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- PDB-1sxy: 1.07 A Crystal Structure of D30N Mutant of Nitrophorin 4 from Rho... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1sxy | ||||||
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Title | 1.07 A Crystal Structure of D30N Mutant of Nitrophorin 4 from Rhodnius Prolixus | ||||||
![]() | Nitrophorin 4 | ||||||
![]() | TRANSPORT PROTEIN / lipocalin / beta barrel / ferric heme | ||||||
Function / homology | ![]() nitrite dismutase / histamine binding / nitric oxide binding / vasodilation / oxidoreductase activity / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Maes, E.M. / Weichsel, A. / Andersen, J.F. / Shepley, D. / Montfort, W.R. | ||||||
![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 99.7 KB | Display | ![]() |
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PDB format | ![]() | 74.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 799.6 KB | Display | ![]() |
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Full document | ![]() | 803 KB | Display | |
Data in XML | ![]() | 12.3 KB | Display | |
Data in CIF | ![]() | 18.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1sxuC ![]() 1sxwC ![]() 1sxxC ![]() 1sy0C ![]() 1sy1C ![]() 1sy2C ![]() 1sy3C ![]() 1d2uS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 20291.678 Da / Num. of mol.: 1 / Mutation: D30N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-NH4 / |
#3: Chemical | ChemComp-HEM / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 37.03 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Ammonium Phosphate 3.2 M, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 20, 2002 / Details: Bent cylindrical Si-mirror (Rh coating) |
Radiation | Monochromator: Si (111) double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.07→19.83 Å / Num. all: 67346 / Num. obs: 67346 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.37 % / Biso Wilson estimate: 5.48 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 24.2 |
Reflection shell | Resolution: 1.07→1.11 Å / Redundancy: 5.22 % / Rmerge(I) obs: 0.201 / Mean I/σ(I) obs: 9.1 / Num. unique all: 6648 / Rsym value: 0.201 / % possible all: 96.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1D2U Resolution: 1.07→19.8 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / SU B: 0.338 / SU ML: 0.018 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.032 / ESU R Free: 0.032 / 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: 8.156 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.07→19.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.07→1.098 Å / Total num. of bins used: 20
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