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- PDB-1ccr: STRUCTURE OF RICE FERRICYTOCHROME C AT 2.0 ANGSTROMS RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1ccr
TitleSTRUCTURE OF RICE FERRICYTOCHROME C AT 2.0 ANGSTROMS RESOLUTION
ComponentsCYTOCHROME C
KeywordsELECTRON TRANSPORT(CYTOCHROME)
Function / homology
Function and homology information


mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / mitochondrial intermembrane space / 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 c / Cytochrome c
Similarity search - Component
Biological speciesOryza sativa (Asian cultivated rice)
MethodX-RAY DIFFRACTION / Resolution: 1.5 Å
AuthorsOchi, H. / Hata, Y. / Tanaka, N. / Kakudo, M. / Sakurai, T. / Aihara, S. / Morita, Y.
Citation
Journal: J.Mol.Biol. / Year: 1983
Title: Structure of rice ferricytochrome c at 2.0 A resolution.
Authors: Ochi, H. / Hata, Y. / Tanaka, N. / Kakudo, M. / Sakurai, T. / Aihara, S. / Morita, Y.
#1: Journal: J.Biochem.(Tokyo) / Year: 1980
Title: Amino Acid Sequence of Cytochrome C from Rice
Authors: Mori, E. / Morita, Y.
#2: Journal: J.Mol.Biol. / Year: 1972
Title: A Preliminary Crystallographic Investigation of Rice Cytochrome C
Authors: Morita, Y. / Ida, S.
#3: Journal: Agric.Biol.Chem. / Year: 1968
Title: Studies on Respiratory Enzymes in Rice Kernel. Part I. Isolation and Purification of Cytochrome C and Peroxidase 556 from Rice Embryo
Authors: Mori, Y. / Ida, S.
History
DepositionMar 14, 1983Processing site: BNL
Revision 1.0Apr 21, 1983Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 2.0Mar 3, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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 / struct_conn / struct_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYTOCHROME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8862
Polymers12,2681
Non-polymers6191
Water82946
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.780, 43.780, 110.050
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Atom site foot note1: RESIDUE LYS 80 AND TML 2 FORM EPSILON-N-TRIMETHYLLYSINE. SEE REMARK 4 ABOVE.
2: RESIDUE LYS 94 AND TML 3 FORM EPSILON-N-TRIMETHYLLYSINE. SEE REMARK 4 ABOVE.

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Components

#1: Protein CYTOCHROME C /


Mass: 12267.986 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa (Asian cultivated rice) / References: UniProt: P00055, UniProt: Q0DI31*PLUS
#2: Chemical ChemComp-HEC / HEME C / Heme C


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


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.74 %
Crystal grow
*PLUS
pH: 6 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13.6 Mammonium sulphate11
22 %(w/v)protein11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2 Å / Num. obs: 44000 / % possible obs: 97.5 % / Rmerge(I) obs: 0.022

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Processing

RefinementRfactor Rwork: 0.19 / Highest resolution: 1.5 Å
Refinement stepCycle: LAST / Highest resolution: 1.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms858 0 49 46 953
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.02
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Refinement
*PLUS
Highest resolution: 2 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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