[English] 日本語
![](img/lk-miru.gif)
- PDB-6hdi: R49A variant of beta-phosphoglucomutase from Lactococcus lactis i... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6hdi | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | R49A variant of beta-phosphoglucomutase from Lactococcus lactis in an open conformer to 2.0 A. | |||||||||
![]() | Beta-phosphoglucomutase![]() | |||||||||
![]() | ![]() ![]() | |||||||||
Function / homology | ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Robertson, A.J. / Bisson, C. / Waltho, J.P. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Transition state of phospho-enzyme hydrolysis in beta-phosphoglucomutase. Authors: Robertson, A.J. / Bisson, C. / Waltho, J.P. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 103.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 78.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 6h8uC ![]() 6h8vC ![]() 6h8wC ![]() 6h8xC ![]() 6h8yC ![]() 6h8zC ![]() 6h90C ![]() 6h93C ![]() 6h94C ![]() 6hdfC ![]() 6hdgC ![]() 6hdhC ![]() 6hdjC ![]() 6hdkC ![]() 6hdlC ![]() 6hdmC ![]() 2wheS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | ![]() Mass: 24153.479 Da / Num. of mol.: 2 / Mutation: K125R, Y206H, R49A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: IL1403 / Gene: pgmB, LL0429, L0001 / Production host: ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-EDO / ![]() #4: Water | ChemComp-HOH / | ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.45 % |
---|---|
Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 24-34% PEG 4000 200mM sodium acetate 50mM TRIS pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 27, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.03→52.64 Å / Num. obs: 29676 / % possible obs: 99.6 % / Redundancy: 3.7 % / CC1/2: 0.992 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.077 / Rrim(I) all: 0.153 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2.03→2.07 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.829 / Num. unique obs: 1446 / CC1/2: 0.525 / Rpim(I) all: 0.488 / Rrim(I) all: 0.965 / % possible all: 99.2 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: 2WHE Resolution: 2.03→52.64 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.886 / SU B: 5.888 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.14 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.03→52.64 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|