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Yorodumi- PDB-2bpo: Crystal structure of the yeast CPR triple mutant: D74G, Y75F, K78A. -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bpo | ||||||
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Title | Crystal structure of the yeast CPR triple mutant: D74G, Y75F, K78A. | ||||||
Components | NADPH-CYTOCHROM P450 REDUCTASE | ||||||
Keywords | REDUCTASE / NADPH-CYTOCHROME P450 REDUCTASE / CPR / DIFLAVIN REDUCTASE / FAD / FMN-BINDING / NADP / ELECTRON TRANSFER | ||||||
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 / ergosterol biosynthetic process / ROS and RNS production in phagocytes / 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 / ergosterol biosynthetic process / ROS and RNS production in phagocytes / 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: 2.9 Å | ||||||
Authors | Yermalitskaya, L.V. / Kim, Y. / Waterman, M.R. / Podust, L.M. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the Yeast Cpr Triple Mutant: D74G, Y75F, K78A. Authors: Yermalitskaya, L.V. / Kim, Y. / 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 | 2bpo.cif.gz | 273.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bpo.ent.gz | 218.2 KB | Display | PDB format |
PDBx/mmJSON format | 2bpo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bp/2bpo ftp://data.pdbj.org/pub/pdb/validation_reports/bp/2bpo | HTTPS FTP |
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-Related structure data
Related structure data | 2bf4S S: Starting model for refinement |
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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: (-0.16692, -0.98565, 0.02499), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 75710.906 Da / Num. of mol.: 2 / Mutation: YES 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 |
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-Non-polymers , 5 types, 194 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Compound details | RESIDUE NUMBERS REFER TO THE UNIPROT SEQUENCE, WITH THE PDB NUMBERING GIVEN IN PARENTHESES. ...RESIDUE NUMBERS REFER TO THE UNIPROT SEQUENCE, WITH THE PDB NUMBERING GIVEN IN PARENTHESE |
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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 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56 % |
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Crystal grow | Temperature: 295 K / pH: 5 Details: 1.6 M AMMONIUM SULFATE 100 MM SODIUM CITRATE, PH 5.0 5 MM NICKEL CHLORIDE 1 MM FMN 1 MM FAD 1 MM NADP, T=22 C. |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 17, 2005 Details: SAGITTAL FOCUSING CRYSTAL AND VERTICALLY FOCUSING MIRROR |
Radiation | Monochromator: SI (220) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 37243 / % possible obs: 92.6 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 136.3 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.8 / % possible all: 78 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BF4 Resolution: 2.9→39.18 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 149934.34 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY OMITTED RESIDUES LYS 564, GLY 565, GLY 566, ASN 567 ARE DUE TO LACK OF ELECTRON DENSITY
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.2759 Å2 / ksol: 0.345189 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→39.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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