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- PDB-6a3l: Crystal structure of cytochrome c' from Shewanella violacea DSS12 -

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Basic information

Entry
Database: PDB / ID: 6a3l
TitleCrystal structure of cytochrome c' from Shewanella violacea DSS12
ComponentsCytochrome c
KeywordsELECTRON TRANSPORT / Cytochrome c' / Shewanella
Function / homology
Function and homology information


electron transfer activity / periplasmic space / iron ion binding / heme binding
Similarity search - Function
Cytochrome c prime / Cytochrome c class II profile. / Cytochrome c, class II / Cytochrome C' / Cytochrome c/b562 / Cytochrome c/b562 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
HEME C / Cytochrome c
Similarity search - Component
Biological speciesShewanella violacea (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsSuka, A. / Oki, H. / Kato, Y. / Kawahara, K. / Ohkubo, T. / Maruno, T. / Kobayashi, Y. / Fujii, S. / Wakai, S. / Sambongi, Y.
CitationJournal: Extremophiles / Year: 2019
Title: Stability of cytochromes c' from psychrophilic and piezophilic Shewanella species: implications for complex multiple adaptation to low temperature and high hydrostatic pressure.
Authors: Suka, A. / Oki, H. / Kato, Y. / Kawahara, K. / Ohkubo, T. / Maruno, T. / Kobayashi, Y. / Fujii, S. / Wakai, S. / Lisdiana, L. / Sambongi, Y.
History
DepositionJun 15, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 2.0Oct 2, 2019Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_site
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_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _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 / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id / _struct_site.details / _struct_site.pdbx_auth_comp_id

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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)29,5634
Polymers28,3262
Non-polymers1,2372
Water1,26170
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-42 kcal/mol
Surface area13280 Å2
Unit cell
Length a, b, c (Å)44.751, 69.707, 45.598
Angle α, β, γ (deg.)90.000, 112.190, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA1 - 129
211chain BB1 - 129

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Components

#1: Protein Cytochrome c /


Mass: 14163.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella violacea (strain JCM 10179 / CIP 106290 / LMG 19151 / DSS12) (bacteria)
Strain: JCM 10179 / CIP 106290 / LMG 19151 / DSS12 / Gene: SVI_0970 / Production host: Escherichia coli (E. coli) / References: UniProt: D4ZGZ2
#2: Chemical ChemComp-HEC / HEME C / 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 / Water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.32 Å3/Da / Density % sol: 47.09 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9.4 / Details: 100 mM CAPS (pH 9.4), 26 % (v/v) PEG 400

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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: Dec 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.14→37.49 Å / Num. obs: 14369 / % possible obs: 99.9 % / Redundancy: 4.25 % / Biso Wilson estimate: 38.44 Å2 / Rmerge(I) obs: 0.096 / Rrim(I) all: 0.11 / Χ2: 1.17 / Net I/σ(I): 7.8 / Num. measured all: 61600 / Scaling rejects: 462
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRrim(I) allΧ2% possible all
2.14-2.224.220.4512.714160.5171.27100
2.22-2.314.240.4112.714260.471.22100
2.31-2.414.290.343.214420.3881.22100
2.41-2.544.260.3113.514340.3561.2100
2.54-2.74.290.2753.814340.3141.19100
2.7-2.94.280.215.314180.2411.2399.9
2.9-3.24.250.1676.714650.1911.2599.9
3.2-3.664.20.09910.114140.1141.1799.4
3.66-4.614.240.06516.314530.0740.9699.7
4.61-37.494.280.04523.414670.0511.0299.9

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Processing

Software
NameVersionClassification
d*TREK9.9.9.8 W9DSSIdata scaling
d*TREKdata reduction
CrystalCleardata collection
PHENIXphasing
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.14→22.572 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 35.2
RfactorNum. reflection% reflection
Rfree0.272 1423 10.03 %
Rwork0.2146 --
obs0.2203 14188 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 78.32 Å2 / Biso mean: 48.2045 Å2 / Biso min: 30.4 Å2
Refinement stepCycle: final / Resolution: 2.14→22.572 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1980 0 86 70 2136
Biso mean--40.37 46.48 -
Num. residues----258
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092118
X-RAY DIFFRACTIONf_angle_d1.0782854
X-RAY DIFFRACTIONf_chiral_restr0.056290
X-RAY DIFFRACTIONf_plane_restr0.007360
X-RAY DIFFRACTIONf_dihedral_angle_d22.478764
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1146X-RAY DIFFRACTION7.559TORSIONAL
12B1146X-RAY DIFFRACTION7.559TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1401-2.21650.34621330.3591241137497
2.2165-2.30520.36141390.33831249138897
2.3052-2.410.40771390.30221267140698
2.41-2.53690.3671440.28751276142099
2.5369-2.69560.35091370.28491284142199
2.6956-2.90330.37711490.28081257140699
2.9033-3.19470.33741440.265313081452100
3.1947-3.65530.27031430.20231272141599
3.6553-4.59890.2051500.16113001450100
4.5989-22.57290.19721450.14951311145699

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