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- PDB-1co6: CRYSTAL STRUCTURE OF FERROCYTOCHROME C2 FROM RHODOPSEUDOMONAS VIRIDIS -

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Basic information

Entry
Database: PDB / ID: 1co6
TitleCRYSTAL STRUCTURE OF FERROCYTOCHROME C2 FROM RHODOPSEUDOMONAS VIRIDIS
ComponentsPROTEIN (CYTOCHROME C2)
KeywordsELECTRON TRANSPORT / ELECTRON TRANSPORT(HEME PROTEIN)
Function / homology
Function and homology information


photosynthesis / electron transfer activity / heme binding / metal ion binding
Similarity search - Function
Cytochrome c, class IA/ IB / Cytochrome c / 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 / Cytochrome c2
Similarity search - Component
Biological speciesBlastochloris viridis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMiki, K. / Sogabe, S.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: Refined crystal structure of ferrocytochrome c2 from Rhodopseudomonas viridis at 1.6 A resolution.
Authors: Sogabe, S. / Miki, K.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1994
Title: Application of Automatic Molecular-Replacement Procedure to Crystal Structure Analysis of Cytochrrome c2 from Rhodopseudomonas Viridis
Authors: Miki, K. / Sogabe, S. / Uno, A. / Ezoe, T. / Kasai, N. / Saeda, M. / Matsuura, Y. / Miki, M.
#2: Journal: FEBS Lett. / Year: 1994
Title: Structure Similarity of Cytochrrome c2 from Rhodopseudomonas Viridis to Mitochondrial Cytochrome C Revealed by its Crystal Structure at 2.7 A Resokution
Authors: Sogabe, S. / Ezoe, T. / Kasai, N. / Saeda, M. / Uno, A. / Miki, M. / Miki, K.
History
DepositionJun 5, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jun 18, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 2.0Mar 3, 2021Group: 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_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (CYTOCHROME C2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2862
Polymers11,6671
Non-polymers6191
Water2,612145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.130, 76.130, 40.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Cell settingtrigonal
Space group name H-MP3221

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Components

#1: Protein PROTEIN (CYTOCHROME C2)


Mass: 11667.220 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Blastochloris viridis (bacteria) / References: UniProt: P00083
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.37 Å3/Da / Density % sol: 57.52 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.5
Details: CRYSTALS WERE GROWN FROM AN AMMONIUM SULFATE SOLUTION AT PH 8.5, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
20.1 MTris-HCl1drop
340 %satammonium sulfate1drop
470 %satammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Jul 15, 1994
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 16166 / % possible obs: 89.1 % / Observed criterion σ(I): 1 / Redundancy: 1 % / Rmerge(I) obs: 0.072

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Processing

Software
NameClassification
PHASERphasing
PROLSQrefinement
WEISdata reduction
PROTEINdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CYT

5cyt


Resolution: 1.6→6 Å / σ(F): 1 / Details: INITIAL REFINEMENT WITH X-PLOR 3.1
RfactorNum. reflection% reflection
Rwork0.182 --
obs-15014 85.2 %
Refinement stepCycle: LAST / Resolution: 1.6→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms821 0 43 145 1009
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.02
X-RAY DIFFRACTIONp_angle_d0.0370.037
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0440.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.1311.5
X-RAY DIFFRACTIONp_mcangle_it1.6962
X-RAY DIFFRACTIONp_scbond_it2.2672
X-RAY DIFFRACTIONp_scangle_it3.4812.5
X-RAY DIFFRACTIONp_plane_restr0.0140.2
X-RAY DIFFRACTIONp_chiral_restr0.1410.15
X-RAY DIFFRACTIONp_singtor_nbd0.1760.3
X-RAY DIFFRACTIONp_multtor_nbd0.2260.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2230.3
X-RAY DIFFRACTIONp_planar_tor2.43
X-RAY DIFFRACTIONp_staggered_tor18.915
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor1520
X-RAY DIFFRACTIONp_special_tor

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