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Yorodumi- PDB-7exo: Structure of legume lectin domain from Methanocaldococcus jannasc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7exo | ||||||
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Title | Structure of legume lectin domain from Methanocaldococcus jannaschii in mannose bound form | ||||||
Components | Legume lectin | ||||||
Keywords | SUGAR BINDING PROTEIN / legume lectin / lectin / Methanocaldococcus jannaschii | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Methanocaldococcus jannaschii DSM 2661 (archaea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Suguna, K. / Khan, F. | ||||||
Citation | Journal: Proteins / Year: 2023 Title: Crystal structure of an L-type lectin domain from archaea. Authors: Khan, F. / Kaza, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7exo.cif.gz | 64.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7exo.ent.gz | 41.9 KB | Display | PDB format |
PDBx/mmJSON format | 7exo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ex/7exo ftp://data.pdbj.org/pub/pdb/validation_reports/ex/7exo | HTTPS FTP |
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-Related structure data
Related structure data | 7elvC 2bqpS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 22661.746 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii DSM 2661 (archaea) Strain: DSM 2661 / Gene: MJ1396 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q58791 |
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#3: Sugar | ChemComp-BMA / |
-Non-polymers , 6 types, 170 molecules
#2: Chemical | #4: Chemical | ChemComp-ACT / | #5: Chemical | #6: Chemical | ChemComp-CA / | #7: Chemical | ChemComp-MN / | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.14 % 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: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 2, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→51.624 Å / Num. obs: 24083 / % possible obs: 100 % / Redundancy: 7.4 % / CC1/2: 0.99 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.75→1.78 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1299 / CC1/2: 0.743 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2BQP Resolution: 1.75→51.624 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.174 / WRfactor Rwork: 0.153 / SU B: 2.089 / SU ML: 0.065 / Average fsc free: 0.9462 / Average fsc work: 0.9519 / Cross valid method: FREE R-VALUE / ESU R: 0.097 / ESU R Free: 0.092 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.486 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→51.624 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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