[English] 日本語
![](img/lk-miru.gif)
- PDB-3c77: 1.08 A crystal structure of nitrophorin 4 from Rhodnius prolixus ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3c77 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | 1.08 A crystal structure of nitrophorin 4 from Rhodnius prolixus containing FE(III) deuteroporphyrin ix complexed with ammonia at ph 7.5 | |||||||||
![]() | Nitrophorin-4 | |||||||||
![]() | TRANSPORT PROTEIN / LIPOCALN / BETA BARREL / FERRIC / HEME ANALOG / FE(III) DEUTEROPORPHYRIN IX / Iron / Metal-binding / Secreted / Vasoactive / Vasodilator | |||||||||
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. / Montfort, W.R. | |||||||||
![]() | ![]() Title: Heme Distortion in Nitrophorin 4: High Resolution Structures of Mutated Positions L123V and L133V and Heme Altered Proteins Authors: Amoia, A.M. / Montfort, W.R. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 110.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 85.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 13.4 KB | Display | |
Data in CIF | ![]() | 20.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3c76C ![]() 3c78C ![]() 1x8pS 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: 20292.664 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#2: Chemical | ChemComp-NH3 / |
#3: Chemical | ChemComp-FDE / |
#4: Water | ChemComp-HOH / |
Nonpolymer details | FE(III) DEUTEROPORPHYRIN IX IS DISORDERED BY A ROTATION OF 180 DEGREES AROUND THE CHA-FE-CHC AXIS ...FE(III) DEUTEROPOR |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.64 Å3/Da / Density % sol: 24.3 % |
---|---|
Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: AMMONIUM PHOSPHATE, pH 7.50, temperature 300.0K, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 31, 2003 / Details: BENT CONICAL SI-MIRROR (RH COATING) |
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: 1.07→21.8 Å / Num. obs: 65307 / % possible obs: 94.9 % / Observed criterion σ(I): 0 / Redundancy: 6.68 % / Biso Wilson estimate: 11.7 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 1.07→1.11 Å / Redundancy: 6.06 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 3.6 / Rsym value: 0.18 / % possible all: 91 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1X8P Resolution: 1.08→21.8 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.968 / SU B: 0.765 / SU ML: 0.018 / Cross valid method: FREE R / σ(F): 0 / ESU R: 0.033 / ESU R Free: 0.033 / Stereochemistry target values: ENGH & HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R. 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: 9.59 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.08→21.8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.08→1.11 Å / Total num. of bins used: 20
|