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- PDB-7elv: Structure of legume lectin domain from Methanocaldococcus jannasc... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7elv | ||||||
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Title | Structure of legume lectin domain from Methanocaldococcus jannaschii in apo form | ||||||
![]() | legume lectin | ||||||
![]() | SUGAR BINDING PROTEIN / lectin | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Suguna, K. / Khan, F. | ||||||
![]() | ![]() Title: Crystal structure of an L-type lectin domain from archaea. Authors: Khan, F. / Kaza, S. #1: ![]() Title: Crystal structures of a beta-trefoil lectin from Entamoeba histolytica in monomeric and a novel disulphide bond-mediated dimeric forms. Authors: Khan, F. / Kurre, D. / Suguna, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 61.3 KB | Display | ![]() |
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PDB format | ![]() | 41.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453.2 KB | Display | ![]() |
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Full document | ![]() | 453.9 KB | Display | |
Data in XML | ![]() | 11.6 KB | Display | |
Data in CIF | ![]() | 16.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7exoC ![]() 2bqpS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules E
#1: Protein | Mass: 22661.746 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: DSM 2661 / Gene: MJ1396 Production host: ![]() ![]() References: UniProt: Q58791 |
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-Non-polymers , 5 types, 165 molecules ![](data/chem/img/MPD.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CA / | #5: Chemical | ChemComp-MN / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.4 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 0.1 M sodium acetate, pH 4.6 and 2 M sodium formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 20, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→51.86 Å / Num. obs: 38198 / % possible obs: 100 % / Redundancy: 17.1 % / CC1/2: 0.99 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 1.5→1.539 Å / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1837 / CC1/2: 0.84 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2BQP Resolution: 1.5→51.86 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.092 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: 60.68 Å2 / Biso mean: 17.6 Å2 / Biso min: 9.85 Å2
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Refinement step | Cycle: final / Resolution: 1.5→51.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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