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- PDB-5b6q: Crystal structure of monomeric cytochrome c5 from Shewanella violacea -

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Basic information

Entry
Database: PDB / ID: 5b6q
TitleCrystal structure of monomeric cytochrome c5 from Shewanella violacea
ComponentsSoluble cytochrome cA
KeywordsELECTRON TRANSPORT / Cytochrome c5 / Protein stability / Shewanella
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-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HEME C / IMIDAZOLE / Soluble cytochrome cA / Soluble cytochrome cA
Similarity search - Component
Biological speciesShewanella violacea (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsMasanari, M. / Fujii, S. / Kawahara, K. / Oki, H. / Tsujino, H. / Maruno, T. / Kobayashi, Y. / Ohkubo, T. / Nishiyama, M. / Harada, Y. ...Masanari, M. / Fujii, S. / Kawahara, K. / Oki, H. / Tsujino, H. / Maruno, T. / Kobayashi, Y. / Ohkubo, T. / Nishiyama, M. / Harada, Y. / Wakai, S. / Sambongi, Y.
CitationJournal: Biosci.Biotechnol.Biochem. / Year: 2016
Title: Comparative study on stabilization mechanism of monomeric cytochrome c5 from deep-sea piezophilic Shewanella violacea
Authors: Masanari, M. / Fujii, S. / Kawahara, K. / Oki, H. / Tsujino, H. / Maruno, T. / Kobayashi, Y. / Ohkubo, T. / Wakai, S. / Sambongi, Y.
History
DepositionJun 1, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 2.0Oct 2, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Soluble cytochrome cA
B: Soluble cytochrome cA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3325
Polymers16,0262
Non-polymers1,3063
Water2,918162
1
A: Soluble cytochrome cA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,6322
Polymers8,0131
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-21 kcal/mol
Surface area4170 Å2
MethodPISA
2
B: Soluble cytochrome cA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7013
Polymers8,0131
Non-polymers6882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-16 kcal/mol
Surface area4310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.588, 50.075, 97.609
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Soluble cytochrome cA / cytochrome c5


Mass: 8013.103 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella violacea (bacteria) / Gene: cytcA / Production host: Escherichia coli (E. coli) / Strain (production host): Jcb387 / References: UniProt: Q9RHJ6, UniProt: D4ZE39*PLUS
#2: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O

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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: 2.03 Å3/Da / Density % sol: 39.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 0.1 M imidazole, 0.2 M NaCl, 0.4 M NaH2PO4, 1.8 M K2HPO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.78→34.951 Å / Num. obs: 12711 / % possible obs: 96.7 % / Redundancy: 6.12 % / Net I/σ(I): 16.1

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Processing

Software
NameVersionClassification
d*TREKdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
CrystalCleardata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→34.951 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.69
RfactorNum. reflection% reflection
Rfree0.2375 1268 10.01 %
Rwork0.214 --
obs0.2164 12662 96.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 47.17 Å2 / Biso mean: 26.7906 Å2 / Biso min: 15.28 Å2
Refinement stepCycle: final / Resolution: 1.78→34.951 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1108 0 91 162 1361
Biso mean--23.72 31.15 -
Num. residues----152
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081245
X-RAY DIFFRACTIONf_angle_d1.6931693
X-RAY DIFFRACTIONf_chiral_restr0.044168
X-RAY DIFFRACTIONf_plane_restr0.007211
X-RAY DIFFRACTIONf_dihedral_angle_d12.338456
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7801-1.85140.30151270.31021149127691
1.8514-1.93560.37091380.32531226136496
1.9356-2.03770.23761400.22261262140297
2.0377-2.16530.26681360.21891242137897
2.1653-2.33250.31781400.27241241138196
2.3325-2.56710.25651390.22571254139396
2.5671-2.93840.24361450.21631301144698
2.9384-3.70150.20131470.19811317146499
3.7015-34.95720.19761560.1721402155899

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