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- PDB-8qj6: Crystal structure of cytochrome domain 1 from PgcA -

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Basic information

Entry
Database: PDB / ID: 8qj6
TitleCrystal structure of cytochrome domain 1 from PgcA
ComponentsLipoprotein cytochrome c
KeywordsELECTRON TRANSPORT / Geobacter sulfurreducens / cytochrome / 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: 1.55 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 12, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3843
Polymers9,7421
Non-polymers6412
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-23 kcal/mol
Surface area3720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.427, 68.427, 27.681
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Lipoprotein cytochrome c


Mass: 9742.112 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter sulfurreducens PCA (bacteria)
Strain: PCA / Gene: pgcA, GSU1761 / Production host: Shewanella oneidensis MR-1 (bacteria) / Strain (production host): LS527 / References: UniProt: Q74CB3
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 1.66 Å3/Da / Density % sol: 26.04 % / Description: Plates
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.3 uL protein at 10 mg per mL in 20 mM HEPES pH 7.8 100 mM NaCl, 0.28 uL Na Malonate pH 7.0 and 0.02 uL 30% W/V PEG 2000 MME

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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: Jul 26, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.55→34.21 Å / Num. obs: 9230 / % possible obs: 97.4 % / Redundancy: 12.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.02 / Rrim(I) all: 0.073 / Χ2: 0.96 / Net I/σ(I): 21.9 / Num. measured all: 118718
Reflection shellResolution: 1.55→1.58 Å / % possible obs: 76.8 % / Redundancy: 8.6 % / Rmerge(I) obs: 0.512 / Num. measured all: 2980 / Num. unique obs: 345 / CC1/2: 0.915 / Rpim(I) all: 0.173 / Rrim(I) all: 0.543 / Χ2: 0.95 / Net I/σ(I) obs: 3.8

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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: 1.55→34.21 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1891 427 4.63 %
Rwork0.1553 --
obs0.1568 9227 97.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→34.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms433 0 44 69 546
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_d0.997
X-RAY DIFFRACTIONf_dihedral_angle_d21.43575
X-RAY DIFFRACTIONf_chiral_restr0.04474
X-RAY DIFFRACTIONf_plane_restr0.00985
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.770.21451560.16452715X-RAY DIFFRACTION92
1.78-2.230.18721430.15422986X-RAY DIFFRACTION100
2.24-34.210.18271280.15393099X-RAY DIFFRACTION100

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