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Yorodumi- PDB-3tgc: Crystal structure of L130R mutant of Nitrophorin 4 from Rhodnius ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3tgc | ||||||
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Title | Crystal structure of L130R mutant of Nitrophorin 4 from Rhodnius prolixus complexed with nitrite at pH 7.4 | ||||||
Components | Nitrophorin-4 | ||||||
Keywords | METAL BINDING PROTEIN / heme / lipocalin / 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: Chem.Biodivers. / Year: 2012 Title: Insertion of an H-Bonding Residue into the Distal Pocket of the Ferriheme Protein Nitrophorin 4: Effect on Nitrite[BOND]Iron Coordination and Nitrite Disproportionation 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 | 3tgc.cif.gz | 90.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tgc.ent.gz | 73.6 KB | Display | PDB format |
PDBx/mmJSON format | 3tgc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3tgc_validation.pdf.gz | 781.3 KB | Display | wwPDB validaton report |
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Full document | 3tgc_full_validation.pdf.gz | 783 KB | Display | |
Data in XML | 3tgc_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | 3tgc_validation.cif.gz | 15.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tg/3tgc ftp://data.pdbj.org/pub/pdb/validation_reports/tg/3tgc | HTTPS FTP |
-Related structure data
Related structure data | |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 20336.699 Da / Num. of mol.: 1 / Mutation: L130R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodnius prolixus (insect) / Production host: Escherichia coli (E. coli) / References: UniProt: Q94734 |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-NO2 / |
#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: 1.93 Å3/Da / Density % sol: 36.35 % |
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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: 0.91841 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Dec 15, 2010 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→30.59 Å / Num. obs: 30602 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.038 |
Reflection shell | Resolution: 1.4→1.44 Å / Rmerge(I) obs: 0.285 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→30.59 Å / SU ML: 0.17 / σ(F): 1.99 / Phase error: 16.24 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.226 Å2 / ksol: 0.455 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.4→30.59 Å
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Refine LS restraints |
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LS refinement shell |
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