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- PDB-1u17: 1.7 A Crystal structure of H60C mutant of Nitrophorin I. Heme com... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1u17 | ||||||
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Title | 1.7 A Crystal structure of H60C mutant of Nitrophorin I. Heme complexed with two molecules imidazole | ||||||
![]() | Nitrophorin 1 | ||||||
![]() | SIGNALING PROTEIN / Lipocalin / beta barrel / heme / imidazole / bis-imidazole heme | ||||||
Function / homology | ![]() histamine binding / nitric oxide binding / vasodilation / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vetter, S.W. / Goodin, D.B. | ||||||
![]() | ![]() Title: 1.7 A Crystal structure of H60C mutant of Nitrophorin I. Heme complexed with two molecules imidazole Authors: Vetter, S.W. / Goodin, D.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 94.7 KB | Display | ![]() |
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PDB format | ![]() | 72.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2np1S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 20607.059 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-IMD / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.44 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M potassium cacodylate pH 5.3, 2.9 M di-ammoium hydrogen phospate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 24, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. obs: 40082 / % possible obs: 99.5 % / Redundancy: 3.9 % / Biso Wilson estimate: 20.3 Å2 / Rsym value: 0.074 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 1.7→1.74 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1 / Rsym value: 0.33 / % possible all: 98.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB Entry 2NP1 Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.028 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 24.646 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20 /
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