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- PDB-6qyc: Crystal structure of MtrC from Shewanella baltica OS185 -

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Basic information

Entry
Database: PDB / ID: 6qyc
TitleCrystal structure of MtrC from Shewanella baltica OS185
ComponentsDecaheme c-type cytochrome, OmcA/MtrC family
KeywordsELECTRON TRANSPORT / Cytochrome / Membrane protein / greek key / multiheme
Function / homologyDecahaem cytochrome, c-type, OmcA/MtrC / Multiheme cytochrome superfamily / HEME C / Multiheme cytochrome MtrC
Function and homology information
Biological speciesShewanella baltica OS185 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.29 Å
AuthorsClarke, T.A. / Edwards, M.J.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilP01819X United Kingdom
Biotechnology and Biological Sciences Research CouncilL023733X United Kingdom
CitationJournal: Cell / Year: 2020
Title: The Crystal Structure of a Biological Insulated Transmembrane Molecular Wire.
Authors: Edwards, M.J. / White, G.F. / Butt, J.N. / Richardson, D.J. / Clarke, T.A.
History
DepositionMar 8, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Decaheme c-type cytochrome, OmcA/MtrC family
B: Decaheme c-type cytochrome, OmcA/MtrC family
C: Decaheme c-type cytochrome, OmcA/MtrC family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,38843
Polymers192,3883
Non-polymers19,00040
Water16,448913
1
A: Decaheme c-type cytochrome, OmcA/MtrC family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,51915
Polymers64,1291
Non-polymers6,38914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Decaheme c-type cytochrome, OmcA/MtrC family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,43514
Polymers64,1291
Non-polymers6,30513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Decaheme c-type cytochrome, OmcA/MtrC family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,43514
Polymers64,1291
Non-polymers6,30513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.520, 291.500, 87.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Decaheme c-type cytochrome, OmcA/MtrC family


Mass: 64129.344 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella baltica OS185 (bacteria) / Gene: NCTC10735_02683 / Production host: Shewanella oneidensis MR-1 (bacteria) / Strain (production host): MR-1 / References: UniProt: P0DSN4*PLUS
#2: Chemical...
ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 913 / Source method: isolated from a natural source / Formula: H2O

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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: 3 Å3/Da / Density % sol: 58.95 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.4 M Sodium Acetate, 5% PEG 6000, 5% PEG 8000, 5% PEG 10000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.72001 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.72001 Å / Relative weight: 1
ReflectionResolution: 2.29→90.52 Å / Num. obs: 104279 / % possible obs: 99.5 % / Redundancy: 12.6 % / Biso Wilson estimate: 50.79 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.033 / Rrim(I) all: 0.117 / Net I/σ(I): 17 / Num. measured all: 1317009 / Scaling rejects: 3
Reflection shellResolution: 2.29→2.35 Å / Redundancy: 10.2 % / Rmerge(I) obs: 1.887 / Num. unique obs: 7485 / CC1/2: 0.475 / Rpim(I) all: 0.612 / Rrim(I) all: 1.986 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Aimless0.6.2data scaling
PDB_EXTRACT3.24data extraction
xia2data reduction
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.29→87.2 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.66
RfactorNum. reflection% reflection
Rfree0.2283 5313 5.1 %
Rwork0.1826 --
obs0.185 104187 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 117.89 Å2 / Biso mean: 52.3964 Å2 / Biso min: 30.4 Å2
Refinement stepCycle: final / Resolution: 2.29→87.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13410 0 1306 914 15630
Biso mean--46.5 51.77 -
Num. residues----1817
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.29-2.3160.38711470.32853265341299
2.316-2.34330.36221750.29733172334798
2.3433-2.37190.31131910.27253155334696
2.3719-2.40190.30891580.25783111326996
2.4019-2.43350.30531550.25223193334897
2.4335-2.46680.34041580.24863275343399
2.4668-2.50210.31061880.238132663454100
2.5021-2.53940.28051910.220632393430100
2.5394-2.57910.27041800.215432873467100
2.5791-2.62140.30051730.216832883461100
2.6214-2.66660.26041960.211532713467100
2.6666-2.71510.28011610.209332803441100
2.7151-2.76730.30221620.218833063468100
2.7673-2.82380.27671550.216233113466100
2.8238-2.88520.26461880.218332663454100
2.8852-2.95230.27941590.220933073466100
2.9523-3.02620.26671860.218333013487100
3.0262-3.1080.25621650.219133073472100
3.108-3.19940.27831720.214532753447100
3.1994-3.30270.28431660.211933253491100
3.3027-3.42080.28261870.204333033490100
3.4208-3.55770.25191740.200833083482100
3.5577-3.71960.24221830.190133313514100
3.7196-3.91580.21542060.167133193525100
3.9158-4.16110.1871780.154433363514100
4.1611-4.48240.17731720.138133603532100
4.4824-4.93340.15492030.134333253528100
4.9334-5.64720.17591830.140433943577100
5.6472-7.11430.20512110.153533953606100
7.1143-87.26320.18151900.155536033793100

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