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Open data
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Basic information
Entry | Database: PDB / ID: 2gtf | ||||||
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Title | Crystal structure of nitrophorin 2 complex with pyrimidine | ||||||
![]() | Nitrophorin-2 | ||||||
![]() | TRANSPORT PROTEIN / beta barrel / lipocalin / ferric heme / pyrimidine | ||||||
Function / homology | ![]() histamine binding / nitric oxide binding / vasodilation / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Weichsel, A. / Montfort, W.R. | ||||||
![]() | ![]() Title: Crystal structures, ligand induced conformational change and heme deformation in complexes of nitrophorin 2, a nitric oxide transport protein from rhodnius prolixus Authors: Weichsel, A. / Berry, R.E. / Walker, F.A. / Montfort, W.R. #1: ![]() Title: The crystal structure of nitrophorin 2. A trifunctional antihemostatic protein from the saliva of Rhodnius prolixus Authors: Andersen, J.F. / 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 | ![]() | 94.9 KB | Display | ![]() |
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PDB format | ![]() | 71.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 802.8 KB | Display | ![]() |
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Full document | ![]() | 806.4 KB | Display | |
Data in XML | ![]() | 11.3 KB | Display | |
Data in CIF | ![]() | 16 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2acpC ![]() 2ah7C ![]() 2al0C ![]() 2allC ![]() 2ammC ![]() 2asnC ![]() 2eu7C ![]() 1peeS 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: 20080.391 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-P1R / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.88 Å3/Da / Density % sol: 34.62 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: sodium citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 11, 2005 / Details: bent Si-mirror |
Radiation | Monochromator: bent Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→23.4 Å / Num. all: 29002 / Num. obs: 29002 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 16 Å2 / Rsym value: 0.08 / Net I/σ(I): 32 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2 / Num. unique all: 4255 / Rsym value: 0.68 / % possible all: 73 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1PEE Resolution: 1.4→23.4 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.53 / SU ML: 0.045 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.09 / ESU R Free: 0.076 / 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: 14.402 Å2
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Refine analyze | Luzzati coordinate error obs: 0.1773 Å / Luzzati sigma a obs: 0.089 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→23.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.437 Å / Total num. of bins used: 20
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