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- PDB-5xee: NMR solution structure of the aromatic mutant H43F H67F cytochrome b5 -

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Basic information

Entry
Database: PDB / ID: 5xee
TitleNMR solution structure of the aromatic mutant H43F H67F cytochrome b5
ComponentsCytochrome b5
KeywordsELECTRON TRANSPORT / aromatic interaction
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 / endoplasmic reticulum membrane / heme binding / 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 / endoplasmic reticulum membrane / heme binding / 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 ...: / 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 / simulated annealing
AuthorsBalakrishnan, S. / Sarma, S.P.
CitationJournal: Biochemistry / Year: 2017
Title: Engineering Aromatic-Aromatic Interactions To Nucleate Folding in Intrinsically Disordered Regions of Proteins
Authors: Balakrishnan, S. / Sarma, S.P.
History
DepositionApr 4, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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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)11,2751
Polymers11,2751
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6360 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Cytochrome b5


Mass: 11275.436 Da / Num. of mol.: 1 / Fragment: UNP residues 2-99 / Mutation: H43F, H67F, T77K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Cyb5a, Cyb5 / 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-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N HSQC
122isotropic23D HN(CA)CB
132isotropic23D CBCA(CO)NH
142isotropic23D HNCA
152isotropic13D HNCO
162isotropic23D HN(CO)CA
171isotropic13D 1H-15N NOESY
183isotropic13D 1H-15N NOESY
191isotropic22D 1H-1H NOESY
1102isotropic23D (H)CCH-TOCSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.5 mM [U-99% 15N] FFcytb5, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution20.5 mM [U-13C; U-15N] FFcytb5, 90% H2O/10% D2O13C 15N90% H2O/10% D2O
solution30.5 mM [U-13C; U-15N; U-2H] FFcytb5, 90% H2O/10% D2O13C 15N 2H90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMFFcytb5[U-99% 15N]1
0.5 mMFFcytb5[U-13C; U-15N]2
0.5 mMFFcytb5[U-13C; U-15N; U-2H]3
Sample conditionsDetails: Proline, Arginine and Glutamate were added to sample for stability
Ionic strength: 50 mM / Label: FFcytb5 with PRE / pH: 7 / Pressure: 101325 Pa / Temperature: 283 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE7001
Varian Uniform NMR SystemVarianUniform NMR System6002

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Processing

NMR software
NameDeveloperClassification
CNSBrunger A. T. et.al.refinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
AnalysisCCPNchemical shift assignment
AnalysisCCPNpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 20

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