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- PDB-7o7g: Crystal structure of the Shewanella oneidensis MR1 MtrC mutant H561M -

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Basic information

Entry
Database: PDB / ID: 7o7g
TitleCrystal structure of the Shewanella oneidensis MR1 MtrC mutant H561M
ComponentsExtracellular iron oxide respiratory system surface decaheme cytochrome c component MtrC
KeywordsELECTRON TRANSPORT / electron transfer activity oxidoreductase activity ion binding cation binding metal ion binding
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsEdwards, M.J. / van Wonderen, J.H. / Newton-Payne, S.E. / Butt, J.N. / Clarke, T.A.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P01819X/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S002499/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/M001989/1 United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Nanosecond heme-to-heme electron transfer rates in a multiheme cytochrome nanowire reported by a spectrally unique His/Met-ligated heme.
Authors: van Wonderen, J.H. / Adamczyk, K. / Wu, X. / Jiang, X. / Piper, S.E.H. / Hall, C.R. / Edwards, M.J. / Clarke, T.A. / Zhang, H. / Jeuken, L.J.C. / Sazanovich, I.V. / Towrie, M. / Blumberger, ...Authors: van Wonderen, J.H. / Adamczyk, K. / Wu, X. / Jiang, X. / Piper, S.E.H. / Hall, C.R. / Edwards, M.J. / Clarke, T.A. / Zhang, H. / Jeuken, L.J.C. / Sazanovich, I.V. / Towrie, M. / Blumberger, J. / Meech, S.R. / Butt, J.N.
History
DepositionApr 13, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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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)78,44628
Polymers71,3081
Non-polymers7,13727
Water14,268792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14910 Å2
ΔGint-262 kcal/mol
Surface area27260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.875, 89.657, 153.900
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: 71308.422 Da / Num. of mol.: 1 / Mutation: H561M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (strain 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, 819 molecules

#2: Chemical
ChemComp-HEC / HEME C


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


Mass: 40.078 Da / Num. of mol.: 4 / 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.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 792 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.56 Å3/Da / Density % sol: 51.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 4.5
Details: 0.4 M sodium acetate pH 4.5, 0.1 M calcium chloride, 19% PEG6000

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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 EIGER2 XE 16M / Detector: PIXEL / Date: Feb 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.6→52.9 Å / Num. obs: 96658 / % possible obs: 99.8 % / Redundancy: 5.5 % / CC1/2: 0.998 / Net I/σ(I): 9.2
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 5.6 % / Num. unique obs: 4516 / CC1/2: 0.673 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LM8

4lm8


Resolution: 1.6→50.06 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.651 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2046 4751 4.9 %RANDOM
Rwork0.1702 ---
obs0.1719 91812 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.21 Å2 / Biso mean: 22.801 Å2 / Biso min: 6.51 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å2-0 Å2-0 Å2
2---0.3 Å20 Å2
3---1.33 Å2
Refinement stepCycle: final / Resolution: 1.6→50.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4693 0 486 792 5971
Biso mean--20.63 34.94 -
Num. residues----627
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0145486
X-RAY DIFFRACTIONr_bond_other_d0.0010.0184845
X-RAY DIFFRACTIONr_angle_refined_deg2.6891.8027573
X-RAY DIFFRACTIONr_angle_other_deg1.4441.67211168
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9965652
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.94525.767215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.14415796
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.321156
X-RAY DIFFRACTIONr_chiral_restr0.1590.2704
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.026379
X-RAY DIFFRACTIONr_gen_planes_other0.0120.021184
LS refinement shellResolution: 1.603→1.644 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 325 -
Rwork0.32 6487 -
all-6812 -
obs--96.61 %

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