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Yorodumi- PDB-1u0x: Crystal structure of nitrophorin 4 under pressure of xenon (200 psi) -
+Open data
-Basic information
Entry | Database: PDB / ID: 1u0x | ||||||
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Title | Crystal structure of nitrophorin 4 under pressure of xenon (200 psi) | ||||||
Components | Nitrophorin 4 | ||||||
Keywords | TRANSPORT PROTEIN / beta-barrel / lipocalin / ferric heme / xenon | ||||||
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 / FOURIER SYNTHESIS / Resolution: 1.45 Å | ||||||
Authors | Nienhaus, K. / Maes, E.M. / Weichsel, A. / Montfort, W.R. / Nienhaus, G.U. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Structural dynamics controls nitric oxide affinity in nitrophorin 4 Authors: Nienhaus, K. / Maes, E.M. / Weichsel, A. / Montfort, W.R. / Nienhaus, G.U. #1: Journal: Biochemistry / Year: 2001 Title: Ligand-Induced Heme Ruffling and Bent NO Geometry in Ultra-High-Resolution Structures of Nitrophorin 4 Authors: Roberts, S.A. / Weichsel, A. / Qui, Y. / Shelnutt, J.A. / Walker, F.A. / Montfort, W.R. #2: Journal: Nat.Struct.Biol. / Year: 2000 Title: Nitric Oxide Binding to Nitrophorin 4 Induces Complete Distal Pocket Burial Authors: Weichsel, A. / Andersen, J.F. / Roberts, S.A. / Montfort, W.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1u0x.cif.gz | 63.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1u0x.ent.gz | 44.6 KB | Display | PDB format |
PDBx/mmJSON format | 1u0x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u0/1u0x ftp://data.pdbj.org/pub/pdb/validation_reports/u0/1u0x | HTTPS FTP |
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-Related structure data
Related structure data | 1d2uS 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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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: 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-HEM / | ||
#3: Chemical | ChemComp-NH3 / | ||
#4: Chemical | #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: 1.9 Å3/Da / Density % sol: 34 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: ammonium phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 1, 2001 / Details: osmic mirrors |
Radiation | Monochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→30.3 Å / Num. all: 26873 / Num. obs: 26873 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 11.8 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 26.9 |
Reflection shell | Resolution: 1.45→1.5 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.113 / Mean I/σ(I) obs: 6.8 / Num. unique all: 2149 / % possible all: 78 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1D2U Resolution: 1.45→30 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.012 / SU ML: 0.04 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.073 / 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: 10.001 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.45→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.488 Å / Rfactor Rfree error: 0.073 / Total num. of bins used: 20
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