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- PDB-8qjg: Crystal structure of cytochrome domain 2 from PgcA -

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Basic information

Entry
Database: PDB / ID: 8qjg
TitleCrystal structure of cytochrome domain 2 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: 1.8 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 13, 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
B: Lipoprotein cytochrome c
C: Lipoprotein cytochrome c
D: Lipoprotein cytochrome c
E: Lipoprotein cytochrome c
F: Lipoprotein cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,89126
Polymers59,8696
Non-polymers5,02220
Water9,692538
1
A: Lipoprotein cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7894
Polymers9,9781
Non-polymers8113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lipoprotein cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6933
Polymers9,9781
Non-polymers7152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Lipoprotein cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8855
Polymers9,9781
Non-polymers9074
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Lipoprotein cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8855
Polymers9,9781
Non-polymers9074
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Lipoprotein cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7894
Polymers9,9781
Non-polymers8113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Lipoprotein cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8515
Polymers9,9781
Non-polymers8734
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.104, 74.101, 56.019
Angle α, β, γ (deg.)90.00, 103.92, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11E-248-

HOH

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Components

#1: Protein
Lipoprotein cytochrome c


Mass: 9978.192 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter sulfurreducens PCA (bacteria)
Gene: pgcA / Production host: Shewanella oneidensis MR-1 (bacteria) / Strain (production host): LS527 / References: UniProt: Q74CB3
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 538 / 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

Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 1:1 mixture of 10 mg per mL protein in 20 mM HEPES pH 7.8 100 mM NaCl, with 2.0 M ammonium sulfate, 5% v/v isopropanol 1.8% PEG 4000.

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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: Jan 29, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.8→42.96 Å / Num. obs: 34881 / % possible obs: 99.6 % / Redundancy: 3.4 % / CC1/2: 0.981 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.085 / Rrim(I) all: 0.16 / Χ2: 0.86 / Net I/σ(I): 5.4 / Num. measured all: 117486
Reflection shellResolution: 1.8→1.84 Å / % possible obs: 93.5 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.36 / Num. measured all: 4784 / Num. unique obs: 1925 / CC1/2: 0.874 / Rpim(I) all: 0.268 / Rrim(I) all: 0.452 / Χ2: 0.95 / Net I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
xia2data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→42.96 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.227 1643 4.72 %
Rwork0.1748 --
obs0.1773 34832 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→42.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2669 0 327 538 3534
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01
X-RAY DIFFRACTIONf_angle_d1.133
X-RAY DIFFRACTIONf_dihedral_angle_d18.563455
X-RAY DIFFRACTIONf_chiral_restr0.049444
X-RAY DIFFRACTIONf_plane_restr0.009527
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.27161320.20852636X-RAY DIFFRACTION95
1.85-1.910.24911320.1942756X-RAY DIFFRACTION100
1.91-1.980.22111260.17532770X-RAY DIFFRACTION100
1.98-2.060.23131570.17662753X-RAY DIFFRACTION100
2.06-2.150.27031370.17692774X-RAY DIFFRACTION100
2.15-2.270.23771350.17352743X-RAY DIFFRACTION100
2.27-2.410.22061310.17722794X-RAY DIFFRACTION100
2.41-2.60.24391310.16312760X-RAY DIFFRACTION100
2.6-2.860.22441510.16842781X-RAY DIFFRACTION100
2.86-3.270.20341360.16542780X-RAY DIFFRACTION100
3.27-4.120.19961390.15382798X-RAY DIFFRACTION100
4.12-42.960.22581360.19732844X-RAY DIFFRACTION99

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