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Yorodumi- PDB-4xmd: Crystal structure of nitrophorin 7 from Rhodnius prolixus at pH 7.8 -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xmd | ||||||
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Title | Crystal structure of nitrophorin 7 from Rhodnius prolixus at pH 7.8 | ||||||
Components | Nitrophorin-7 | ||||||
Keywords | TRANSPORT PROTEIN / Heme / NO transpoter / oxidoreductase | ||||||
Function / homology | Function and homology information intracellular nitric oxide homeostasis / vasodilation in another organism / response to histamine / nitrite dismutase / negative regulation of coagulation / histamine binding / nitric oxide binding / platelet aggregation / oxidoreductase activity / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Rhodnius prolixus (insect) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Ogata, H. | ||||||
Citation | Journal: F1000Res / Year: 2015 Title: Structure and dynamics of the membrane attaching nitric oxide transporter nitrophorin 7. Authors: Knipp, M. / Ogata, H. / Soavi, G. / Cerullo, G. / Allegri, A. / Abbruzzetti, S. / Bruno, S. / Viappiani, C. / Bidon-Chanal, A. / Luque, F.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xmd.cif.gz | 100.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xmd.ent.gz | 74.8 KB | Display | PDB format |
PDBx/mmJSON format | 4xmd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xm/4xmd ftp://data.pdbj.org/pub/pdb/validation_reports/xm/4xmd | HTTPS FTP |
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-Related structure data
Related structure data | 4xmcC 4xmeC 4xmfC 4xmgC 4xmhC 3mvfS 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: 20759.660 Da / Num. of mol.: 1 / Fragment: UNP residues 22-205 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodnius prolixus (insect) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6PQK2, nitrite dismutase |
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#2: Chemical | ChemComp-HEM / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.69 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 25%(w/v) PEG 3350, 0.1 M bis-Tris propane pH 7.8, 0.02 M HEPES pH 6.8, 0.25%(w/v) naphthalene-1,3,6-trisulfonic acid trisodium salt hydrate, 0.25%(w/v) 2,6-naphthalenedisulfonic acid ...Details: 25%(w/v) PEG 3350, 0.1 M bis-Tris propane pH 7.8, 0.02 M HEPES pH 6.8, 0.25%(w/v) naphthalene-1,3,6-trisulfonic acid trisodium salt hydrate, 0.25%(w/v) 2,6-naphthalenedisulfonic acid disodium salt, 0.25%(w/v) 4-aminobenzoic acid, 0.25%(w/v) 5-sulfosalicylic acid dehydrate. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jul 28, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→30.42 Å / Num. obs: 23143 / % possible obs: 99.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 1.6→1.64 Å / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 3 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3MVF Resolution: 1.6→30.42 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 21.25 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→30.42 Å
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Refine LS restraints |
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LS refinement shell |
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