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- PDB-2ofr: 1.00 A Crystal Structure Of V36A/D129A/L130A Mutant of Nitrophori... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ofr | ||||||
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Title | 1.00 A Crystal Structure Of V36A/D129A/L130A Mutant of Nitrophorin 4 From Rhodnius Prolixus Complexed With Nitric Oxide at pH 5.6 | ||||||
![]() | Nitrophorin-4 | ||||||
![]() | TRANSPORT PROTEIN / lipocalin / beta barrel / flexible loop mutant | ||||||
Function / homology | ![]() nitrite dismutase / histamine binding / nitric oxide binding / vasodilation / oxidoreductase activity / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Amoia, A.M. | ||||||
![]() | ![]() Title: Ligand Protection and Nitric Oxide Interactions with Heme in Nitrophorin 4: Kinetic and Structural Analyses of a Loop Mutant Authors: Amoia, A.M. / Montfort, W.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 113 KB | Display | ![]() |
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PDB format | ![]() | 86.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 829 KB | Display | ![]() |
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Full document | ![]() | 833.4 KB | Display | |
Data in XML | ![]() | 12.9 KB | Display | |
Data in CIF | ![]() | 19.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1sxxS 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 20178.520 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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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: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.21 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: ammonium phosphate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 1, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1→52.85 Å / Num. obs: 79668 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 37 |
Reflection shell | Resolution: 1→1.04 Å / Redundancy: 4 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 5.33 / Rsym value: 0.39 / % possible all: 90.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1SXX Resolution: 1→9.47 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.551 / SU ML: 0.014 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.026 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 7.202 Å2
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Refine analyze | Luzzati coordinate error obs: 0.136 Å / Luzzati d res low obs: 4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1→9.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1→1.026 Å / Total num. of bins used: 20
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