[English] 日本語
![](img/lk-miru.gif)
- PDB-6z2o: Crystal structure of wild type OgpA from Akkermansia muciniphila ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6z2o | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of wild type OgpA from Akkermansia muciniphila in P 21 21 21 | ||||||
![]() | O-glycan protease | ||||||
![]() | HYDROLASE / O-glycan endopeptidase / mucins / OgpA. metalloprotease | ||||||
Function / homology | metal ion binding / Peptidase M43 pregnancy-associated plasma-A domain-containing protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Trastoy, B. / Naegali, A. / Anso, I. / Sjogren, J. / Guerin, M.E. | ||||||
![]() | ![]() Title: Structural basis of mammalian mucin processing by the human gut O-glycopeptidase OgpA from Akkermansia muciniphila. Authors: Trastoy, B. / Naegeli, A. / Anso, I. / Sjogren, J. / Guerin, M.E. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 93.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 66.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 435.1 KB | Display | |
Data in XML | ![]() | 17 KB | Display | |
Data in CIF | ![]() | 25.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6z2dSC ![]() 6z2pC ![]() 6z2qC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 41856.137 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: Amuc_1119 / Production host: ![]() ![]() | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-ZN / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.7 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 100mM sodium imidazole/MES monohydrate pH 6.5, 100mM carboxylic acids mixture (sodium formate, ammonium acetate, sodium citrate tribasic dihydrate, sodium potassium tartrate tetrahydrate and ...Details: 100mM sodium imidazole/MES monohydrate pH 6.5, 100mM carboxylic acids mixture (sodium formate, ammonium acetate, sodium citrate tribasic dihydrate, sodium potassium tartrate tetrahydrate and sodium oxamate) and 50% (w/v) of precipitant mix based on 25% (w/v) MPD, 25% (w/v) PEG 1000 and 25% (w/v) PEG 3350 (Morpheus protein crystallization screen). |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 16, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1702 Å / Relative weight: 1 |
Reflection | Resolution: 1.649→29.632 Å / Num. obs: 52999 / % possible obs: 99.66 % / Redundancy: 12.6 % / Biso Wilson estimate: 23.23 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.08763 / Rrim(I) all: 0.09136 / Net I/σ(I): 16.95 |
Reflection shell | Resolution: 1.649→1.708 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.5749 / Mean I/σ(I) obs: 3.29 / Num. unique obs: 5089 / CC1/2: 0.1835 / CC star: 0.905 / Rrim(I) all: 0.6045 / % possible all: 97.03 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 6Z2D Resolution: 1.649→29.632 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.19 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 73.31 Å2 / Biso mean: 27.9432 Å2 / Biso min: 15.42 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.649→29.632 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|