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Yorodumi- PDB-2jec: crystal structure of recombinant DiocleA grandiflora lectin mutan... -
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-Basic information
Entry | Database: PDB / ID: 2jec | ||||||
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Title | crystal structure of recombinant DiocleA grandiflora lectin mutant E123A-H131N-K132Q complexed witH 5-bromo-4-chloro-3-indolyl-a-D- mannose | ||||||
Components | LECTIN ALPHA CHAIN | ||||||
Keywords | SUGAR BINDING PROTEIN / CONA-LIKE / METAL-BINDING / LEGUME LECTIN / CARBOHYDRATE BINDING PROTEIN / SUGAR-BINDING PROTEIN | ||||||
Function / homology | Function and homology information D-mannose binding / toxin activity / carbohydrate binding / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | DIOCLEA GRANDIFLORA (mucana) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jec.cif.gz | 209.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jec.ent.gz | 167.9 KB | Display | PDB format |
PDBx/mmJSON format | 2jec.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2jec_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 2jec_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 2jec_validation.xml.gz | 43.6 KB | Display | |
Data in CIF | 2jec_validation.cif.gz | 63.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/je/2jec ftp://data.pdbj.org/pub/pdb/validation_reports/je/2jec | HTTPS FTP |
-Related structure data
Related structure data | 2jdzC 2je7C 2je9SC 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: 25750.516 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) DIOCLEA GRANDIFLORA (mucana) / Plasmid: PET-32A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P08902 #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-MN / #4: Sugar | ChemComp-XMM / #5: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, GLU 123 TO ALA ENGINEERED RESIDUE IN CHAIN A, HIS 131 TO ASN ...ENGINEERED | Sequence details | THE AMINO ACID SEQUENCES WERE OBTAINED FROM THE DEDUCED DNA. THESE SEQUENCES WERE CONFIRMED BY DNA ...THE AMINO ACID SEQUENCES WERE OBTAINED FROM THE DEDUCED DNA. THESE SEQUENCES WERE CONFIRMED BY DNA SEQUENCE OF ALL CLONES. THE INSERTIONS | |
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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: 2.61 Å3/Da / Density % sol: 52.98 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.5 Details: CRYSTALS WERE GROWN BY THE HANGING DROP VAPOUR DIFFUSION METHOD USING 18% PEG 8000, 0.1M CACODYLATE, PH 6.5 AND 0.2M ZINC ACETATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.9796 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 21, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 2→28.9 Å / Num. obs: 73352 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2JE9 Resolution: 2→88.04 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.914 / SU B: 3.521 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.16 / 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: 19.04 Å2
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Refinement step | Cycle: LAST / Resolution: 2→88.04 Å
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Refine LS restraints |
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