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- PDB-8qc9: Crystal structure of the outer membrane decaheme cytochrome MtrC ... -

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Basic information

Entry
Database: PDB / ID: 8qc9
TitleCrystal structure of the outer membrane decaheme cytochrome MtrC (A293Boc-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: 2 Å
AuthorsNash, B.W. / Lockwood, C.J. / Edwards, M.J. / Whiting, K. / 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

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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)79,41324
Polymers72,5371
Non-polymers6,87623
Water14,142785
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13910 Å2
ΔGint-263 kcal/mol
Surface area27680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.078, 90.021, 154.522
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 72536.680 Da / Num. of mol.: 1 / Mutation: A293Boc-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

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Non-polymers , 5 types, 808 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.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 785 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.54 Å3/Da / Density % sol: 51.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 200 mM Na acetate pH 5.0, 100 mM CaCl2 and 21% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→58.63 Å / Num. obs: 50997 / % possible obs: 100 % / Redundancy: 13.4 % / CC1/2: 0.991 / Rmerge(I) obs: 0.346 / Net I/σ(I): 6.1
Reflection shellResolution: 2→2.05 Å / Redundancy: 13.9 % / Num. unique obs: 3730 / CC1/2: 0.602 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→58.63 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2143 2629 5.17 %
Rwork0.1731 --
obs0.1752 50847 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→58.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4702 0 467 785 5954
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_d1.096
X-RAY DIFFRACTIONf_dihedral_angle_d18.6891781
X-RAY DIFFRACTIONf_chiral_restr0.056755
X-RAY DIFFRACTIONf_plane_restr0.007915
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.28261360.25362498X-RAY DIFFRACTION100
2.04-2.080.29561290.23782488X-RAY DIFFRACTION100
2.08-2.120.2781290.24112536X-RAY DIFFRACTION100
2.12-2.160.26231410.2252458X-RAY DIFFRACTION100
2.16-2.210.28331460.20432522X-RAY DIFFRACTION100
2.21-2.270.29161330.20522495X-RAY DIFFRACTION100
2.27-2.330.22931230.20212516X-RAY DIFFRACTION100
2.33-2.40.26031320.19352510X-RAY DIFFRACTION100
2.4-2.480.2471350.19252517X-RAY DIFFRACTION100
2.48-2.570.23161360.19282516X-RAY DIFFRACTION100
2.57-2.670.21061140.18382560X-RAY DIFFRACTION100
2.67-2.790.2431350.18482521X-RAY DIFFRACTION100
2.79-2.940.23651350.17932527X-RAY DIFFRACTION100
2.94-3.120.19761440.17292553X-RAY DIFFRACTION100
3.12-3.360.20091470.16672535X-RAY DIFFRACTION100
3.36-3.70.20251360.15332558X-RAY DIFFRACTION100
3.7-4.240.16181570.13792565X-RAY DIFFRACTION100
4.24-5.330.17491560.12372618X-RAY DIFFRACTION100
5.34-58.630.1791650.15262725X-RAY DIFFRACTION100

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