[English] 日本語
![](img/lk-miru.gif)
- PDB-5hv4: Crystal Structure of a Prolyl 4-Hydroxylase Complexed with Alpha-... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5hv4 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of a Prolyl 4-Hydroxylase Complexed with Alpha-ketoglutarate from the Pathogenic Bacterium Bacillus anthracis in C2221 | ||||||
![]() | 2OG-Fe(II) oxygenase | ||||||
![]() | OXIDOREDUCTASE / P4H / Dioxygenase / Cupin / Fe(II)/alpha-ketoglutarate | ||||||
Function / homology | ![]() procollagen-proline 4-dioxygenase activity / L-ascorbic acid binding / iron ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Schnicker, N.J. / Dey, M. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Structural analysis of cofactor binding for a prolyl 4-hydroxylase from the pathogenic bacterium Bacillus anthracis. Authors: Schnicker, N.J. / Dey, M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 57.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 39.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 437.2 KB | Display | |
Data in XML | ![]() | 10.4 KB | Display | |
Data in CIF | ![]() | 14.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5hv0C ![]() 3itqS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 24708.592 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: GBAA_4459, AB163_21210, AB164_16730, AB165_11640, AB166_03610, AB167_21505, AB168_05660, AB169_05325, AB170_09560, AB171_10145, AB893_21665, ADK17_22720, ADK18_21540, ADT20_05380, ADT21_14515, BF27_3254 Production host: ![]() ![]() | ||||||||
---|---|---|---|---|---|---|---|---|---|
#2: Chemical | ChemComp-CD / #3: Chemical | ChemComp-AKG / | #4: Chemical | ChemComp-K / #5: Water | ChemComp-HOH / | Sequence details | Authors state that this is a cloning artifact from the restriction site. | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.94 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 0.1 M HEPES pH 7.8, 0.05 M Cadmium sulfate, 0.9 M Sodium acetate tri-hydrate, 0.1 M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: NOIR-1 / Detector: CCD / Date: Mar 2, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→52.372 Å / Num. obs: 10150 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 24.68 Å2 / Rsym value: 0.098 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 2.35→2.48 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 1.9 / % possible all: 99.9 |
-Phasing
Phasing | Method: ![]() |
---|
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3ITQ Resolution: 2.35→52.37 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.57 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→52.37 Å
| |||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||
LS refinement shell |
|