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- PDB-4lmh: Crystal structure of the outer membrane decaheme cytochrome OmcA -

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Basic information

Entry
Database: PDB / ID: 4lmh
TitleCrystal structure of the outer membrane decaheme cytochrome OmcA
ComponentsExtracellular iron oxide respiratory system surface decaheme cytochrome c component OmcA
KeywordsELECTRON TRANSPORT / Greek key beta barrel / Electron transport c-type cytochrome / Outer membrane
Function / homologyDecahaem cytochrome, c-type, OmcA/MtrC / : / Multiheme cytochrome c family profile. / Multiheme cytochrome superfamily / cellular response to iron ion / electron transfer activity / metal ion binding / HEME C / Extracelllular iron oxide respiratory system surface decaheme cytochrome c component OmcA
Function and homology information
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsEdwards, M.J. / Baiden, N. / Clarke, T.A.
CitationJournal: FEBS Letters / Year: 2014
Title: Insights into electron transfer at the microbe-mineral interface: the X-ray crystal structures of Shewanella oneidensis MtrC and OmcA
Authors: Edwards, M.J. / Baiden, N. / Clarke, T.A. / Richardson, D.J.
History
DepositionJul 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software

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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 OmcA
B: Extracellular iron oxide respiratory system surface decaheme cytochrome c component OmcA
C: Extracellular iron oxide respiratory system surface decaheme cytochrome c component OmcA
D: Extracellular iron oxide respiratory system surface decaheme cytochrome c component OmcA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)352,07668
Polymers325,7654
Non-polymers26,31164
Water31,4901748
1
A: Extracellular iron oxide respiratory system surface decaheme cytochrome c component OmcA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,01917
Polymers81,4411
Non-polymers6,57816
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Extracellular iron oxide respiratory system surface decaheme cytochrome c component OmcA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,01917
Polymers81,4411
Non-polymers6,57816
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Extracellular iron oxide respiratory system surface decaheme cytochrome c component OmcA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,01917
Polymers81,4411
Non-polymers6,57816
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Extracellular iron oxide respiratory system surface decaheme cytochrome c component OmcA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,01917
Polymers81,4411
Non-polymers6,57816
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.640, 245.380, 135.630
Angle α, β, γ (deg.)90.00, 97.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Extracellular iron oxide respiratory system surface decaheme cytochrome c component OmcA


Mass: 81441.352 Da / Num. of mol.: 4 / Fragment: unp residues 28-735
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: omcA, SO_1779 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8EG33
#2: Chemical...
ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 40 / 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-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1748 / 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: 4.69 Å3/Da / Density % sol: 73.76 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Bis TRIS Propane, 0.1 M MgCl2, 15% PEG 20000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 14, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.7→58.14 Å / Num. all: 161304 / Num. obs: 161304 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 36.21 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.091
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 3.1 / Num. unique all: 11901 / Rsym value: 0.377 / % possible all: 98.4

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Processing

Software
NameVersionClassification
XDSdata scaling
SHELXSphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
xia2data reduction
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.7→50.97 Å / SU ML: 0.38 / σ(F): 1.34 / Phase error: 22.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2304 8080 5.01 %Random
Rwork0.1929 ---
obs0.1948 161229 98.43 %-
all-161229 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20.125 Å2 / ksol: 0.321 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.6317 Å2-0 Å20.4906 Å2
2--0.2512 Å20 Å2
3---0.3805 Å2
Refinement stepCycle: LAST / Resolution: 2.7→50.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20903 0 1792 1748 24443
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01323618
X-RAY DIFFRACTIONf_angle_d0.88932494
X-RAY DIFFRACTIONf_dihedral_angle_d14.5857889
X-RAY DIFFRACTIONf_chiral_restr0.0553216
X-RAY DIFFRACTIONf_plane_restr0.0034070
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.73070.40722590.31445183X-RAY DIFFRACTION99
2.7307-2.76280.34342680.28785002X-RAY DIFFRACTION98
2.7628-2.79650.34282530.27835156X-RAY DIFFRACTION99
2.7965-2.83190.32652480.26595203X-RAY DIFFRACTION100
2.8319-2.86920.29372770.24985113X-RAY DIFFRACTION99
2.8692-2.90850.29222570.25065164X-RAY DIFFRACTION99
2.9085-2.950.27062640.24675157X-RAY DIFFRACTION99
2.95-2.99410.28752910.24185066X-RAY DIFFRACTION99
2.9941-3.04080.29892730.22625129X-RAY DIFFRACTION100
3.0408-3.09070.27313000.22945186X-RAY DIFFRACTION100
3.0907-3.1440.2682650.21495129X-RAY DIFFRACTION99
3.144-3.20110.24722430.21485173X-RAY DIFFRACTION99
3.2011-3.26270.26382460.21475117X-RAY DIFFRACTION99
3.2627-3.32930.26512850.21565091X-RAY DIFFRACTION98
3.3293-3.40170.25132700.20075029X-RAY DIFFRACTION97
3.4017-3.48080.23862950.19735082X-RAY DIFFRACTION99
3.4808-3.56780.24012790.20515167X-RAY DIFFRACTION99
3.5678-3.66420.24132720.20265026X-RAY DIFFRACTION98
3.6642-3.7720.23282630.19625065X-RAY DIFFRACTION98
3.772-3.89370.22532630.1915136X-RAY DIFFRACTION99
3.8937-4.03280.22692910.18185105X-RAY DIFFRACTION99
4.0328-4.19420.21062790.16325073X-RAY DIFFRACTION98
4.1942-4.3850.19692640.15415033X-RAY DIFFRACTION96
4.385-4.61610.17472520.1445082X-RAY DIFFRACTION98
4.6161-4.90510.1692690.14485087X-RAY DIFFRACTION98
4.9051-5.28340.17992710.14445086X-RAY DIFFRACTION98
5.2834-5.81450.18452630.16175139X-RAY DIFFRACTION98
5.8145-6.65420.20242620.17725083X-RAY DIFFRACTION97
6.6542-8.37760.18223070.16115016X-RAY DIFFRACTION97
8.3776-50.97910.16782510.16565071X-RAY DIFFRACTION96

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