+
Open data
-
Basic information
Entry | Database: PDB / ID: 8h81 | ||||||
---|---|---|---|---|---|---|---|
Title | Trans-3/4-proline-hydroxylase H11 with 4-Hydroxyl-proline | ||||||
![]() | Phytanoyl-CoA dioxygenase | ||||||
![]() | STRUCTURAL PROTEIN / L-proline / Trans / Hydroxylase / AKG / HYDROLASE | ||||||
Function / homology | phytanoyl-CoA dioxygenase activity / Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / metal ion binding / 4-HYDROXYPROLINE / Phytanoyl-CoA dioxygenase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gong, W.M. / Hu, X.Y. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Structures of L-proline trans-hydroxylase reveal the catalytic specificity and provide deeper insight into AKG-dependent hydroxylation. Authors: Hu, X. / Huang, X. / Liu, J. / Zheng, P. / Gong, W. / Yang, L. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 130.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 99.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 746.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 750 KB | Display | |
Data in XML | ![]() | 13.6 KB | Display | |
Data in CIF | ![]() | 19 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8h7tC ![]() 8h7vC ![]() 8h7yC ![]() 8h85C ![]() 6lns S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 29867.504 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() |
---|---|
#2: Chemical | ChemComp-HYP / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.43 Å3/Da / Density % sol: 64.13 % |
---|---|
Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.7M Sodium citrate tribasic dihydrate and 0.1M Bis-Tris propane (pH 7.0) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 24, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→75.29 Å / Num. obs: 36880 / % possible obs: 99.9 % / Redundancy: 24.4 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.012 / Rrim(I) all: 0.059 / Χ2: 0.843 / Net I/σ(I): 152.6 |
Reflection shell | Resolution: 1.84→1.87 Å / Redundancy: 25.1 % / Rmerge(I) obs: 0.529 / Mean I/σ(I) obs: 7.8 / Num. unique obs: 1801 / CC1/2: 0.97 / CC star: 0.992 / Rpim(I) all: 0.107 / Rrim(I) all: 0.54 / Χ2: 0.46 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 6LNS ![]() 6lns Resolution: 1.84→24.63 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 4.308 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 130.04 Å2 / Biso mean: 36.834 Å2 / Biso min: 14.9 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.84→24.63 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.84→1.888 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|