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- PDB-1jex: SOLUTION STRUCTURE OF A67V MUTANT OF RAT FERRO CYTOCHROME B5 -

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Basic information

Entry
Database: PDB / ID: 1jex
TitleSOLUTION STRUCTURE OF A67V MUTANT OF RAT FERRO CYTOCHROME B5
ComponentsCYTOCHROME B5
KeywordsELECTRON TRANSPORT / CYTOCHROME B5 / SOLUTION STRUCTURES
Function / homology
Function and homology information


Vitamin C (ascorbate) metabolism / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / response to cadmium ion / mitochondrial outer membrane / electron transfer activity / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / enzyme binding / endoplasmic reticulum ...Vitamin C (ascorbate) metabolism / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / response to cadmium ion / mitochondrial outer membrane / electron transfer activity / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / enzyme 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 / Roll / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome b5
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsShahzad, N. / Dangi, B. / Blankman, J.I. / Guiles, R.D.
CitationJournal: To be Published
Title: MUTAGENIC MODULATION OF THE ENTROPY CHANGE ON OXIDATION OF CYTOCHROME B5: AN ANALYSIS OF THE CONTRIBUTION OF CONFORMATIONAL ENTROPY
Authors: SHAHZAD, N. / DANGI, B. / BLANKMAN, J.I. / GUILES, R.D.
History
DepositionJun 19, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details / _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 B5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4582
Polymers10,8421
Non-polymers6161
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with acceptable covalent geometry, structures with the least restraint violations, target function
RepresentativeModel #1fewest violations, lowest energy

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Components

#1: Protein CYTOCHROME B5 /


Mass: 10841.962 Da / Num. of mol.: 1 / Mutation: A67V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: PET3C / Production host: Escherichia coli (E. coli) / References: UniProt: P00173
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121HNHA
1313D 15N-separated NOESY

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Sample preparation

DetailsContents: 2MM F35Y CYTOCHROME B5;1MM PHOSPHATE BUFFER; PURGED WITH NITROGEN GAS AND REDUCED BY ADDING FEW GRAINS OF SODIUM DITHIONATE AND SEALED USING OXY-ACETYLENE TORCH; 0.05 MM TSP AS INTERNAL REFERENCE
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 1 mM / pH: 7.0 / Pressure: ambient / Temperature: 313 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guentert, P.refinement
XwinNMR2.1Brukercollection
Felix97MSIdata analysis
NMRPipe1.8Delaglio, F.processing
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: THE STRUCTURE WAS CALCULATED USING 1177 NOE RESTRAINTS AND 75 DIHEDRAL ANGLE RESTRAINTS; RESIDUES 1-3 AND 89-94 WERE NOT INCLUDED IN THE REFINED MODEL BECAUSE OF A LACK OF RESTRAINTS IN ...Details: THE STRUCTURE WAS CALCULATED USING 1177 NOE RESTRAINTS AND 75 DIHEDRAL ANGLE RESTRAINTS; RESIDUES 1-3 AND 89-94 WERE NOT INCLUDED IN THE REFINED MODEL BECAUSE OF A LACK OF RESTRAINTS IN THESE PRESUMABLY UNSTRUCTURED REGIONS OF THE PROTEIN.
NMR representativeSelection criteria: fewest violations, lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry, structures with the least restraint violations, target function
Conformers calculated total number: 200 / Conformers submitted total number: 20

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