of molelcules
Total (without water)10,6391
Polymers10,6391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.833, 31.634, 68.631
Angle α, β, γ (deg.)90.00, 116.83, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein SufE-like protein, chloroplastic / Protein EMBRYO DEFECTIVE 1374 / Protein SULFUR E / AtSUFE / Protein SULFUR E 1 / AtSUFE1


Mass: 10639.063 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 277-371
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SUFE, EMB1374, SUFE1, At4g26500, M3E9.70 / Production host: Escherichia coli (E. coli) / References: UniProt: Q84W65
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.18 Å3/Da / Density % sol: 43.61 %
Crystal growTemperature: 278 K / Method: oil microbatch method / pH: 6.5
Details: 12% PEG20000, 6% ethylene glycol, 0.02 M trimethylamine HCl and 0.1 M MES, pH 6.5, Oil microbatch method, temperature 278K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97911 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 5, 2012
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 1.698→46.182 Å / Num. all: 20575 / Num. obs: 20573 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 23.3 Å2 / Rmerge(I) obs: 0.032 / Net I/σ(I): 20.6
Reflection shellResolution: 1.698→1.79 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 2.6 / Num. unique all: 2902 / % possible all: 97.2

-
Processing

Software
NameVersionClassification
Proxima1 SOLEILdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1V60

1v60


Resolution: 1.698→46.182 Å / SU ML: 0.23 / σ(F): 0 / σ(I): 0 / Phase error: 22.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2132 1053 5.12 %RANDOM
Rwork0.1913 ---
all0.1924 20575 --
obs0.1924 20573 99.47 %-
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.557 Å2 / ksol: 0.415 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.8388 Å2-0 Å21.078 Å2
2---0.1159 Å2-0 Å2
3---6.9547 Å2
Refinement stepCycle: LAST / Resolution: 1.698→46.182 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1360 0 0 165 1525
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061386
X-RAY DIFFRACTIONf_angle_d1.0661860
X-RAY DIFFRACTIONf_dihedral_angle_d14.134532
X-RAY DIFFRACTIONf_chiral_restr0.067211
X-RAY DIFFRACTIONf_plane_restr0.005241
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6981-1.77540.33191180.28822368X-RAY DIFFRACTION97
1.7754-1.8690.27221350.24552423X-RAY DIFFRACTION100
1.869-1.98610.30271320.22612431X-RAY DIFFRACTION100
1.9861-2.13950.1881100.192414X-RAY DIFFRACTION100
2.1395-2.35480.2251410.19142433X-RAY DIFFRACTION100
2.3548-2.69550.19741120.19122475X-RAY DIFFRACTION100
2.6955-3.39590.24011540.18612432X-RAY DIFFRACTION100
3.3959-46.19870.17341510.17352537X-RAY DIFFRACTION100

+
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://pdbjlvh1.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