+Open data
-Basic information
Entry | Database: PDB / ID: 1i7p | ||||||
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Title | CRYSTAL STRUCTURE OF RAT B5R IN COMPLEX WITH FAD | ||||||
Components | NADH-CYTOCHROME B5 REDUCTASE | ||||||
Keywords | OXYGEN STORAGE/TRANSPORT / ELECTRON TRANSPORT / HEMOGLOBINEMIA / ERYTHROCYTE FUNCTION / FAD-BINDING / NADH-BINDING / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
Function / homology | Function and homology information Phase I - Functionalization of compounds / nitric-oxide synthase complex / Vitamin C (ascorbate) metabolism / cytochrome-b5 reductase / cytochrome-b5 reductase activity, acting on NAD(P)H / nitrite reductase (NO-forming) activity / Neutrophil degranulation / AMP binding / cholesterol biosynthetic process / nitric oxide biosynthetic process ...Phase I - Functionalization of compounds / nitric-oxide synthase complex / Vitamin C (ascorbate) metabolism / cytochrome-b5 reductase / cytochrome-b5 reductase activity, acting on NAD(P)H / nitrite reductase (NO-forming) activity / Neutrophil degranulation / AMP binding / cholesterol biosynthetic process / nitric oxide biosynthetic process / FAD binding / lipid droplet / mitochondrial membrane / ADP binding / NAD binding / flavin adenine dinucleotide binding / mitochondrial outer membrane / endoplasmic reticulum membrane / mitochondrion Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Bewley, M.C. / Marohnic, C.C. / Barber, M.J. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: The structure and biochemistry of NADH-dependent cytochrome b5 reductase are now consistent. Authors: Bewley, M.C. / Marohnic, C.C. / Barber, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i7p.cif.gz | 73 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i7p.ent.gz | 52.4 KB | Display | PDB format |
PDBx/mmJSON format | 1i7p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1i7p_validation.pdf.gz | 461.5 KB | Display | wwPDB validaton report |
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Full document | 1i7p_full_validation.pdf.gz | 468.3 KB | Display | |
Data in XML | 1i7p_validation.xml.gz | 8.5 KB | Display | |
Data in CIF | 1i7p_validation.cif.gz | 12.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i7/1i7p ftp://data.pdbj.org/pub/pdb/validation_reports/i7/1i7p | HTTPS FTP |
-Related structure data
Related structure data | 1ib0C 1ndhS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31315.178 Da / Num. of mol.: 1 / Fragment: SOLUBLE DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: DIA1 / Plasmid: PET 23B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P20070, cytochrome-b5 reductase |
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#2: Chemical | ChemComp-FAD / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 59.43 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG 6000, MPD, SODIUM HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 99 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1 Å |
Detector | Type: BRANDEIS - B4 / Detector: CCD / Date: Oct 11, 2000 / Details: MONOCHROMATOR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→40 Å / Num. all: 26333 / Num. obs: 26290 / % possible obs: 99.8 % / Observed criterion σ(F): 3.2 / Observed criterion σ(I): 11.5 / Redundancy: 6.5 % / Biso Wilson estimate: 13.4 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 5 % / Rmerge(I) obs: 0.216 / Num. unique all: 2530 / % possible all: 99.1 |
Reflection | *PLUS Redundancy: 6.2 % |
Reflection shell | *PLUS % possible obs: 99.1 % / Redundancy: 5.3 % / Mean I/σ(I) obs: 3.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PROTEIN ATOMS OF 1NDH Resolution: 2→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 30 Å / σ(F): 0 / Rfactor obs: 0.215 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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