[English] 日本語
Yorodumi
- PDB-9eov: Crystal structure of domains I and II from the outer membrane cyt... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9eov
TitleCrystal structure of domains I and II from the outer membrane cytochrome MtrC
ComponentsExtracellular iron oxide respiratory system surface decaheme cytochrome c component MtrC
KeywordsELECTRON TRANSPORT / Multiheme cytochrome / Shewanella oneidensis / Truncation / Extracellular electron transfer / Redox.
Function / homology
Function and homology information


oxidoreductase activity / metal ion binding
Similarity search - Function
: / Decaheme cytochrome c component MtrC/MtrF N-terminal domain / Decahaem cytochrome, c-type, OmcA/MtrC / : / Outer membrane cytochrome MtrC/MtrF-like, domains II/IV / : / Multiheme cytochrome superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
HEME C / Extracellular iron oxide respiratory system surface decaheme cytochrome c component MtrC
Similarity search - Component
Biological speciesShewanella oneidensis MR-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsNash, B.W. / Morales Florez, A. / Lockwood, C.W.J. / Edwards, M.J. / Butt, J.N. / Clarke, T.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T008717/1 United Kingdom
CitationJournal: Protein Sci. / Year: 2025
Title: Extracellular catalysis of environmental substrates by Shewanella oneidensis MR-1 occurs via active sites on the C-terminal domains of MtrC.
Authors: Morales-Florez, A. / Lockwood, C.W.J. / Nash, B.W. / Edwards, M.J. / van Wonderen, J.H. / Sachdeva, A. / Butt, J.N. / Clarke, T.A.
History
DepositionMar 15, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Extracellular iron oxide respiratory system surface decaheme cytochrome c component MtrC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,82110
Polymers34,5181
Non-polymers3,3039
Water6,612367
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6610 Å2
ΔGint-104 kcal/mol
Surface area13280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.275, 77.350, 96.531
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Extracellular iron oxide respiratory system surface decaheme cytochrome c component MtrC


Mass: 34518.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis MR-1 (bacteria) / Gene: mtrC, SO_1778 / Production host: Shewanella oneidensis MR-1 (bacteria) / References: UniProt: Q8EG34
#2: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 367 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.07 Å3/Da / Density % sol: 69.8 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M magnesium acetate tetrahydrate, 0.1 M sodium cacodylate, 20% w/v polyethylene glycol (PEG) 8000, pH 6.5.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 20, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.8→60.36 Å / Num. obs: 52210 / % possible obs: 99.9 % / Redundancy: 12.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.175 / Rpim(I) all: 0.051 / Rrim(I) all: 0.182 / Χ2: 0.66 / Net I/σ(I): 7.1 / Num. measured all: 648930
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 12.7 % / Rmerge(I) obs: 1.156 / Num. unique obs: 3060 / CC1/2: 0.896 / Rpim(I) all: 0.338 / Χ2: 0.26

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→58.87 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2207 2529 4.85 %
Rwork0.1875 --
obs0.1891 52134 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→58.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2112 0 228 367 2707
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02
X-RAY DIFFRACTIONf_angle_d2.057
X-RAY DIFFRACTIONf_dihedral_angle_d17.622814
X-RAY DIFFRACTIONf_chiral_restr0.088329
X-RAY DIFFRACTIONf_plane_restr0.02425
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.830.40921490.36872694X-RAY DIFFRACTION100
1.83-1.870.3381340.30972758X-RAY DIFFRACTION100
1.87-1.910.28561460.2832687X-RAY DIFFRACTION100
1.91-1.960.27691500.26412730X-RAY DIFFRACTION100
1.96-2.010.24731580.24052706X-RAY DIFFRACTION100
2.01-2.060.27361510.25052737X-RAY DIFFRACTION100
2.06-2.120.21661350.21412714X-RAY DIFFRACTION100
2.12-2.190.20511410.19842751X-RAY DIFFRACTION100
2.19-2.270.24091390.19132713X-RAY DIFFRACTION100
2.27-2.360.18741360.19072761X-RAY DIFFRACTION100
2.36-2.470.21371220.1832742X-RAY DIFFRACTION100
2.47-2.60.23541260.17972762X-RAY DIFFRACTION100
2.6-2.760.24851600.17952761X-RAY DIFFRACTION100
2.76-2.970.22371310.18862767X-RAY DIFFRACTION100
2.97-3.270.22561150.18912780X-RAY DIFFRACTION99
3.27-3.740.23171340.17022805X-RAY DIFFRACTION100
3.74-4.720.15661450.14272785X-RAY DIFFRACTION99
4.72-58.870.18251570.14412952X-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://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