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- PDB-1i8c: SOLUTION STRUCTURE OF THE WATER-SOLUBLE FRAGMENT OF RAT HEPATIC A... -

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Basic information

Entry
Database: PDB / ID: 1i8c
TitleSOLUTION STRUCTURE OF THE WATER-SOLUBLE FRAGMENT OF RAT HEPATIC APOCYTOCHROME B5
ComponentsCYTOCHROME B5
KeywordsELECTRON TRANSPORT / apo hemoprotein
Function / homology
Function and homology information


Vitamin C (ascorbate) metabolism / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / response to cadmium ion / electron transfer activity / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / enzyme binding / endoplasmic reticulum / metal ion binding / membrane
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
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / distance geometry simulated annealing, molecular dynamics
AuthorsFalzone, C.J. / Wang, Y. / Vu, B.C. / Scott, N.L. / Bhattacharya, S. / Lecomte, J.T.
Citation
Journal: Biochemistry / Year: 2001
Title: Structural and dynamic perturbations induced by heme binding in cytochrome b5.
Authors: Falzone, C.J. / Wang, Y. / Vu, B.C. / Scott, N.L. / Bhattacharya, S. / Lecomte, J.T.
#1: Journal: Biochemistry / Year: 1996
Title: Design Challenges for Hemoproteins: The Solution Structure of Apocytochrome b5
Authors: Falzone, C.J. / Mayer, M.R. / Whiteman, E.L. / Moore, C.D. / Lecomte, J.T.J.
History
DepositionMar 13, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYTOCHROME B5


Theoretical massNumber of molelcules
Total (without water)11,2291
Polymers11,2291
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 100structures with the lowest energy
Representative

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Components

#1: Protein CYTOCHROME B5 / APOCYTOCHROME B5


Mass: 11229.305 Da / Num. of mol.: 1 / Fragment: WATER-SOLUBLE DOMAIN (RESIDUES 1-98)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: PET3D / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00173

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1223D 15N-separated NOESY
1332D-NOESY
1442D-NOESY
NMR detailsText: The amino acid sequence numbering follows the bovine scheme, with the first four residues given negative values. These four residues are disordered and not included in the coordinates.

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM apocytochrome b5, 13C,15N90% H2O/10% D2O
21 mM apocytochrome b5, 15N90% H2O/10% D2O
32 mM apocytochrome b590% H2O/10% D2O
42 mM apocytochrome b5100% D2O
Sample conditionsIonic strength: low / pH: 6.2 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX5001
Bruker AVANCEBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.5Brukercollection
Felix97MSIprocessing
Felix97MSIdata analysis
X-PLOR3.851Brungerstructure solution
X-PLOR3.851Brungerrefinement
RefinementMethod: distance geometry simulated annealing, molecular dynamics
Software ordinal: 1
Details: His 26, 27, 39, 63, and 80 were protonated at the NE2 position in accordance to 15N NMR data. His 15 has a high pK and was protonated at the ND1 and NE2 positions. Additional details are ...Details: His 26, 27, 39, 63, and 80 were protonated at the NE2 position in accordance to 15N NMR data. His 15 has a high pK and was protonated at the ND1 and NE2 positions. Additional details are provided in the primary citation.
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 1

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