[English] 日本語
Yorodumi
- PDB-8qbz: Crystal structure of the outer membrane decaheme cytochrome MtrC ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8qbz
TitleCrystal structure of the outer membrane decaheme cytochrome MtrC (E344Boc-Lys)
ComponentsExtracellular iron oxide respiratory system surface decaheme cytochrome c component MtrC
KeywordsELECTRON TRANSPORT / Boc-Lys / Cytochrome / Electron transport.
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
ACETATE ION / 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: 1.9 Å
AuthorsEdwards, M.J. / Lockwood, C.J. / Whiting, K. / Nash, B.W. / Butt, J.N. / Clarke, T.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Leverhulme TrustRPG-2020-085 United Kingdom
CitationJournal: Acs Synth Biol / Year: 2024
Title: Genetic Code Expansion in Shewanella oneidensis MR-1 Allows Site-Specific Incorporation of Bioorthogonal Functional Groups into a c -Type Cytochrome.
Authors: Lockwood, C.W.J. / Nash, B.W. / Newton-Payne, S.E. / van Wonderen, J.H. / Whiting, K.P.S. / Connolly, A. / Sutton-Cook, A.L. / Crook, A. / Aithal, A.R. / Edwards, M.J. / Clarke, T.A. / Sachdeva, A. / Butt, J.N.
History
DepositionAug 25, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
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)79,42025
Polymers72,4791
Non-polymers6,94124
Water17,276959
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14220 Å2
ΔGint-249 kcal/mol
Surface area27300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.967, 89.664, 153.545
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 1 molecules A

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


Mass: 72478.648 Da / Num. of mol.: 1 / Mutation: E344Boc-Lys
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

-
Non-polymers , 5 types, 983 molecules

#2: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 959 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 21% PEG 6000, 0.1 M CaCl2, 0.2 M Sodium acetate, pH 5.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.7085 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7085 Å / Relative weight: 1
ReflectionResolution: 1.9→89.66 Å / Num. obs: 58591 / % possible obs: 99.7 % / Redundancy: 11.3 % / CC1/2: 0.92 / Rmerge(I) obs: 0.451 / Rpim(I) all: 0.15 / Rrim(I) all: 0.476 / Net I/σ(I): 5.3 / Num. measured all: 659243
Reflection shellResolution: 1.9→1.93 Å / % possible obs: 92.3 % / Redundancy: 10.7 % / Rmerge(I) obs: 1.39 / Num. measured all: 28551 / Num. unique obs: 2661 / CC1/2: 0.483 / Rpim(I) all: 0.457 / Rrim(I) all: 1.465 / Net I/σ(I) obs: 1.2

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→50.12 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.508 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21577 2957 5.1 %RANDOM
Rwork0.1737 ---
obs0.17586 55540 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.245 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å2-0 Å2-0 Å2
2---0.24 Å20 Å2
3---0.46 Å2
Refinement stepCycle: 1 / Resolution: 1.9→50.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4698 0 471 959 6128
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0145444
X-RAY DIFFRACTIONr_bond_other_d0.0010.0154801
X-RAY DIFFRACTIONr_angle_refined_deg2.6711.8047492
X-RAY DIFFRACTIONr_angle_other_deg1.3711.67311061
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1335639
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.81225.607214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.24215785
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.162156
X-RAY DIFFRACTIONr_chiral_restr0.1470.2698
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026273
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021175
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2841.7562563
X-RAY DIFFRACTIONr_mcbond_other1.2711.7512544
X-RAY DIFFRACTIONr_mcangle_it2.0022.6223183
X-RAY DIFFRACTIONr_mcangle_other2.0022.6233184
X-RAY DIFFRACTIONr_scbond_it1.6141.8032881
X-RAY DIFFRACTIONr_scbond_other1.6141.8042882
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5832.6134310
X-RAY DIFFRACTIONr_long_range_B_refined6.07422.3467020
X-RAY DIFFRACTIONr_long_range_B_other5.38620.9536634
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.947 Å
RfactorNum. reflection% reflection
Rfree0.279 196 -
Rwork0.278 3851 -
obs--94.78 %

+
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