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- PDB-6r2q: Structure of the Mtr complex -

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Basic information

Entry
Database: PDB / ID: 6r2q
TitleStructure of the Mtr complex
Components
  • Cystathionine beta-synthase
  • Decaheme c-type cytochrome, OmcA/MtrC family
  • Uncharacterized protein
KeywordsELECTRON TRANSPORT / Cytochrome / Membrane protein / greek key / multiheme
Function / homology
Function and homology information


cell outer membrane
Similarity search - Function
Decaheme cytochrome, c-type, DmsE / Decahaem-associated outer membrane protein, MtrB/PioB / Putative outer membrane beta-barrel porin, MtrB/PioB / Doubled CXXCH motif / : / Cytochrome c-type protein NrfB-like / : / Doubled CXXCH motif (Paired_CXXCH_1) / : / Decaheme cytochrome c component MtrC/MtrF N-terminal domain ...Decaheme cytochrome, c-type, DmsE / Decahaem-associated outer membrane protein, MtrB/PioB / Putative outer membrane beta-barrel porin, MtrB/PioB / Doubled CXXCH motif / : / Cytochrome c-type protein NrfB-like / : / Doubled CXXCH motif (Paired_CXXCH_1) / : / 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 c family profile. / TonB-dependent receptor-like, beta-barrel domain superfamily / Porin domain superfamily / Multiheme cytochrome superfamily
Similarity search - Domain/homology
HEME C / Cystathionine beta-synthase / Uncharacterized protein / Decaheme c-type cytochrome, OmcA/MtrC family / Outer membrane protein MtrB / Multiheme cytochrome MtrA / Multiheme cytochrome MtrC
Similarity search - Component
Biological speciesShewanella baltica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.697 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 18, 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

Downloads & links

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Assembly

Deposited unit
A: Cystathionine beta-synthase
B: Uncharacterized protein
C: Decaheme c-type cytochrome, OmcA/MtrC family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,12227
Polymers181,5913
Non-polymers12,53024
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, Edwards MJ, White GF, Lockwood CW, Lawes MC, Martel A, Harris G, Scott DJ, Richardson DJ, Butt JN, Clarke TA. (2018) Structural modeling of an outer membrane electron conduit from a ...Evidence: SAXS, Edwards MJ, White GF, Lockwood CW, Lawes MC, Martel A, Harris G, Scott DJ, Richardson DJ, Butt JN, Clarke TA. (2018) Structural modeling of an outer membrane electron conduit from a metal-reducing bacterium suggests electron transfer via periplasmic redox partners. J Biol Chem. 293, 8103-8112, equilibrium centrifugation, Hartshorne RS, Reardon CL, Ross D, Nuester J, Clarke TA, Gates AJ, Mills PC, Fredrickson JK, Zachara JM, Shi L, Beliaev AS, Marshall MA, Tien M, Brantley S, Butt JN, Richardson DJ (2009) Characterization of an electron conduit between bacteria and the extracellullar environment PNAS, 106, 22169-74
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38670 Å2
ΔGint-503 kcal/mol
Surface area61960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)212.042, 234.165, 99.192
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein Cystathionine beta-synthase / Cytochrome c-type protein NrfB


Mass: 36096.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Shewanella baltica (bacteria) / References: UniProt: A0A165K349, UniProt: P0DSN3*PLUS
#2: Protein Uncharacterized protein


Mass: 77362.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Shewanella baltica (bacteria) / References: UniProt: A0A165K351, UniProt: P0DSN2*PLUS
#3: Protein Decaheme c-type cytochrome, OmcA/MtrC family


Mass: 68131.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Shewanella baltica (bacteria) / References: UniProt: A0A379ZX38, UniProt: P0DSN4*PLUS

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Non-polymers , 3 types, 46 molecules

#4: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#5: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 22 / 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: 3.71 Å3/Da / Density % sol: 66.82 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis-Tris, 0.01 M LDAO, 0.4 M Calcium chloride, 40 % MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97624 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Sep 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
Reflection

Entry-ID: 6R2Q / Diffraction-ID: 1

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)CC1/2Rmerge(I) obsRpim(I) allNet I/σ(I)
2.697-106.0214975894.15.50.9970.0910.04213.3
2.694-106.0216761798.75.89.9
Reflection shellResolution: 2.697→2.814 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 2.6 / Num. unique obs: 2489 / CC1/2: 0.908 / % possible all: 97.1

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
SHELXDEphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.697→73.25 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 30.23
RfactorNum. reflection% reflection
Rfree0.2573 2470 4.97 %
Rwork0.2241 --
obs0.2258 49734 72.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 220.71 Å2 / Biso mean: 62.5529 Å2 / Biso min: 9.31 Å2
Refinement stepCycle: final / Resolution: 2.697→73.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11577 0 1496 22 13095
Biso mean--54.52 37.58 -
Num. residues----1522
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6966-2.74840.4528510.33871026107729
2.7484-2.80450.4074490.31191154120332
2.8045-2.86550.3202640.30651269133335
2.8655-2.93220.3423650.30911436150140
2.9322-3.00550.2989700.30591618168845
3.0055-3.08680.3587990.32891743184249
3.0868-3.17760.3144940.29961947204154
3.1776-3.28020.33621220.2842262238463
3.2802-3.39740.34281340.26472671280575
3.3974-3.53340.27041920.26123236342890
3.5334-3.69420.31081630.23683574373799
3.6942-3.8890.26791940.21763568376299
3.889-4.13260.23751910.19343589378099
4.1326-4.45170.20881840.17313579376399
4.4517-4.89960.22582010.16773601380299
4.8996-5.60840.212140.18383589380399
5.6084-7.0650.23881830.22383662384599
7.065-73.27670.24782000.24643740394098

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