[English] 日本語
Yorodumi
- PDB-5nq6: Crystal structure of the inhibited form of the redox-sensitive Su... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5nq6
TitleCrystal structure of the inhibited form of the redox-sensitive SufE-like sulfur acceptor CsdE from Escherichia coli at 2.40 Angstrom Resolution
ComponentsSulfur acceptor protein CsdE
KeywordsSULFUR-ACCEPTOR PROTEIN / SULFUR-BINDING PROTEIN / L-CYSTEINE DESULFURASE / TRANSPERSULFURATION / SULFUR TRAFFICKING
Function / homologyCysteine desulfurase, sulphur acceptor subunit CsdE / Fe-S metabolism associated domain, SufE-like / Fe-S metabolism associated domain / cyclic threonylcarbamoyladenosine biosynthetic process / sulfur carrier activity / Sulfur acceptor protein CsdE
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsPenya-Soler, E. / Aranda, J. / Lopez-Estepa, M. / Gomez, S. / Garces, F. / Coll, M. / Fernandez, F.J. / Vega, M.C.
Funding support Spain, Belgium, 7items
OrganizationGrant numberCountry
Instituto de Salud Carlos IIIPI12/01667 Spain
Spanish Ministry of Economy and CompetitivenessPET2008_0101 Spain
Spanish Ministry of Economy and CompetitivenessBIO2009-11184 Spain
Spanish Ministry of Economy and CompetitivenessBFU2010-22260-C02-02 Spain
Spanish Ministry of Economy and CompetitivenessCTQ2015-66206-C2-2-R Spain
Regional Government of MadridS2010/BD-2316 Spain
European CommissionComplexINC (Contract No. 279039) Belgium
Citation
Journal: PLoS ONE / Year: 2017
Title: Insights into the inhibited form of the redox-sensitive SufE-like sulfur acceptor CsdE.
Authors: Pena-Soler, E. / Aranda, J. / Lopez-Estepa, M. / Gomez, S. / Garces, F. / Coll, M. / Fernandez, F.J. / Tunon, I. / Vega, M.C.
#1: Journal: ACS Catalysis / Year: 2016
Title: Mechanism of Sulfur Transfer Across Protein-Protein Interfaces: The Cysteine Desulfurase Model System
Authors: Fernandez, F.J. / Arda, A. / Lopez-Estepa, M. / Aranda, J. / Penya-Soler, E. / Garces, F. / Round, A. / Campos-Olivas, R. / Bruix, M. / Coll, M. / Tunon, I. / Jimenez-Barbero, J. / Vega, M.C.
History
DepositionApr 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sulfur acceptor protein CsdE
B: Sulfur acceptor protein CsdE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3858
Polymers33,8292
Non-polymers5576
Water84747
1
A: Sulfur acceptor protein CsdE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0983
Polymers16,9141
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sulfur acceptor protein CsdE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2875
Polymers16,9141
Non-polymers3724
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.433, 58.433, 150.452
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.1917, -0.9796, -0.0597), (-0.6609, -0.0839, -0.7457), (0.7255, 0.1824, -0.6636)
Vector: -22.2917, 5.5074, 54.6333)

-
Components

#1: Protein Sulfur acceptor protein CsdE


Mass: 16914.271 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: csdE, ygdK, b2811, JW2782 / Plasmid: pET3a / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / References: UniProt: P0AGF2
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.2 Å3/Da / Density % sol: 44.09 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M sodium citrate (pH 6.5), 20% (w/v) PEG monomethyl ether (PEG-MME) 2000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.4→47.964 Å / Num. obs: 12231 / % possible obs: 99.3 % / Observed criterion σ(I): 3 / Redundancy: 7.5 % / Biso Wilson estimate: 44.88 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.2
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.6 / % possible all: 96.6

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→47.964 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2486 583 4.79 %
Rwork0.1909 --
obs0.1937 12176 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→47.964 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2156 0 35 47 2238
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082253
X-RAY DIFFRACTIONf_angle_d1.0083044
X-RAY DIFFRACTIONf_dihedral_angle_d18.5081354
X-RAY DIFFRACTIONf_chiral_restr0.05346
X-RAY DIFFRACTIONf_plane_restr0.006392
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.64160.33781510.26422782X-RAY DIFFRACTION98
2.6416-3.02380.31741440.2312855X-RAY DIFFRACTION100
3.0238-3.80950.24371560.1832883X-RAY DIFFRACTION100
3.8095-47.97360.21421320.17073073X-RAY DIFFRACTION99

+
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