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- PDB-8qk0: Crystal structure of cytochrome domain 3 from PgcA -

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Basic information

Entry
Database: PDB / ID: 8qk0
TitleCrystal structure of cytochrome domain 3 from PgcA
ComponentsLipoprotein cytochrome c
KeywordsELECTRON TRANSPORT / Cytochrome / Geobacter sulfurreducens / extracellular electron transfer / mineral reduction.
Function / homology
Function and homology information


electron transfer activity / heme binding / metal ion binding / membrane
Similarity search - Function
: / Cytochrome C oxidase, cbb3-type, subunit III / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
HEME C / Lipoprotein cytochrome c
Similarity search - Component
Biological speciesGeobacter sulfurreducens PCA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsNash, B.W. / Edwards, M.J. / Clarke, T.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T008717/1 United Kingdom
CitationJournal: Protein Sci. / Year: 2024
Title: Tethered heme domains in a triheme cytochrome allow for increased electron transport distances.
Authors: Nash, B.W. / Fernandes, T.M. / Burton, J.A.J. / Morgado, L. / van Wonderen, J.H. / Svistunenko, D.A. / Edwards, M.J. / Salgueiro, C.A. / Butt, J.N. / Clarke, T.A.
History
DepositionSep 14, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipoprotein cytochrome c
C: Lipoprotein cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7539
Polymers21,3322
Non-polymers1,4217
Water3,225179
1
A: Lipoprotein cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3314
Polymers10,6661
Non-polymers6643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Lipoprotein cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4235
Polymers10,6661
Non-polymers7574
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.564, 55.033, 37.456
Angle α, β, γ (deg.)90.00, 99.30, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Lipoprotein cytochrome c


Mass: 10666.068 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter sulfurreducens PCA (bacteria)
Strain: PCA / Gene: pgcA / Production host: Shewanella oneidensis MR-1 (bacteria) / Strain (production host): LS527 / References: UniProt: Q74CB3
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 1.8 Å3/Da / Density % sol: 31.72 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1:1 mixture of 20 mg per mL protein in 20 mM HEPES 100 mM NaCl pH 7.8 with 2.3 M Na Malonate pH 7.0, 1.8% Jeffamine ED-2001

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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: May 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.9→44.28 Å / Num. obs: 12027 / % possible obs: 99.8 % / Redundancy: 6.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.056 / Rrim(I) all: 0.147 / Χ2: 0.95 / Net I/σ(I): 8.2 / Num. measured all: 81356
Reflection shellResolution: 1.9→1.94 Å / % possible obs: 97.9 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.631 / Num. measured all: 4008 / Num. unique obs: 760 / CC1/2: 0.842 / Rpim(I) all: 0.301 / Rrim(I) all: 0.702 / Χ2: 1.01 / Net I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→44.28 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2632 599 4.99 %
Rwork0.221 --
obs0.2232 11995 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→44.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1028 0 96 179 1303
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d1.096
X-RAY DIFFRACTIONf_dihedral_angle_d16.745382
X-RAY DIFFRACTIONf_chiral_restr0.057160
X-RAY DIFFRACTIONf_plane_restr0.016196
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.090.30581420.23472815X-RAY DIFFRACTION99
2.09-2.390.26511510.21922832X-RAY DIFFRACTION100
2.39-3.020.26011470.22512857X-RAY DIFFRACTION100
3.02-44.280.25281590.21542892X-RAY DIFFRACTION100

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