[English] 日本語
![](img/lk-miru.gif)
- PDB-4okc: Structure, interactions and evolutionary implications of a domain... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4okc | ||||||
---|---|---|---|---|---|---|---|
Title | Structure, interactions and evolutionary implications of a domain-swapped lectin dimer from Mycobacterium smegmatis | ||||||
![]() | LysM domain protein | ||||||
![]() | SUGAR BINDING PROTEIN / Beta-prism II fold / bacterial lectin / protein-carbohydrate interactions / Beta-Prism II / Carbohydrate binding / Carbohydrate/Sugar Binding | ||||||
Function / homology | ![]() Agglutinin, subunit A / Bulb-type lectin domain / Bulb-type lectin domain / Bulb-type lectin domain superfamily / Bulb-type lectin domain profile. / Bulb-type mannose-specific lectin / Orthogonal Prism / Lysin motif / LysM domain superfamily / LysM domain ...Agglutinin, subunit A / Bulb-type lectin domain / Bulb-type lectin domain / Bulb-type lectin domain superfamily / Bulb-type lectin domain profile. / Bulb-type mannose-specific lectin / Orthogonal Prism / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Patra, D. / Mishra, P. / Surolia, A. / Vijayan, M. | ||||||
![]() | ![]() Title: Structure, interactions and evolutionary implications of a domain-swapped lectin dimer from Mycobacterium smegmatis. Authors: Patra, D. / Mishra, P. / Surolia, A. / Vijayan, M. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2011 Title: Cloning, expression, purification, crystallization and preliminary X-ray studies of the mannose-binding lectin domain of MSMEG_3662 from Mycobacterium smegmatis Authors: Patra, D. / Sharma, A. / Chandran, D. / Vijayan, M. #2: Journal: J.Biosci. / Year: 2007 Title: Multiplicity of carbohydrate-binding sites in beta-prism fold lectins: occurrence and possible evolutionary implications Authors: Sharma, A. / Chandran, D. / Singh, D.D. / Vijayan, M. #3: Journal: Proteins / Year: 2013 Title: Identification of mycobacterial lectins from genomic data Authors: Abhinav, K.V. / Sharma, A. / Vijayan, M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 56.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 40.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 446 KB | Display | |
Data in XML | ![]() | 12.8 KB | Display | |
Data in CIF | ![]() | 17.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4oitC ![]() 4oizC ![]() 1xd5S C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 12541.867 Da / Num. of mol.: 2 / Fragment: mannose-binding lectin domain, UNP residues 1-105 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.71 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.2M tri-sodium citrate, 0.1M Na HEPES, 6% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 10, 2011 / Details: mirrors |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→40 Å / Num. obs: 9500 / % possible obs: 94.2 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.25→2.37 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.3 / Num. unique all: 1365 / % possible all: 92.3 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1xd5 Resolution: 2.25→35.36 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.884 / SU B: 8.171 / SU ML: 0.202 / Cross valid method: THROUGHOUT / ESU R: 0.546 / ESU R Free: 0.281 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.519 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→35.36 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.25→2.308 Å / Total num. of bins used: 20
|