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Yorodumi- PDB-3mvf: Crystal Structure of Nitrophorin 4 from Rhodnius prolixus Complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mvf | ||||||
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Title | Crystal Structure of Nitrophorin 4 from Rhodnius prolixus Complexed with Nitrite at pH 7.4 | ||||||
Components | Nitrophorin-4 | ||||||
Keywords | TRANSPORT PROTEIN / heme / hemoglobin / iron / lipocalin / nitric oxide / nitrite / nitrophorin | ||||||
Function / homology | Function and homology information nitrite dismutase / histamine binding / nitric oxide binding / vasodilation / oxidoreductase activity / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Rhodnius prolixus (insect) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Ogata, H. / He, C. / Knipp, M. | ||||||
Citation | Journal: Biochemistry / Year: 2010 Title: Formation of the complex of nitrite with the ferriheme b beta-barrel proteins nitrophorin 4 and nitrophorin 7. Authors: He, C. / Ogata, H. / Knipp, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mvf.cif.gz | 92.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mvf.ent.gz | 75.6 KB | Display | PDB format |
PDBx/mmJSON format | 3mvf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3mvf_validation.pdf.gz | 789.9 KB | Display | wwPDB validaton report |
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Full document | 3mvf_full_validation.pdf.gz | 792.1 KB | Display | |
Data in XML | 3mvf_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | 3mvf_validation.cif.gz | 17.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mv/3mvf ftp://data.pdbj.org/pub/pdb/validation_reports/mv/3mvf | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 20292.664 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodnius prolixus (insect) / Plasmid: pET17 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q94734 | ||
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#2: Chemical | ChemComp-HEM / | ||
#3: Chemical | #4: 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: 1.94 Å3/Da / Density % sol: 36.75 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: Ammonium phosphate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91892 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 23, 2010 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91892 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→30.53 Å / Num. obs: 30694 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.038 |
Reflection shell | Resolution: 1.4→1.44 Å / Rmerge(I) obs: 0.193 / % possible all: 93.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→15 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.765 / SU ML: 0.033 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.999 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -8.2211 Å / Origin y: -0.3259 Å / Origin z: -13.2321 Å
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