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- PDB-1b5a: RAT FERROCYTOCHROME B5 A CONFORMATION, NMR, 1 STRUCTURE -

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Basic information

Entry
Database: PDB / ID: 1b5a
TitleRAT FERROCYTOCHROME B5 A CONFORMATION, NMR, 1 STRUCTURE
ComponentsFERROCYTOCHROME B5
KeywordsELECTRON TRANSPORT
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 / distance geometry
AuthorsDangi, B. / Sarma, S. / Yan, C. / Banville, D. / Guiles, R.D.
CitationJournal: Biochemistry / Year: 1998
Title: The origin of differences in the physical properties of the equilibrium forms of cytochrome b5 revealed through high-resolution NMR structures and backbone dynamic analyses.
Authors: Dangi, B. / Sarma, S. / Yan, C. / Banville, D.L. / Guiles, R.D.
History
DepositionApr 6, 1998Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Aug 8, 2018Group: Data collection / Experimental preparation / Source and taxonomy
Category: entity_src_gen / pdbx_nmr_details ...entity_src_gen / pdbx_nmr_details / pdbx_nmr_exptl_sample / pdbx_nmr_exptl_sample_conditions / pdbx_nmr_representative / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _entity_src_gen.gene_src_genus / _entity_src_gen.host_org_genus ..._entity_src_gen.gene_src_genus / _entity_src_gen.host_org_genus / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_vector_type / _pdbx_nmr_exptl_sample_conditions.ionic_strength / _pdbx_nmr_exptl_sample_conditions.ionic_strength_units / _pdbx_nmr_exptl_sample_conditions.label / _pdbx_nmr_exptl_sample_conditions.pH_units / _pdbx_nmr_exptl_sample_conditions.pressure / _pdbx_nmr_spectrometer.field_strength / _pdbx_nmr_spectrometer.manufacturer / _pdbx_nmr_spectrometer.model
Revision 1.5Apr 10, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: FERROCYTOCHROME B5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4302
Polymers10,8141
Non-polymers6161
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 200CLOSEST TO THE AVERAGE STRUCTURE, LOW TARGET FUNCTION
RepresentativeModel #1closest to the average structure, low target function

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Components

#1: Protein FERROCYTOCHROME B5


Mass: 10813.908 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: HEME AS PROSTHETIC GROUP, WITH H63 AND H39 AS AXIAL LIGANDS
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: PET3C / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) PLYSS / 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
111NOESY
121DQF-COSY
131TOCSY
141N15 3D NOESY-HMQC
151N15 3D TOCSY-HMQC
1613D (H)CCH-TOCSY
171HNCO
181CBCA(CO)NH
191HSQC
1101HCACO< HNHA
NMR detailsText: THIS STRUCTURE REPRESENTS THE A CONFORMATION OF THE RAT FERROCYTOCHROME B5. IT IS THE STRUCTURE CLOSEST TO THE AVERAGE AS ANALYZED BY X-PLOR. 200 STRUCTURES WERE CALCULATED USING DIANA 2.1 AND ...Text: THIS STRUCTURE REPRESENTS THE A CONFORMATION OF THE RAT FERROCYTOCHROME B5. IT IS THE STRUCTURE CLOSEST TO THE AVERAGE AS ANALYZED BY X-PLOR. 200 STRUCTURES WERE CALCULATED USING DIANA 2.1 AND ONE STRUCTURE WAS CHOSEN TO REPRESENT THE FINAL RESULTS. THE STRUCTURE WAS DETERMINED USING 2D AND 3D EXPERIMENTS INCLUDING DISTANCE AND ANGULAR RESTRAINTS FROM HNHA.

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Sample preparation

DetailsType: solution
Contents: [U-13C; U-15N] Cytochrome b5, 100 mM phosphate buffer, 0.5 mM TSP, pH 7.0, 90% H2O/10% D2O
Details: The sample was reduced by purging with nitrogen prior to addition of sodium dithionite.
Label: sample_1 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
Cytochrome b5[U-13C; U-15N]1
100 mMphosphate buffernatural abundance2
0.5 mMTSPnatural abundance3
Sample conditionsIonic strength: 100 mM / Label: sample_conditions / pH: 7.0 / Pressure: ambient / Temperature: 313 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX6001
Varian UNITYPLUSVarianUNITYPLUS5002

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR software
NameVersionDeveloperClassification
DIANA2.1WUTHRICHrefinement
DIANA2.1WUTHRICHstructure calculation
X-PLORrefinement
X-PLORdata analysis
RefinementMethod: distance geometry / Software ordinal: 1
NMR representativeSelection criteria: closest to the average structure, low target function
NMR ensembleConformer selection criteria: CLOSEST TO THE AVERAGE STRUCTURE, LOW TARGET FUNCTION
Conformers calculated total number: 200 / Conformers submitted total number: 1

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