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- PDB-8yts: The structure of the cytochrome c546/556 from Thioalkalivibrio pa... -

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Basic information

Entry
Database: PDB / ID: 8yts
TitleThe structure of the cytochrome c546/556 from Thioalkalivibrio paradoxus with unusual UV-Vis spectral features at atomic resolution
ComponentsCytochrome C
KeywordsELECTRON TRANSPORT / Cytochrome c546/556 / Monoheme cytochrome / Q-bands splitting / room temperature / two conformations of the propianate group
Function / homology
Function and homology information


electron transfer activity / heme binding / metal ion binding
Similarity search - Function
: / Cytochrome c / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
HEME C / Cytochrome C
Similarity search - Component
Biological speciesThioalkalivibrio paradoxus ARh 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.15 Å
AuthorsVarfolomeeva, L.A. / Solovieva, A.Y. / Dergousova, N.I. / Boyko, K.M. / Tikhonova, T.V. / Popov, V.O.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2025
Title: Relationship between the structure and physicochemical properties of cytochrome c 546/556 from the bacterium Thioalkalivibrio paradoxus ARh1.
Authors: Varfolomeeva, L.A. / Solovieva, A.Y. / Shipkov, N.S. / Sluchanko, N.N. / Boyko, K.M. / Khrenova, M.G. / Tikhonova, T.V. / Popov, V.O.
History
DepositionMar 26, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Jul 23, 2025Group: Database references / Category: citation / citation_author
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.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Jul 30, 2025Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome C
B: Cytochrome C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2904
Polymers22,0532
Non-polymers1,2372
Water3,369187
1
A: Cytochrome C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6452
Polymers11,0261
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6452
Polymers11,0261
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.416, 37.601, 97.117
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cytochrome C


Mass: 11026.460 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thioalkalivibrio paradoxus ARh 1 (bacteria)
References: UniProt: W0DLP1
#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.: 187 / 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: 288 K / Method: vapor diffusion, hanging drop / pH: 3.5 / Details: 0.1 M Citric acid, pH 3.5, 30% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.8 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.15→48.56 Å / Num. obs: 47379 / % possible obs: 98.5 % / Redundancy: 3.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.022 / Rrim(I) all: 0.043 / Χ2: 0.56 / Net I/σ(I): 13.1 / Num. measured all: 165902
Reflection shellResolution: 1.15→1.17 Å / % possible obs: 95.7 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.174 / Num. measured all: 7250 / Num. unique obs: 2270 / CC1/2: 0.922 / Rpim(I) all: 0.108 / Rrim(I) all: 0.206 / Χ2: 0.13 / Net I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
CRANK2phasing
DIALSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.15→48.56 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.986 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.14417 2275 4.8 %RANDOM
Rwork0.11406 ---
obs0.11552 45054 97.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.26 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2--0.01 Å2-0 Å2
3----0.11 Å2
Refinement stepCycle: 1 / Resolution: 1.15→48.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1240 0 86 187 1513
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0121422
X-RAY DIFFRACTIONr_bond_other_d0.0030.0161236
X-RAY DIFFRACTIONr_angle_refined_deg2.6291.7691958
X-RAY DIFFRACTIONr_angle_other_deg0.9021.6532817
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9335170
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.36126.41867
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.14815198
X-RAY DIFFRACTIONr_dihedral_angle_4_deg1.554151
X-RAY DIFFRACTIONr_chiral_restr0.1790.2179
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.021700
X-RAY DIFFRACTIONr_gen_planes_other0.020.02302
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4251.562682
X-RAY DIFFRACTIONr_mcbond_other1.374681
X-RAY DIFFRACTIONr_mcangle_it1.87938.307852
X-RAY DIFFRACTIONr_mcangle_other1.938853
X-RAY DIFFRACTIONr_scbond_it2.285740
X-RAY DIFFRACTIONr_scbond_other2.287736
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6671105
X-RAY DIFFRACTIONr_long_range_B_refined2.8041725
X-RAY DIFFRACTIONr_long_range_B_other2.5431684
X-RAY DIFFRACTIONr_rigid_bond_restr3.77231370
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 2435 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.14 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.15→1.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.167 154 -
Rwork0.184 3233 -
obs--95.89 %

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