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- PDB-2cdv: REFINED STRUCTURE OF CYTOCHROME C3 AT 1.8 ANGSTROMS RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 2cdv
TitleREFINED STRUCTURE OF CYTOCHROME C3 AT 1.8 ANGSTROMS RESOLUTION
ComponentsCYTOCHROME C3
KeywordsHEME PROTEIN OF ELECTRON TRANSPORT
Function / homology
Function and homology information


anaerobic respiration / periplasmic space / electron transfer activity / heme binding / metal ion binding
Similarity search - Function
Class III cytochrome C / Class III cytochrome C family / Cytochrome c, class III / Cytochrome C3 / Cytochrome C3 / Multiheme cytochrome superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
HEME C / Cytochrome c3
Similarity search - Component
Biological speciesDesulfovibrio vulgaris (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsHiguchi, Y. / Kusunoki, M. / Matsuura, Y. / Yasuoka, N. / Kakudo, M.
Citation
Journal: J.Mol.Biol. / Year: 1984
Title: Refined structure of cytochrome c3 at 1.8 A resolution
Authors: Higuchi, Y. / Kusunoki, M. / Matsuura, Y. / Yasuoka, N. / Kakudo, M.
#1: Journal: J.Biochem.(Tokyo) / Year: 1981
Title: On Cytochrome C3 Folding
Authors: Higuchi, Y. / Kusunoki, M. / Yasuoka, N. / Kakudo, M. / Yagi, T.
#2: Journal: J.Biochem.(Tokyo) / Year: 1981
Title: The Structure of Cytochrome C3 from Desulfovibrio Vulgaris Miyazaki at 2.5 Angstroms Resolution
Authors: Higuchi, Y. / Bando, S. / Kusunoki, M. / Matsuura, Y. / Yasuoka, N. / Kakudo, M. / Yamanaka, T. / Yagi, T. / Inokuchi, H.
#3: Journal: J.Biochem.(Tokyo) / Year: 1980
Title: Amino Acid Sequence of Cytochrome C3 from Desulfovibrio Vulgaris, Miyazaki
Authors: Shinkai, W. / Hase, T. / Yagi, T. / Matsubara, H.
#4: Journal: J.Biochem.(Tokyo) / Year: 1979
Title: Crystallographic Data for Cytochrome C3 from Two Strains of Desulfovibrio Vulgaris, Miyazaki
Authors: Bando, S. / Matsuura, Y. / Tanaka, N. / Yasuoka, N. / Kakudo, M. / Yagi, T. / Inokuchi, H.
History
DepositionNov 15, 1983Processing site: BNL
SupersessionFeb 2, 1984ID: 1CDV
Revision 1.0Feb 2, 1984Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
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_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _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_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_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 / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Oct 23, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYTOCHROME C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0315
Polymers11,5571
Non-polymers2,4744
Water84747
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.900, 68.100, 34.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CYTOCHROME C3


Mass: 11557.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris (bacteria) / References: UniProt: P00132
#2: Chemical
ChemComp-HEC / HEME C


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


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.72 Å3/Da / Density % sol: 54.76 %
Crystal grow
*PLUS
Temperature: 11 ℃ / pH: 7.3 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.0-2.5 %(w/v)protein1drop
250 mMTris-HCl1drop
360-65 %(v/v)ethanol1drop
470-75 %(v/v)ethanol1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 12162 / Num. measured all: 74360 / Rmerge(I) obs: 0.043

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Processing

RefinementHighest resolution: 1.8 Å /
RfactorNum. reflection
Rwork0.176 -
obs-9907
Refinement stepCycle: LAST / Highest resolution: 1.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms801 0 172 47 1020
Refinement
*PLUS
Lowest resolution: 6 Å / Rfactor obs: 0.176
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONo_bond_d0.0170.018
X-RAY DIFFRACTIONo_angle_d0.0310.026
X-RAY DIFFRACTIONo_planar_d0.0290.03
X-RAY DIFFRACTIONo_plane_restr0.0290.03
X-RAY DIFFRACTIONo_chiral_restr0.250.4
X-RAY DIFFRACTIONo_mcbond_it0.961
X-RAY DIFFRACTIONo_scbond_it1.411
X-RAY DIFFRACTIONo_mcangle_it1.551.5
X-RAY DIFFRACTIONo_scangle_it2.321.5

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