[English] 日本語
![](img/lk-miru.gif)
- PDB-4mdy: Crystal structure of periplasmic solute binding protein from Myco... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4mdy | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of periplasmic solute binding protein from Mycobacterium smegmatis str. MC2 155 | ||||||
![]() | Periplasmic binding protein | ||||||
![]() | TRANSPORT PROTEIN / MCSG / STRUCTURAL GENOMICS / PSI-BIOLOGY / MIDWEST CENTER FOR STRUCTURAL GENOMICS / Protein Structure Initiative / ABC transporter system / solute binding protein | ||||||
Function / homology | ![]() ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chang, C. / Wu, R. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
![]() | ![]() Title: Crystal structure of periplasmic solute binding protein from Mycobacterium smegmatis str. MC2 155 Authors: Chang, C. / Wu, R. / Endres, M. / Joachimiak, A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 125.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 102.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 425.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 426.1 KB | Display | |
Data in XML | ![]() | 13.8 KB | Display | |
Data in CIF | ![]() | 19.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 31493.086 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#2: Chemical | ChemComp-PEG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.69 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 0.2M Sodium Citrate, 0.1 M Phosphate-citrate, 20 % PEG 8000, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 16, 2012 |
Radiation | Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97899 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→50 Å / Num. all: 25588 / Num. obs: 24908 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 23.1 |
Reflection shell | Resolution: 1.78→1.81 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.992 / Mean I/σ(I) obs: 1.92 / Num. unique all: 1170 / % possible all: 97.3 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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: 78.07 Å2 / Biso mean: 25.3141 Å2 / Biso min: 11.72 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.78→31.82 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.779→1.825 Å / Total num. of bins used: 20
|