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

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Basic information

Entry
Database: PDB / ID: 8qbq
TitleCrystal structure of the outer membrane decaheme cytochrome MtrC (A430Boc-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: 1.81 Å
AuthorsNash, B.W. / Lockwood, C.J. / Whiting, K. / Butt, J.N. / Clarke, T.A. / Edwards, M.J.
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

Downloads & links

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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)79,78830
Polymers72,5371
Non-polymers7,25129
Water17,619978
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15220 Å2
ΔGint-232 kcal/mol
Surface area27180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.904, 89.609, 154.031
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: A430Boc-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, 1007 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 978 / 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: 2.52 Å3/Da / Density % sol: 51.13 % / Description: Plates
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2 M 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: Jan 29, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.55→58.4 Å / Num. obs: 95747 / % possible obs: 89.6 % / Redundancy: 11.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.039 / Rrim(I) all: 0.14 / Net I/σ(I): 10.3 / Num. measured all: 1078151
Reflection shellResolution: 1.55→1.58 Å / % possible obs: 53 % / Redundancy: 3.9 % / Rmerge(I) obs: 1.36 / Num. measured all: 10966 / Num. unique obs: 2787 / CC1/2: 0.355 / Rpim(I) all: 0.737 / Rrim(I) all: 1.557 / Net I/σ(I) obs: 0.4

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
xia2data scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→44.8 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 16.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1866 3388 5.02 %
Rwork0.1548 --
obs0.1564 67487 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.81→44.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4706 0 491 978 6175
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d1.057
X-RAY DIFFRACTIONf_dihedral_angle_d17.7111792
X-RAY DIFFRACTIONf_chiral_restr0.059754
X-RAY DIFFRACTIONf_plane_restr0.008915
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.840.27311180.22212607X-RAY DIFFRACTION97
1.84-1.860.26331270.20182634X-RAY DIFFRACTION100
1.86-1.890.22861300.17732666X-RAY DIFFRACTION100
1.89-1.920.21771430.16172615X-RAY DIFFRACTION100
1.92-1.960.18591400.16382666X-RAY DIFFRACTION100
1.96-1.990.21031470.16122601X-RAY DIFFRACTION100
1.99-2.030.22691390.1572666X-RAY DIFFRACTION100
2.03-2.070.18021440.15652633X-RAY DIFFRACTION100
2.07-2.120.20191350.1632634X-RAY DIFFRACTION100
2.12-2.170.17221120.15852690X-RAY DIFFRACTION100
2.17-2.220.19021330.15412635X-RAY DIFFRACTION100
2.22-2.280.21441540.15832640X-RAY DIFFRACTION100
2.28-2.350.20461440.1582652X-RAY DIFFRACTION100
2.35-2.420.21751690.15622657X-RAY DIFFRACTION100
2.42-2.510.20361460.16082636X-RAY DIFFRACTION100
2.51-2.610.18381410.15742660X-RAY DIFFRACTION100
2.61-2.730.20031390.16352676X-RAY DIFFRACTION100
2.73-2.870.19151530.15732677X-RAY DIFFRACTION100
2.87-3.050.21131520.15832658X-RAY DIFFRACTION100
3.05-3.290.18671630.15882693X-RAY DIFFRACTION100
3.29-3.620.16521310.14662701X-RAY DIFFRACTION100
3.62-4.140.15771600.142728X-RAY DIFFRACTION100
4.15-5.220.13681430.12662760X-RAY DIFFRACTION100
5.22-44.80.16641250.15442914X-RAY DIFFRACTION100

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