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- PDB-351c: STRUCTURE OF CYTOCHROME C551 FROM P. AERUGINOSA REFINED AT 1.6 AN... -

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Basic information

Entry
Database: PDB / ID: 351c
TitleSTRUCTURE OF CYTOCHROME C551 FROM P. AERUGINOSA REFINED AT 1.6 ANGSTROMS RESOLUTION AND COMPARISON OF THE TWO REDOX FORMS
ComponentsCYTOCHROME C551
KeywordsELECTRON TRANSPORT
Function / homology
Function and homology information


periplasmic space / electron transfer activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome c, class ID / 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
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome c-551
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.6 Å
AuthorsMatsuura, Y. / Takano, T. / Dickerson, R.E.
Citation
Journal: J.Mol.Biol. / Year: 1982
Title: Structure of cytochrome c551 from Pseudomonas aeruginosa refined at 1.6 A resolution and comparison of the two redox forms.
Authors: Matsuura, Y. / Takano, T. / Dickerson, R.E.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1978
Title: Pseudomonas Cytochrome C551 at 2.0 Angstroms Resolution. Enlargement of the Cytochrome C Family
Authors: Almassy, R.J. / Dickerson, R.E.
#2: Journal: J.Mol.Biol. / Year: 1976
Title: The Cytochrome Fold and the Evolution of Bacterial Energy Metabolism
Authors: Dickerson, R.E. / Timkovich, R. / Almassy, R.J.
History
DepositionJul 20, 1981Processing site: BNL
SupersessionOct 2, 1981ID: 251C
Revision 1.0Oct 2, 1981Provider: repository / Type: Initial release
Revision 1.1Mar 25, 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 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_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.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

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Assembly

Deposited unit
A: CYTOCHROME C551
A: PROTOPORPHYRIN IX CONTAINING FE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3212
Polymers8,7051
Non-polymers6161
Water1,20767
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.500, 49.270, 49.640
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 C551


Mass: 8704.892 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / References: UniProt: P00099
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.07 Å3/Da / Density % sol: 40.6 %
Crystal grow
*PLUS
Method: microdialysis / PH range low: 5.7 / PH range high: 5.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
140-60 %ammonium sulfate11
21 M11NaCl
30.05 Mammonium phosphate11

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Data collection

Reflection
*PLUS
Num. obs: 8670

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Processing

RefinementHighest resolution: 1.6 Å /
RfactorNum. reflection
Rwork0.195 -
obs-8670
Refinement stepCycle: LAST / Highest resolution: 1.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms610 0 43 67 720
Refinement
*PLUS
Rfactor obs: 0.195
Solvent computation
*PLUS
Displacement parameters
*PLUS

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