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- PDB-7qth: Crystal structure of the Shewanella oneidensis MR1 MtrC mutant C453A -

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Basic information

Entry
Database: PDB / ID: 7qth
TitleCrystal structure of the Shewanella oneidensis MR1 MtrC mutant C453A
ComponentsExtracellular iron oxide respiratory system surface decaheme cytochrome c component MtrC
KeywordsELECTRON TRANSPORT / ELECTRON TRANSFER ACTIVITY / OXIDOREDUCTASE ACTIVITY
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. / Clarke, T.A.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/K009885/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/L023733/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/H007288/1 United Kingdom
CitationJournal: Mbio / Year: 2023
Title: A Cysteine Pair Controls Flavin Reduction by Extracellular Cytochromes during Anoxic/Oxic Environmental Transitions.
Authors: Norman, M.P. / Edwards, M.J. / White, G.F. / Burton, J.A.J. / Butt, J.N. / Richardson, D.J. / Louro, R.O. / Paquete, C.M. / Clarke, T.A.
History
DepositionJan 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)78,58831
Polymers71,2831
Non-polymers7,30430
Water15,097838
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15210 Å2
ΔGint-250 kcal/mol
Surface area27410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.061, 89.797, 154.286
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 71283.312 Da / Num. of mol.: 1 / Mutation: C453A
Source method: isolated from a genetically manipulated source
Details: C453A / Source: (gene. exp.) Shewanella oneidensis MR-1 (bacteria) / Strain: MR-1 / Gene: mtrC, SO_1778 / Production host: Shewanella oneidensis MR-1 (bacteria) / References: UniProt: Q8EG34

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Non-polymers , 5 types, 868 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.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 838 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.11 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 21% PEG 6000, 0.1 M CaCl2, 0.2 M Sodium acetate, pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→154.29 Å / Num. obs: 58700 / % possible obs: 99.5 % / Redundancy: 6.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.042 / Rrim(I) all: 0.107 / Net I/σ(I): 14 / Num. measured all: 385137 / Scaling rejects: 22
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.9-1.945.90.4412177936990.9020.1980.484499.3
9.11-154.295.70.03235506270.9990.0140.0353599

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Processing

SoftwareName: REFMAC / Version: 5.8.0267 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LM8

4lm8


Resolution: 1.9→77.73 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.1815 / WRfactor Rwork: 0.1404 / FOM work R set: 0.8824 / SU B: 2.769 / SU ML: 0.08 / SU R Cruickshank DPI: 0.1305 / SU Rfree: 0.126 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1956 2892 4.9 %RANDOM
Rwork0.1513 ---
obs0.1535 55739 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.82 Å2 / Biso mean: 17.464 Å2 / Biso min: 0.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å2-0 Å2-0 Å2
2---0.4 Å20 Å2
3---0.35 Å2
Refinement stepCycle: final / Resolution: 1.9→77.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4694 0 542 838 6074
Biso mean--15.75 28.8 -
Num. residues----627
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0145545
X-RAY DIFFRACTIONr_bond_other_d0.0010.0154876
X-RAY DIFFRACTIONr_angle_refined_deg2.8131.8167666
X-RAY DIFFRACTIONr_angle_other_deg1.481.67911238
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0915652
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.1725.721215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.29815794
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.683156
X-RAY DIFFRACTIONr_chiral_restr0.1620.2706
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.026437
X-RAY DIFFRACTIONr_gen_planes_other0.0120.021179
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 201 -
Rwork0.231 4034 -
all-4235 -
obs--99.09 %

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