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- PDB-5b3i: Homo-dimeric structure of cytochrome c' from Thermophilic Hydroge... -

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Basic information

Entry
Database: PDB / ID: 5b3i
TitleHomo-dimeric structure of cytochrome c' from Thermophilic Hydrogenophilus thermoluteolus
ComponentsCytochrome c prime
KeywordsELECTRON TRANSPORT / cytochrome c' / class II cytochrome c protein / heme protein
Function / homology
Function and homology information


electron transfer activity / periplasmic space / iron ion binding / heme binding
Similarity search - Function
Cytochrome c prime, subgroup / 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 prime
Similarity search - Component
Biological speciesHydrogenophilus thermoluteolus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.89 Å
AuthorsFujii, S. / Oki, H. / Kawahara, K. / Yamane, D. / Yamanaka, M. / Maruno, T. / Kobayashi, Y. / Masanari, M. / Wakai, S. / Nishihara, H. ...Fujii, S. / Oki, H. / Kawahara, K. / Yamane, D. / Yamanaka, M. / Maruno, T. / Kobayashi, Y. / Masanari, M. / Wakai, S. / Nishihara, H. / Ohkubo, T. / Sambongi, Y.
CitationJournal: Protein Sci. / Year: 2017
Title: Structural and functional insights into thermally stable cytochrome c' from a thermophile
Authors: Fujii, S. / Oki, H. / Kawahara, K. / Yamane, D. / Yamanaka, M. / Maruno, T. / Kobayashi, Y. / Masanari, M. / Wakai, S. / Nishihara, H. / Ohkubo, T. / Sambongi, Y.
History
DepositionFeb 29, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references
Revision 2.0Oct 2, 2019Group: Advisory / Atomic model ...Advisory / 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_validate_close_contact / 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.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_validate_close_contact.auth_comp_id_2 / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id / _struct_site.details / _struct_site.pdbx_auth_comp_id
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome c prime
B: Cytochrome c prime
C: Cytochrome c prime
D: Cytochrome c prime
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8708
Polymers59,3964
Non-polymers2,4744
Water13,998777
1
A: Cytochrome c prime
B: Cytochrome c prime
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9354
Polymers29,6982
Non-polymers1,2372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-63 kcal/mol
Surface area13350 Å2
MethodPISA
2
C: Cytochrome c prime
D: Cytochrome c prime
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9354
Polymers29,6982
Non-polymers1,2372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-63 kcal/mol
Surface area13440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.243, 72.923, 132.365
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-428-

HOH

21A-443-

HOH

31B-470-

HOH

41D-460-

HOH

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Components

#1: Protein
Cytochrome c prime


Mass: 14848.938 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Hydrogenophilus thermoluteolus (bacteria) / References: UniProt: F7J213
#2: Chemical
ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 777 / 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: 2.2 Å3/Da / Density % sol: 43.97 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8.1 / Details: 18% PEG 4000, 0.1M Tris-HCl

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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: Nov 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.89→43.52 Å / Num. obs: 41938 / % possible obs: 97.7 % / Redundancy: 9.57 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.104 / Rrim(I) all: 0.104 / Χ2: 0.58 / Net I/σ(I): 11 / Num. measured all: 404512 / Scaling rejects: 3034
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2Rejects% possible all
1.89-1.966.10.3423.82145335180.61083.6
1.96-2.047.960.3314.43234040590.635096.3
2.04-2.139.850.3055.34155142070.649699.6
2.13-2.249.870.2795.64188142300.6312199.6
2.24-2.389.890.2326.44218242490.6115299.8
2.38-2.579.960.1867.74250542480.5920199.8
2.57-2.8210.110.1459.74355442900.58192100
2.82-3.2310.430.09413.84507743000.55212100
3.23-4.0710.640.0620.34650943480.52242100
4.07-43.5210.180.04625.14746044890.52175898.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
CrystalClear1.3.5data collection
d*TREK8.0SSIdata reduction
d*TREK8.0SSIdata scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BBH

1bbh


Resolution: 1.89→41.953 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 21.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2431 1997 4.77 %
Rwork0.1955 --
obs0.1978 41871 97.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.89→41.953 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4148 0 172 777 5097
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124408
X-RAY DIFFRACTIONf_angle_d1.6555964
X-RAY DIFFRACTIONf_dihedral_angle_d13.4191668
X-RAY DIFFRACTIONf_chiral_restr0.064620
X-RAY DIFFRACTIONf_plane_restr0.007764
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.93730.33351160.3022313X-RAY DIFFRACTION80
1.9373-1.98970.30271330.26762657X-RAY DIFFRACTION93
1.9897-2.04820.271400.23732816X-RAY DIFFRACTION98
2.0482-2.11430.28391440.22932882X-RAY DIFFRACTION100
2.1143-2.18990.25251430.21162853X-RAY DIFFRACTION100
2.1899-2.27750.26531450.20662888X-RAY DIFFRACTION100
2.2775-2.38120.29421440.20012882X-RAY DIFFRACTION100
2.3812-2.50670.25181450.19642891X-RAY DIFFRACTION100
2.5067-2.66370.26031450.20312898X-RAY DIFFRACTION100
2.6637-2.86940.2351470.19962915X-RAY DIFFRACTION100
2.8694-3.1580.26571460.19232929X-RAY DIFFRACTION100
3.158-3.61480.19761470.17272943X-RAY DIFFRACTION100
3.6148-4.55340.20551490.15882984X-RAY DIFFRACTION100
4.5534-41.96310.21381530.17563023X-RAY DIFFRACTION97

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