[English] 日本語
![](img/lk-miru.gif)
- PDB-3np1: CRYSTAL STRUCTURE OF THE COMPLEX OF NITROPHORIN 1 FROM RHODNIUS P... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3np1 | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF THE COMPLEX OF NITROPHORIN 1 FROM RHODNIUS PROLIXUS WITH CYANIDE | ||||||
![]() | NITROPHORIN 1![]() | ||||||
![]() | NITRIC OXIDE TRANSPORT / FERRIC HEME / ![]() ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Weichsel, A. / Andersen, J.F. / Champagne, D.E. / Walker, F.A. / Montfort, W.R. | ||||||
![]() | ![]() Title: Crystal structures of a nitric oxide transport protein from a blood-sucking insect. Authors: Weichsel, A. / Andersen, J.F. / Champagne, D.E. / Walker, F.A. / Montfort, W.R. #1: ![]() Title: Nitric Oxide Binding and Crystallization of Recombinant Nitrophorin I, a Nitric Oxide Transport Protein from the Blood-Sucking Bug Rhodnius Prolixus Authors: Andersen, J.F. / Champagne, D.E. / Weichsel, A. / Ribeiro, J.M. / Balfour, C.A. / Dress, V. / Montfort, W.R. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 84.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 68.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 1np1SC ![]() 2np1C S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.697379, -0.038635, -0.715661), Vector ![]() |
-
Components
#1: Protein | ![]() Mass: 20510.867 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ![]() #3: Chemical | ![]() #4: Chemical | ![]() #5: Water | ChemComp-HOH / | ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48 % | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow![]() | pH: 7.5 Details: 2.8 M AMMONIUM PHOSPHATE, 0.1 M TRIS.HCL, PH 7.5, ROOM TEMPERATURE | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: Andersen, J.F., (1997) Biochemistry, 36, 4423. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Oct 17, 1997 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.3→28 Å / Num. obs: 16620 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 25 Å2 / Rsym value: 0.056 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.22 / % possible all: 97.2 |
Reflection | *PLUS Num. measured all: 46715 / Rmerge(I) obs: 0.053 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() Starting model: PDB ENTRY 1NP1 Resolution: 2.3→15 Å / Rfactor Rfree error: 0.013 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT CORRECTION WITH K = 0.3435, B = 94.9.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati sigma a obs: 0.42 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→15 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | NCS model details: UNRESTRAINED | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.4 Å / Rfactor Rfree error: 0.081 / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|