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- PDB-1e8e: Solution Structure of Methylophilus methylotrophus Cytochrome c''... -

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Basic information

Entry
Database: PDB / ID: 1e8e
TitleSolution Structure of Methylophilus methylotrophus Cytochrome c''. Insights into the Structural Basis of Haem-Ligand Detachment
ComponentsCYTOCHROME C''
KeywordsOXIDOREDUCTASE(CYTOCHROME) / CYTOCHROME C'' / LIGAND DETACHMENT / REDOX-BOHR EFFECT / PARAMAGNETIC
Function / homology
Function and homology information


electron transfer activity / heme binding / metal ion binding
Similarity search - Function
Protein of unknown function DUF1924, Cytochrome c-type protein SHP-like / Domain of unknown function (DUF1924) / 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''
Similarity search - Component
Biological speciesMETHYLOPHILUS METHYLOTROPHUS (bacteria)
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS WITH SIMULATED ANNEALING
AuthorsBrennan, L. / Turner, D.L. / Fareleira, P. / Santos, H.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Solution Structure of Methylophilus Methylotrophus Cytochrome C": Insights Into the Structural Basis of Haem-Ligand Detachment
Authors: Brennan, L. / Turner, D.L. / Fareleira, P. / Santos, H.
#1: Journal: Eur.J.Biochem. / Year: 1993
Title: Characterization of the Haem Environment in Methylophilus Methylotrophus Ferricytochrome C'' by 1H-NMR
Authors: Costa, H.S. / Santos, H. / Turner, D.L.
#2: Journal: Eur.J.Biochem. / Year: 1992
Title: Involvement of a Labile Axial Histidine in Coupling Electron and Proton Transfer in Methylophilus Methylotrophus Cytochrome C''
Authors: Costa, H.S. / Santos, H. / Turner, D.L. / Xavier, A.V.
#3: Journal: Biochim.Biophys.Acta / Year: 1988
Title: Characterization and NMR Studies of a Novel Cytochrome C Isolated from Methylophilus Methylotrophus which Shows a Redox-Linked Change Os Spin-State
Authors: Santos, H. / Turner, D.L.
History
DepositionSep 20, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 15, 2020Group: Derived calculations / Other / Category: pdbx_database_status / struct_conn
Item: _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 23, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 C''
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3182
Polymers13,6991
Non-polymers6191
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 400LEAST RESTRAINT VIOLATION
RepresentativeModel #1

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Components

#1: Protein CYTOCHROME C''


Mass: 13699.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: C-TYPE CYTOCHROME, FULLY OXIDISED FORM / Source: (natural) METHYLOPHILUS METHYLOTROPHUS (bacteria) / References: UniProt: Q9RQB9
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D-1H-NOESY
1212D-1H-TOCSY
1312D-1H-COSY
1413D(15N
1511H)-TOCSY-HSQC
1613D(15N
1711H)-NOESY-HSQC

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Sample preparation

DetailsContents: 10 MM PHOSPATE BUFFER
Sample conditionspH: 5.6 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 750 MHz

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Processing

NMR software
NameDeveloperClassification
PARADYANAD.L.TURNER,L.BRENNAN,S.G.CHAMBERLIN, R.O.LOURO, A.V.XAVIERrefinement
PARADYANAstructure solution
RefinementMethod: TORSION ANGLE DYNAMICS WITH SIMULATED ANNEALING / Software ordinal: 1
Details: DIPOLAR SHIFTS WERE USED AS RESTRAINTS IN AN EXTENDED VERSION OF DYANA CALLED PARADYANA. D.L.TURNER,L,BRENNAN,S.G.CHAMBERLIN, R.O.LOURO,A.V.XAVIER (1998)DETERMINATION OF SOLUTION STRUCTURES ...Details: DIPOLAR SHIFTS WERE USED AS RESTRAINTS IN AN EXTENDED VERSION OF DYANA CALLED PARADYANA. D.L.TURNER,L,BRENNAN,S.G.CHAMBERLIN, R.O.LOURO,A.V.XAVIER (1998)DETERMINATION OF SOLUTION STRUCTURES OF PARAMAGNETIC PROTEINS BY NMR.EUR.BIOPHYS.J.27,367-375.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 400 / Conformers submitted total number: 20

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