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- PDB-8hn3: Soluble domain of cytochrome c-556 from Chlorobaculum tepidum -

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Basic information

Entry
Database: PDB / ID: 8hn3
TitleSoluble domain of cytochrome c-556 from Chlorobaculum tepidum
ComponentsCytochrome c-556
KeywordsELECTRON TRANSPORT / cytochrome c / photosynthesis / green sulfur bacteria / cytochrome bc complex
Function / homology
Function and homology information


electron transfer activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome c, class IE / Cytochrome C oxidase, cbb3-type, subunit III / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
ACETATE ION / HEME C / Cytochrome c-555, membrane-bound
Similarity search - Component
Biological speciesChlorobaculum tepidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsKishimoto, H. / Azai, C. / Yamamoto, T. / Mutoh, R. / Nakaniwa, T. / Tanaka, H. / Kurisu, G. / Oh-oka, H.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)15K21122 Japan
Japan Society for the Promotion of Science (JSPS)T18K061530 Japan
Japan Science and TechnologyJPMJCR20E1 Japan
Japan Society for the Promotion of Science (JSPS)19H04724 Japan
CitationJournal: Curr Res Struct Biol / Year: 2023
Title: Soluble domains of cytochrome c-556 and Rieske iron-sulfur protein from Chlorobaculum tepidum: Crystal structures and interaction analysis.
Authors: Kishimoto, H. / Azai, C. / Yamamoto, T. / Mutoh, R. / Nakaniwa, T. / Tanaka, H. / Miyanoiri, Y. / Kurisu, G. / Oh-Oka, H.
History
DepositionDec 7, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification
Revision 2.0Aug 12, 2026Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_modification_feature / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order / pdbx_validate_chiral
Item: _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight
Description: Metalloprotein remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome c-556
B: Cytochrome c-556
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0978
Polymers16,5132
Non-polymers1,5846
Water3,459192
1
A: Cytochrome c-556
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0654
Polymers8,2561
Non-polymers8093
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome c-556
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0324
Polymers8,2561
Non-polymers7763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.024, 85.024, 123.932
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-223-

HOH

21A-255-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Cytochrome c-556 / Cytochrome c-555 / membrane-bound


Mass: 8256.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlorobaculum tepidum (bacteria) / Gene: CT0073 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q8KG95

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Non-polymers , 5 types, 198 molecules

#2: Chemical ChemComp-HEC / HEME C


Mass: 620.519 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H36FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#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: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.92 Å3/Da / Density % sol: 68.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 0.1 M sodium acetate trihydrate pH 4.4, 1.8 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 32195 / % possible obs: 99.9 % / Redundancy: 20.7 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 95.6
Reflection shellResolution: 1.65→1.68 Å / Rmerge(I) obs: 0.24 / Num. unique obs: 3113

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data scaling
HKL-2000data reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.65→36.82 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.961 / SU B: 0.936 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17357 1972 6.1 %RANDOM
Rwork0.15304 ---
obs0.15427 30276 98.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.112 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 1.65→36.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1130 0 106 192 1428
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0330.0191264
X-RAY DIFFRACTIONr_bond_other_d0.0030.021177
X-RAY DIFFRACTIONr_angle_refined_deg3.3112.0821731
X-RAY DIFFRACTIONr_angle_other_deg1.38232715
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8755158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.12126.75737
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.64315193
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.217152
X-RAY DIFFRACTIONr_chiral_restr0.1420.2171
X-RAY DIFFRACTIONr_gen_planes_refined0.0390.0211454
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02248
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_it2.0481.753639
X-RAY DIFFRACTIONr_mcbond_other2.0181.743637
X-RAY DIFFRACTIONr_mcangle_it2.8552.608794
X-RAY DIFFRACTIONr_mcangle_other2.8552.612795
X-RAY DIFFRACTIONr_scbond_it3.781.959624
X-RAY DIFFRACTIONr_scbond_other3.7691.959624
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8642.785938
X-RAY DIFFRACTIONr_long_range_B_refined5.91315.6541782
X-RAY DIFFRACTIONr_long_range_B_other5.5714.7481695
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.692 Å
RfactorNum. reflection% reflection
Rfree0.183 138 -
Rwork0.145 2153 -
obs--97.08 %

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