+Open data
-Basic information
Entry | Database: PDB / ID: 1b5b | ||||||
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Title | RAT FERROCYTOCHROME B5 B CONFORMATION, NMR, 1 STRUCTURE | ||||||
Components | FERROCYTOCHROME B5 | ||||||
Keywords | ELECTRON 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 / 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 | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | SOLUTION NMR / distance geometry | ||||||
Authors | Dangi, B. / Sarma, S. / Yan, C. / Banville, D. / Guiles, R.D. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b5b.cif.gz | 44.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b5b.ent.gz | 30.2 KB | Display | PDB format |
PDBx/mmJSON format | 1b5b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1b5b_validation.pdf.gz | 452 KB | Display | wwPDB validaton report |
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Full document | 1b5b_full_validation.pdf.gz | 456.7 KB | Display | |
Data in XML | 1b5b_validation.xml.gz | 4.4 KB | Display | |
Data in CIF | 1b5b_validation.cif.gz | 5.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b5/1b5b ftp://data.pdbj.org/pub/pdb/validation_reports/b5/1b5b | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | 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 |
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#2: Chemical | ChemComp-HEM / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | 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 ...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. |
-Sample preparation
Details | Type: 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 | ||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 100 mM / Label: sample_conditions / pH: 7 / Pressure: ambient / Temperature: 313 K | ||||||||||||||||
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer |
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-Processing
Software |
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NMR software |
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Refinement | Method: distance geometry / Software ordinal: 1 | ||||||||||||||||||||
NMR representative | Selection criteria: closest to the average structure, low target function | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: CLOSEST TO THE AVERAGE STRUCTURE, LOW TARGET FUNCTION Conformers calculated total number: 200 / Conformers submitted total number: 1 |