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Yorodumi- PDB-2je7: Crystal structure of recombinant Dioclea guianensis lectin S131H ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2je7 | ||||||
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Title | Crystal structure of recombinant Dioclea guianensis lectin S131H complexed with 5-bromo-4-chloro-3-indolyl-a-D-mannose | ||||||
Components | LECTIN ALPHA CHAIN | ||||||
Keywords | SUGAR BINDING PROTEIN / CARBOHYDRATE BINDING PROTEIN / CONA-LIKE / METAL-BINDING / LEGUME LECTIN / RECOMBINANT LECTIN / SUGAR-BINDING PROTEIN | ||||||
Function / homology | Function and homology information D-mannose binding / toxin activity / carbohydrate binding / metal ion binding Similarity search - Function | ||||||
Biological species | DIOCLEA GUIANENSIS (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Nagano, C.S. / Sanz, L. / Cavada, B.S. / Calvete, J.J. | ||||||
Citation | Journal: Biochem.J. / Year: 2008 Title: Insights Into the Structural Basis of the Ph- Dependent Dimer-Tetramer Equilibrium Through Crystallographic Analysis of Recombinant Diocleinae Lectins. Authors: Nagano, C.S. / Calvete, J.J. / Barettino, D. / Perez, A. / Cavada, B.S. / Sanz, L. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2je7.cif.gz | 118.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2je7.ent.gz | 91.2 KB | Display | PDB format |
PDBx/mmJSON format | 2je7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2je7_validation.pdf.gz | 776.2 KB | Display | wwPDB validaton report |
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Full document | 2je7_full_validation.pdf.gz | 778 KB | Display | |
Data in XML | 2je7_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | 2je7_validation.cif.gz | 20.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/je/2je7 ftp://data.pdbj.org/pub/pdb/validation_reports/je/2je7 | HTTPS FTP |
-Related structure data
Related structure data | 2jdzC 2je9C 2jecC 1h9wS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 25704.430 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) DIOCLEA GUIANENSIS (plant) / Plasmid: RDGUIAS131H/PET32A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P81637 | ||
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#2: Chemical | ChemComp-MN / | ||
#3: Chemical | ChemComp-CA / | ||
#4: Sugar | ChemComp-XMM / | ||
#5: Water | ChemComp-HOH / | ||
Compound details | ENGINEEREDSequence details | THE AMINOACID SEQUENCE DEDUCED FROM CDNA PRESENTS CONFLICTS WITH THE AMINOACID SEQUENCE DETERMINED ...THE AMINOACID SEQUENCE DEDUCED FROM CDNA PRESENTS CONFLICTS WITH THE AMINOACID SEQUENCE DETERMINED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 51.6 % / Description: NONE |
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Crystal grow | pH: 7 Details: CRYSTALS WERE GROWN WITH 0.6M NACL, 0.1 HEPES, PH 7.0. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9763 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 24, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→44 Å / Num. obs: 31757 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 1.65→1.74 Å / Redundancy: 3 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1H9W Resolution: 1.65→63.5 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.462 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 20.62 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→63.5 Å
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Refine LS restraints |
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