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Yorodumi- PDB-2bn4: A second FMN-binding site in yeast NADPH-cytochrome P450 reductas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bn4 | ||||||
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Title | A second FMN-binding site in yeast NADPH-cytochrome P450 reductase suggests a novel mechanism of electron transfer by diflavin reductase | ||||||
Components | NADPH CYTOCHROME P450 REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / DIFLAVIN REDUCTASE / CPR / ELECTRON TRANSFER / FMN-BINDING / FAD / FLAVOPROTEIN / NADPH / OXIDOREDUCTASE. | ||||||
Function / homology | Function and homology information Nitric oxide stimulates guanylate cyclase / Ion homeostasis / Peroxisomal protein import / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Extra-nuclear estrogen signaling / VEGFR2 mediated vascular permeability / ROS and RNS production in phagocytes / ergosterol biosynthetic process / NADPH dehydrogenase activity ...Nitric oxide stimulates guanylate cyclase / Ion homeostasis / Peroxisomal protein import / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Extra-nuclear estrogen signaling / VEGFR2 mediated vascular permeability / ROS and RNS production in phagocytes / ergosterol biosynthetic process / NADPH dehydrogenase activity / NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / FMN binding / NADP binding / flavin adenine dinucleotide binding / mitochondrial outer membrane / electron transfer activity / endoplasmic reticulum membrane / mitochondrion / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å | ||||||
Authors | Podust, L.M. / Lepesheva, G.I. / Kim, Y. / Yermalitskaya, L.V. / Yermalitsky, V.N. / Lamb, D.C. / Kelly, S.L. / Waterman, M.R. | ||||||
Citation | Journal: Structure / Year: 2006 Title: A Second Fmn-Binding Site in Yeast Nadph-Cytochrome P450 Reductase Suggests a Mechanism of Electron Transfer by Diflavin Reductases. Authors: Lamb, D.C. / Kim, Y. / Yermalitskaya, L.V. / Yermalitsky, V.N. / Lepesheva, G.I. / Kelly, S.L. / Waterman, M.R. / Podust, L.M. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bn4.cif.gz | 268.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bn4.ent.gz | 213.9 KB | Display | PDB format |
PDBx/mmJSON format | 2bn4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2bn4_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 2bn4_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 2bn4_validation.xml.gz | 58.1 KB | Display | |
Data in CIF | 2bn4_validation.cif.gz | 77.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bn/2bn4 ftp://data.pdbj.org/pub/pdb/validation_reports/bn/2bn4 | HTTPS FTP |
-Related structure data
Related structure data | 2bf4SC 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.059, -0.99816, 0.01411), Vector: |
-Components
#1: Protein | Mass: 75843.047 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HMS174(DE3) / References: UniProt: P16603, NADPH-hemoprotein reductase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Compound details | FUNCTION: TRANSFER OF TWO REDUCING EQUIVALENTS IN A FORM OF THE HYDRIDE ION FROM NADPH VIA FAD AND ...FUNCTION: TRANSFER OF TWO REDUCING EQUIVALENT | Sequence details | RESIDUES NUMBERING IN THE ENTRY BEGINS FROM THE START METHIONINE 33 N-TERMINUS RESIDUES ARE ...RESIDUES NUMBERING IN THE ENTRY BEGINS FROM THE START METHIONINE | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 51 % |
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Crystal grow | Temperature: 293 K / pH: 5 Details: 1.6 M AMMONIUM SULFATE 100 MM SODIUM CITRATE (PH 5.0) 1 MM FAD 1 MM NADPH T=20 C |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 / Wavelength: 0.97918 Å |
Detector | Type: SBC-2 / Detector: CCD / Date: Mar 10, 2004 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL (SI111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 33851 / % possible obs: 94.4 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 24.8 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2 / % possible all: 75.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BF4 Resolution: 2.91→43.41 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 281615.6 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 Stereochemistry target values: MAXIMUM LIKELIHOOD TARGET USING AMPLITUDES
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 34.5167 Å2 / ksol: 0.325633 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 66.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.91→43.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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Xplor file |
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