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Basic information

Entry
Database: PDB / ID: 1cyj
TitleCYTOCHROME C6
ComponentsCYTOCHROME C6
KeywordsELECTRON TRANSPORT PROTEIN (CYTOCHROME) / PHOTOSYNTHESIS / CHLAMYDOMONAS
Function / homology
Function and homology information


chloroplast thylakoid lumen / photosynthesis / electron transfer activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome c6 / Cytochrome c, class IC / 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 / Cytochrome c6, chloroplastic
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsKerfeld, C.A. / Yeates, T.O.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: The structure of chloroplast cytochrome c6 at 1.9 A resolution: evidence for functional oligomerization.
Authors: Kerfeld, C.A. / Anwar, H.P. / Interrante, R. / Merchant, S. / Yeates, T.O.
#1: Journal: J.Biol.Chem. / Year: 1991
Title: Isolation and Structural Characterization of the Chlamydomonas Reinhardtii Gene for Cytochrome C6
Authors: Hill, K.L. / Li, H.H. / Singer, J. / Merchant, S.
History
DepositionMay 9, 1995Processing site: BNL
Revision 1.0Jan 29, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 2.0Mar 10, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_database_status / 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.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_database_status.process_site / _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_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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.ptnr1_symmetry / _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.ptnr2_symmetry / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700SHEET DUE TO INCOMPLETE ELECTRON DENSITY, THE CE1, CE2, CZ AND OH OF TYR 90 IS MISSING. A SHORT TWO- ...SHEET DUE TO INCOMPLETE ELECTRON DENSITY, THE CE1, CE2, CZ AND OH OF TYR 90 IS MISSING. A SHORT TWO-STRANDED ANTI-PARALLEL BETA-SHEET IS FORMED BY RESIDUES 54 - 63, ENCLOSING A TYPE II' TURN BETWEEN RESIDUES 57 AND 60. THERE ARE TWO INTERSTRAND HYDROGEN BONDS BETWEEN RESIDUES 57 AND 60.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYTOCHROME C6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8796
Polymers9,8111
Non-polymers1,0685
Water1,29772
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.600, 81.600, 81.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-430-

HOH

21A-441-

HOH

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Components

#1: Protein CYTOCHROME C6 / CYTOCHROME C553


Mass: 9810.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / Organelle: CHLOROPLAST / Strain: CC124 / References: UniProt: P08197
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-HEC / HEME C


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


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.68 %
Crystal
*PLUS
Density % sol: 49.3 %
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18.8 mg/mlprotein 1drop
225 mMMES1reservoir
325 %PEG33501reservoir
4150 mM1reservoirCdCl2

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Data collection

Diffraction sourceWavelength: 1.54
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 22, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→57.6 Å / Num. obs: 5709 / % possible obs: 78.6 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.072
Reflection
*PLUS
Rmerge(I) obs: 0.072
Reflection shell
*PLUS
Mean I/σ(I) obs: 4.9

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
R-AXISdata reduction
MSCdata reduction
X-PLOR3.1phasing
RefinementResolution: 1.9→10 Å / σ(F): 0
Details: NO RESTRAINTS WERE PLACED ON CADMIUM IONS DURING REFINEMENT. CONSEQUENTLY THERE ARE CLOSE CONTACTS BETWEEN SOLVENT MOLECULES AND SIDE-CHAIN ATOMS INVOLVED IN CADMIUM LIGATION. FROM 2FO-FC ...Details: NO RESTRAINTS WERE PLACED ON CADMIUM IONS DURING REFINEMENT. CONSEQUENTLY THERE ARE CLOSE CONTACTS BETWEEN SOLVENT MOLECULES AND SIDE-CHAIN ATOMS INVOLVED IN CADMIUM LIGATION. FROM 2FO-FC ELECTRON DENSITY AND ITS PROXIMITY TO SOLVENT MOLECULES, THE ATOM AT POSITION 422 APPEARS TO BE AN ION. HOWEVER SINCE IT DID NOT REFINE SATISFACTORILY AS A CADMIUM ION IT WAS MODELLED AS SOLVENT, RESULTING IN CLOSE INTERMOLECULAR CONTACTS WITH SOLVENT MOLECULES 456 AND 469.
RfactorNum. reflection
Rwork0.187 -
obs0.187 6412
Displacement parametersBiso mean: 21.1 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms684 0 47 72 803
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.665
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it4
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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