+
Open data
-
Basic information
Entry | Database: PDB / ID: 2amm | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of L122V/L132V mutant of nitrophorin 2 | ||||||
![]() | Nitrophorin 2 | ||||||
![]() | TRANSPORT PROTEIN / beta barrel / lipocalin / ferric heme / double mutant | ||||||
Function / homology | ![]() histamine binding / nitric oxide binding / vasodilation / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Weichsel, A. / Berry, R.E. / Walker, F.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 Authors: Andersen, J.F. / Montfort, W.R. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 55.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 38.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 795.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 796.4 KB | Display | |
Data in XML | ![]() | 11.3 KB | Display | |
Data in CIF | ![]() | 15.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2acpC ![]() 2ah7C ![]() 2al0C ![]() 2allC ![]() 2asnC ![]() 2eu7C ![]() 2gtfC ![]() 1peeS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 20052.336 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#2: Chemical | ChemComp-HEM / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.64 Å3/Da / Density % sol: 24.3 % |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 31, 2003 / Details: bent Si-mirror |
Radiation | Monochromator: diamond (111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1808 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→18 Å / Num. all: 12989 / Num. obs: 12989 / % possible obs: 84 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 18.8 Å2 / Rsym value: 0.036 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 10.6 / Num. unique all: 872 / Rsym value: 0.058 / % possible all: 49 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1PEE Resolution: 1.9→18 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.921 / SU B: 3.233 / SU ML: 0.098 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.188 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.648 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati sigma a obs: 0.171 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→18 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
|