[English] 日本語
Yorodumi
- PDB-9wt9: Crystal structure of a multiheme cytochrome c selenoprotein mutan... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9wt9
TitleCrystal structure of a multiheme cytochrome c selenoprotein mutant (MccSep U325A)
ComponentsCytochrome c,Multiheme cytochrome c selenoprotein mutant (MccSep U325A)
KeywordsELECTRON TRANSPORT / multiheme / cytochrome c / selenoprotein
Function / homologyMultiheme cytochrome superfamily / HEME C / Cytochrome c / Uncharacterized protein
Function and homology information
Biological speciesGeobacter sulfurreducens PCA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMihara, H. / Yoshizawa, T. / Izu, Y. / Inoue, M. / Aono, R. / Zhang, W. / Shibamoto, N. / Tobe, R. / Kurihara, T. / Matsumura, H.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)24K01994 Japan
Japan Society for the Promotion of Science (JSPS)23K18033 Japan
Japan Society for the Promotion of Science (JSPS)25H02292 Japan
CitationJournal: To Be Published
Title: Multiheme selenoenzyme essential for elemental sulfur respiration
Authors: Mihara, H. / Yoshizawa, T. / Izu, Y. / Inoue, M. / Aono, R. / Zhang, W. / Shibamoto, N. / Tobe, R. / Kurihara, T. / Matsumura, H.
History
DepositionSep 16, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytochrome c,Multiheme cytochrome c selenoprotein mutant (MccSep U325A)
B: Cytochrome c,Multiheme cytochrome c selenoprotein mutant (MccSep U325A)
C: Cytochrome c,Multiheme cytochrome c selenoprotein mutant (MccSep U325A)
D: Cytochrome c,Multiheme cytochrome c selenoprotein mutant (MccSep U325A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,54993
Polymers198,7624
Non-polymers17,78789
Water18,7001038
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.170, 122.650, 116.450
Angle α, β, γ (deg.)90.000, 92.150, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Cytochrome c,Multiheme cytochrome c selenoprotein mutant (MccSep U325A)


Mass: 49690.590 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter sulfurreducens PCA (bacteria)
Gene: GSU2937, GSU2936 / Production host: Geobacter sulfurreducens PCA (bacteria) / References: UniProt: Q748R4, UniProt: Q748R5

-
Non-polymers , 5 types, 1127 molecules

#2: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 44 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1038 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M ammonium sulfate, 0.1M HEPES (pH 7.5), 10% PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Nov 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→48.53 Å / Num. obs: 215383 / % possible obs: 99.84 % / Redundancy: 7 % / Biso Wilson estimate: 32.46 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08064 / Net I/σ(I): 14.33
Reflection shellResolution: 1.8→1.864 Å / Num. unique obs: 21438 / CC1/2: 0.601 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→48.53 Å / SU ML: 0.2572 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.2239
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2242 10751 5 %
Rwork0.1869 204388 -
obs0.1887 215139 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.22 Å2
Refinement stepCycle: LAST / Resolution: 1.8→48.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13108 0 1181 1038 15327
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009214810
X-RAY DIFFRACTIONf_angle_d1.053820262
X-RAY DIFFRACTIONf_chiral_restr0.05661947
X-RAY DIFFRACTIONf_plane_restr0.00842504
X-RAY DIFFRACTIONf_dihedral_angle_d17.41992063
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.433540.41776763X-RAY DIFFRACTION99.64
1.82-1.840.3963530.3726775X-RAY DIFFRACTION99.64
1.84-1.860.40093570.36226793X-RAY DIFFRACTION99.82
1.86-1.890.34363570.33196793X-RAY DIFFRACTION99.83
1.89-1.910.34963580.32136783X-RAY DIFFRACTION99.71
1.91-1.940.31753600.30036818X-RAY DIFFRACTION99.82
1.94-1.970.31833580.27996804X-RAY DIFFRACTION99.79
1.97-20.29383550.2766734X-RAY DIFFRACTION99.82
2-2.030.30073590.25946826X-RAY DIFFRACTION99.74
2.03-2.060.27813560.25226761X-RAY DIFFRACTION99.85
2.06-2.10.27283580.23676793X-RAY DIFFRACTION99.79
2.1-2.130.27593590.23666821X-RAY DIFFRACTION99.92
2.13-2.180.27563580.23686816X-RAY DIFFRACTION99.89
2.18-2.220.28473560.23536770X-RAY DIFFRACTION99.97
2.22-2.270.2663590.22816807X-RAY DIFFRACTION99.89
2.27-2.320.26223590.21586822X-RAY DIFFRACTION99.85
2.32-2.380.28223590.21066836X-RAY DIFFRACTION99.93
2.38-2.440.24653570.20366776X-RAY DIFFRACTION99.82
2.44-2.510.24683590.19726835X-RAY DIFFRACTION99.9
2.51-2.60.24753570.18946811X-RAY DIFFRACTION99.92
2.6-2.690.25813590.18736814X-RAY DIFFRACTION99.9
2.69-2.80.24853580.1986806X-RAY DIFFRACTION99.93
2.8-2.920.25433590.20336814X-RAY DIFFRACTION99.86
2.92-3.080.24623590.19476828X-RAY DIFFRACTION99.85
3.08-3.270.22453590.18446810X-RAY DIFFRACTION99.92
3.27-3.520.21863600.1786850X-RAY DIFFRACTION99.89
3.52-3.880.18623600.166838X-RAY DIFFRACTION99.93
3.88-4.440.16383620.13556871X-RAY DIFFRACTION99.97
4.44-5.590.15813620.1336880X-RAY DIFFRACTION99.97
5.59-48.530.17143650.14796940X-RAY DIFFRACTION99.58

+
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