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- PDB-1cgn: CYTOCHROME C' -

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Basic information

Entry
Database: PDB / ID: 1cgn
TitleCYTOCHROME C'
ComponentsCYTOCHROME C
KeywordsELECTRON TRANSPORT (CYTOCHROME)
Function / homology
Function and homology information


electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome c prime, subgroup / Cytochrome c, class II / Cytochrome c prime / Cytochrome C' / Cytochrome c class II profile. / Cytochrome c/b562 / Cytochrome c/b562 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
HEME C / Cytochrome c'
Similarity search - Component
Biological speciesAchromobacter xylosoxidans (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.15 Å
AuthorsDobbs, A.J. / Faber, H.R. / Anderson, B.F. / Baker, E.N.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Three-dimensional structure of cytochrome c' from two Alcaligenes species and the implications for four-helix bundle structures.
Authors: Dobbs, A.J. / Anderson, B.F. / Faber, H.R. / Baker, E.N.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Atomic Structure of a Cytochrome C' with an Unusual Ligand-Controlled Dimer Dissociation at 1.8 Angstroms Resolution
Authors: Ren, Z. / Meyer, T.E. / Mcree, D.E.
#2: Journal: J.Biochem.(Tokyo) / Year: 1992
Title: Three-Dimensional Structure of Ferricytochrome C' from Rhodospirillum Rubrum at 2.8 Angstroms Resolution
Authors: Yasui, M. / Harada, S. / Kai, Y. / Kasai, N. / Kusunoki, M. / Matsura, Y.
#3: Journal: J.Mol.Biol. / Year: 1985
Title: Structure of Ferricytochrome C' from Rhodospirillum Molischianum at 1.67 Angstroms
Authors: Finzel, B.C. / Weber, P.C. / Hardman, K.D. / Salemme, F.R.
#4: Journal: J.Mol.Biol. / Year: 1981
Title: Crystallographic Structure of Rhodospirillum Molischianum Ferricytochrome C' at 2.5 Angstroms Resolution
Authors: Weber, P.C. / Howard, A. / Xoung, N.H. / Salemme, F.R.
#5: Journal: Biochem.J. / Year: 1973
Title: The Amino Acid Sequence of Cytochrome C' from Alcaligenes Sp. N.C.I.B. 11015
Authors: Ambler, R.P.
History
DepositionMay 1, 1995Processing site: BNL
Revision 1.0Jul 31, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 25, 2019Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Polymer sequence
Category: entity_poly / pdbx_database_status ...entity_poly / pdbx_database_status / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.process_site ..._entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.process_site / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 3.0Jan 22, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
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_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _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.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id
Revision 3.1Oct 16, 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 C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1942
Polymers13,5751
Non-polymers6191
Water1,35175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.600, 54.600, 180.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsSYMMETRY THE CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS PRESENTED BELOW GENERATE THE SUBUNITS OF THE POLYMERIC MOLECULE. APPLIED TO RESIDUES: PCA 1 .. HEM 128 SYMMETRY OPERATION TO GENERATE THE SECOND MOLECULE OF THE DIMERIC PARTICLE SYMMETRY1 1 -1.000000 0.000000 0.000000 0.00000 SYMMETRY2 1 0.000000 1.000000 0.000000 0.00000 SYMMETRY3 1 0.000000 0.000000 -1.000000 90.20000

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Components

#1: Protein CYTOCHROME C


Mass: 13575.380 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Achromobacter xylosoxidans (bacteria) / References: UniProt: P00138
#2: Chemical ChemComp-HEC / HEME C


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


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.86 Å3/Da / Density % sol: 56.96 %
Crystal grow
*PLUS
Temperature: 37 ℃ / pH: 6 / Method: vapor diffusion / Details: Norris, G. E., (1979) J.Mol.Biol., 135, 309.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112 mg/mlprotein1drop
20.1 Mphosphate1drop
350 %satammonium sulfate1drop
462-66 %satammonium sulfate1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Mar 20, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRedundancy: 7.4 % / Rmerge(I) obs: 0.032
Reflection
*PLUS
Highest resolution: 2.15 Å / Num. obs: 8220 / % possible obs: 90 % / Observed criterion σ(I): 0 / Num. measured all: 60526 / Rmerge(I) obs: 0.032

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Processing

Software
NameVersionClassification
TNT5Crefinement
SUPPLIEDSOFTWAREdata reduction
RefinementResolution: 2.15→20 Å / σ(F): 0 /
RfactorNum. reflection
obs0.167 8220
Refinement stepCycle: LAST / Resolution: 2.15→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms910 0 43 75 1028
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 22.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.013
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg2.1

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