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- PDB-8h28: Crystal structure of the K87V mutant of cytochrome c' from Shewan... -

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Basic information

Entry
Database: PDB / ID: 8h28
TitleCrystal structure of the K87V mutant of cytochrome c' from Shewanella benthica DB6705
ComponentsClass II cytochrome c
KeywordsELECTRON TRANSPORT / cytochrome c' / Shewanella benthica
Function / homology
Function and homology information


electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome c, class II / Cytochrome c prime / Cytochrome C' / Cytochrome c class II profile. / Cytochrome c/b562
Similarity search - Domain/homology
HEME C / Class II cytochrome c
Similarity search - Component
Biological speciesShewanella sp. DB6705 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsFujii, S. / Sakaguchi, R. / Oki, H. / Kawahara, K. / Ohkubo, T. / Fujiyoshi, S. / Sambongi, Y.
Funding support Japan, 2items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)26240045 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)16K07692 Japan
CitationJournal: J.Struct.Biol. / Year: 2023
Title: Contribution of a surface salt bridge to the protein stability of deep-sea Shewanella benthica cytochrome c'.
Authors: Fujii, S. / Sakaguchi, R. / Oki, H. / Kawahara, K. / Ohkubo, T. / Fujiyoshi, S. / Sambongi, Y.
History
DepositionOct 5, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 11, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2024Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Class II cytochrome c
B: Class II cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6114
Polymers28,3742
Non-polymers1,2372
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-42 kcal/mol
Surface area13300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.773, 68.259, 45.507
Angle α, β, γ (deg.)90.000, 112.036, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Class II cytochrome c


Mass: 14187.186 Da / Num. of mol.: 2 / Mutation: K87V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella sp. DB6705 (bacteria) / Strain: DB6705 / Gene: cycP / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2Z6I6U9
#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: 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: 2.27 Å3/Da / Density % sol: 45.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 400 mM sodium phosphate monobasic / 1600 mM potassium phosphate dibasic, 100 mM imidazole / hydrochloric acid pH 8.0, and 200 mM sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.06→42.18 Å / Num. obs: 15616 / % possible obs: 99 % / Redundancy: 3.62 % / Rmerge(I) obs: 0.096 / Rrim(I) all: 0.113 / Χ2: 1.16 / Net I/σ(I): 7 / Num. measured all: 56943 / Scaling rejects: 429
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRrim(I) allΧ2% possible allRejects
2.06-2.133.610.4661.9550915280.5471.4197.9
2.13-2.223.610.4182551115260.491.3597.85
2.22-2.323.610.3542.5558115420.4151.2798.520
2.32-2.443.610.2962.9563815510.3481.2798.433
2.44-2.63.620.263.4566415540.3041.249932
2.6-2.83.620.24.5574015710.2331.2198.948
2.8-3.083.620.1326.9569715590.1551.1499.757
3.08-3.523.640.08210.6585615920.0961.0199.963
3.52-4.443.660.05116.8582015770.0590.8699.745
4.44-42.183.590.04817.8592716160.0570.8599.6126

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Processing

Software
NameVersionClassification
d*TREK9.9.9.8 W9DSSIdata reduction
d*TREK9.9.9.8 W9DSSIdata scaling
PHENIX1.20.1-4487refinement
PDB_EXTRACT3.27data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A3K

6a3k


Resolution: 2.06→37.43 Å / SU ML: 0.273 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.781
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2545 1549 9.94 %
Rwork0.2021 14031 -
obs0.2072 15580 98.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.3 Å2
Refinement stepCycle: LAST / Resolution: 2.06→37.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1984 0 86 179 2249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01322126
X-RAY DIFFRACTIONf_angle_d1.2972880
X-RAY DIFFRACTIONf_chiral_restr0.0782292
X-RAY DIFFRACTIONf_plane_restr0.0063366
X-RAY DIFFRACTIONf_dihedral_angle_d17.2869774
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.130.34621390.30031242X-RAY DIFFRACTION97.8
2.13-2.20.32011390.27051264X-RAY DIFFRACTION97.84
2.2-2.290.29551360.2631258X-RAY DIFFRACTION98.24
2.29-2.390.32951420.25421274X-RAY DIFFRACTION98.06
2.4-2.520.29951420.2561263X-RAY DIFFRACTION98.8
2.52-2.680.34181390.25631269X-RAY DIFFRACTION98.88
2.68-2.890.31881410.23461277X-RAY DIFFRACTION99.3
2.89-3.180.29461410.2191290X-RAY DIFFRACTION99.51
3.18-3.630.24111450.18621290X-RAY DIFFRACTION99.86
3.64-4.580.17411460.14891304X-RAY DIFFRACTION99.79
4.58-37.430.21531390.16781300X-RAY DIFFRACTION98.02

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