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Yorodumi- PDB-1sxw: 1.05 A Crystal Structure of D30A Mutant of Nitrophorin 4 from Rho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1sxw | ||||||
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Title | 1.05 A Crystal Structure of D30A Mutant of Nitrophorin 4 from Rhodnius Prolixus Complexed with Nitric Oxide | ||||||
Components | Nitrophorin 4 | ||||||
Keywords | TRANSPORT PROTEIN / lipocalin / beta barrel / ferrous heme / nitric oxide | ||||||
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 / FOURIER SYNTHESIS / Resolution: 1.05 Å | ||||||
Authors | Maes, E.M. / Weichsel, A. / Andersen, J.F. / Shepley, D. / Montfort, W.R. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: Role of binding site loops in controlling nitric oxide release: structure and kinetics of mutant forms of nitrophorin 4 Authors: Maes, E.M. / Weichsel, A. / Andersen, J.F. / Shepley, D. / Montfort, W.R. #1: Journal: Biochemistry / Year: 2001 Title: Ligand-Induced Heme Ruffling and Bent NO Geometry in Ultra-High-Resolution Structures of Nitrophorin 4 | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1sxw.cif.gz | 106.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1sxw.ent.gz | 80.9 KB | Display | PDB format |
PDBx/mmJSON format | 1sxw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sx/1sxw ftp://data.pdbj.org/pub/pdb/validation_reports/sx/1sxw | HTTPS FTP |
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-Related structure data
Related structure data | 1sxuC 1sxxC 1sxyC 1sy0C 1sy1C 1sy2C 1sy3C 1koiS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 20248.654 Da / Num. of mol.: 1 / Mutation: D30A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodnius prolixus (insect) / Organ: salivary gland / Plasmid: pET17b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q94734 |
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#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-HEM / |
#4: Chemical | ChemComp-NO / |
#5: 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: 1.97 Å3/Da / Density % sol: 37.55 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: Ammonium Phosphate 3.2 M, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 3, 2002 / Details: Bent conical Si-mirror (Rh coating) |
Radiation | Monochromator: Bent Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.05→21.9 Å / Num. all: 71942 / Num. obs: 71942 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.98 % / Biso Wilson estimate: 6.84 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 1.05→1.09 Å / Redundancy: 2.15 % / Rmerge(I) obs: 0.259 / Mean I/σ(I) obs: 2.2 / Num. unique all: 7226 / Rsym value: 0.259 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 1KOI Resolution: 1.05→16.24 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.954 / SU B: 0.371 / SU ML: 0.019 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.032 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 8.166 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.05→16.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.05→1.077 Å / Total num. of bins used: 20
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