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- PDB-155c: THE STRUCTURE OF PARACOCCUS DENITRIFICANS CYTOCHROME C550 -

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Entry
Database: PDB / ID: 155c
TitleTHE STRUCTURE OF PARACOCCUS DENITRIFICANS CYTOCHROME C550
ComponentsCYTOCHROME C550
KeywordsELECTRON TRANSPORT
Function / homology
Function and homology information


electron transfer activity / heme binding / metal ion binding
Similarity search - Function
Cytochrome c, class IA/ IB / 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
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome c-550
Similarity search - Component
Biological speciesParacoccus denitrificans (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsTimkovich, R.
Citation
Journal: J.Biol.Chem. / Year: 1976
Title: The structure of Paracoccus denitrificans cytochrome c550.
Authors: Timkovich, R. / Dickerson, R.E.
History
DepositionAug 1, 1976Processing site: BNL
Revision 1.0Aug 20, 1976Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYTOCHROME C550
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8922
Polymers14,2751
Non-polymers6161
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.700, 82.170, 31.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: SIDE CHAIN ATOMS FOR RESIDUES 122 TO 134 ARE NOT INCLUDED BECAUSE THE SEQUENCE IN THIS REGION IS NOT DEFINITIVELY KNOWN. THE RESIDUES HAVE BEEN LABELLED AS UNK.

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Components

#1: Protein CYTOCHROME C550


Mass: 14275.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (bacteria) / References: UniProt: P00096
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
Has protein modificationY
Sequence detailsSIDE CHAIN ATOMS FOR RESIDUES 122 TO 134 ARE NOT INCLUDED BECAUSE THE SEQUENCE IN THIS REGION IS ...SIDE CHAIN ATOMS FOR RESIDUES 122 TO 134 ARE NOT INCLUDED BECAUSE THE SEQUENCE IN THIS REGION IS NOT DEFINITIVELY KNOWN. THE RESIDUES HAVE BEEN LABELLED AS UNK.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.94 Å3/Da / Density % sol: 36.55 %

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

RefinementHighest resolution: 2.5 Å
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms974 0 43 0 1017
Refinement
*PLUS
Highest resolution: 2.5 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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