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- PDB-1hko: NMR structure of bovine cytochrome b5 -

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Basic information

Entry
Database: PDB / ID: 1hko
TitleNMR structure of bovine cytochrome b5
ComponentsCYTOCHROME B5
KeywordsELECTRON TRANSPORT / CYTOCHROME / ELECTRON TRANSFER PROTEIN / HEME
Function / homology
Function and homology information


Vitamin C (ascorbate) metabolism / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / mitochondrial outer membrane / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / metal ion binding
Similarity search - Function
: / Flavocytochrome B2; Chain A, domain 1 / Cytochrome b5-like heme/steroid binding domain / Cytochrome b5, heme-binding site / Cytochrome b5 family, heme-binding domain signature. / Cytochrome b5 family, heme-binding domain profile. / Cytochrome b5-like heme/steroid binding domain / Cytochrome b5-like heme/steroid binding domain superfamily / Cytochrome b5-like Heme/Steroid binding domain / Cytochrome b5-like Heme/Steroid binding domain ...: / Flavocytochrome B2; Chain A, domain 1 / Cytochrome b5-like heme/steroid binding domain / Cytochrome b5, heme-binding site / Cytochrome b5 family, heme-binding domain signature. / Cytochrome b5 family, heme-binding domain profile. / Cytochrome b5-like heme/steroid binding domain / Cytochrome b5-like heme/steroid binding domain superfamily / Cytochrome b5-like Heme/Steroid binding domain / Cytochrome b5-like Heme/Steroid binding domain / Roll / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome b5
Similarity search - Component
Biological speciesBOS TAURUS (cattle)
MethodSOLUTION NMR
AuthorsMuskett, F.W. / Whitford, D.
CitationJournal: J.Mol.Biol. / Year: 1996
Title: The Solution Structure of Bovine Ferricytochrome B5 Determined Using Heteronuclear NMR Methods.
Authors: Muskett, F.W. / Kelly, G.P. / Whitford, D.
History
SupersessionMar 10, 2003ID: 1WDB
DepositionMar 10, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2003Provider: repository / Type: Initial release
Revision 1.1May 15, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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

Downloads & links

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Assembly

Deposited unit
A: CYTOCHROME B5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4282
Polymers11,8121
Non-polymers6161
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)42 / 100LEAST RESTRAINT VIOLATION
RepresentativeModel #6

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Components

#1: Protein CYTOCHROME B5


Mass: 11811.950 Da / Num. of mol.: 1 / Fragment: HEME BINDING DOMAIN, RESIDUES 1-104
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOS TAURUS (cattle) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00171
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
Compound detailsCYTOCHROME B5 IS A MEMBRANE BOUND HEMOPROTEIN WHICH FUNCTIONS AS AN ELECTRON CARRIER FOR SEVERAL ...CYTOCHROME B5 IS A MEMBRANE BOUND HEMOPROTEIN WHICH FUNCTIONS AS AN ELECTRON CARRIER FOR SEVERAL MEMBRANE BOUND OXYGENASES.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N-1H HSQC
12115N-1H TOCSY-HSQC
13115N-1H NOESY HSQC
141CBCANH
151CBCA(CO)NH
161(H)CCH-TOCSY
171(HB)CB(CGCD)HD/HE
18113C-EDITED NOESY HSQC
NMR detailsText: THE STRUCTURE WAS DETERMINED FROM A COMBINATION OF TRIPLE RESONANCE NMR EXPERIMENTS ON 13C, 15N LABELED CYTOCHROME B5

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Sample preparation

Sample conditionspH: 7 / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX6001
Varian UNITYVarianUNITY6002
Varian UNITYPLUSVarianUNITYPLUS5003

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Processing

NMR software
NameDeveloperClassification
DYANAGUNTERT,WUTHRICHrefinement
DYANAstructure solution
RefinementSoftware ordinal: 1 / Details: 5 CYCLES OF REDAC PROCEDURE
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 100 / Conformers submitted total number: 42

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