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Yorodumi- PDB-2bv4: 1.0A Structure of Chromobacterium Violaceum Lectin in Complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bv4 | ||||||
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Title | 1.0A Structure of Chromobacterium Violaceum Lectin in Complex with alpha-methyl-mannoside | ||||||
Components | LECTIN CV-IIL | ||||||
Keywords | LECTIN / MANNOSE / CHROMOBACTERIUM VIOLACEUM | ||||||
Function / homology | Function and homology information | ||||||
Biological species | CHROMOBACTERIUM VIOLACEUM (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å | ||||||
Authors | Pokorna, M. / Cioci, G. / Perret, S. / Rebuffet, E. / Adam, J. / Gilboa-Garber, N. / Mitchell, E.P. / Imberty, A. / Wimmerova, M. | ||||||
Citation | Journal: Biochemistry / Year: 2006 Title: Unusual Entropy Driven Affinity of Chromobacterium Violaceum Lectin Cv-Iil Towards Fucose and Mannose Authors: Pokorna, M. / Cioci, G. / Perret, S. / Rebuffet, E. / Kostlanova, N. / Adam, J. / Gilboa-Garber, N. / Mitchell, E.P. / Imberty, A. / Wimmerova, M. | ||||||
History |
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Remark 700 | SHEET DETERMIMATION METHOD: PROVIDED BY DEPOSITOR |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bv4.cif.gz | 120.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bv4.ent.gz | 92.9 KB | Display | PDB format |
PDBx/mmJSON format | 2bv4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2bv4_validation.pdf.gz | 336.2 KB | Display | wwPDB validaton report |
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Full document | 2bv4_full_validation.pdf.gz | 336.1 KB | Display | |
Data in XML | 2bv4_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | 2bv4_validation.cif.gz | 17.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bv/2bv4 ftp://data.pdbj.org/pub/pdb/validation_reports/bv/2bv4 | HTTPS FTP |
-Related structure data
Related structure data | 2boiC 1gztS C: citing same article (ref.) S: Starting model for refinement |
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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: 11848.111 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CHROMOBACTERIUM VIOLACEUM (bacteria) / Plasmid: PET25(B) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TUNER(DE3) / References: UniProt: Q7NX84 #2: Chemical | ChemComp-CA / #3: Sugar | #4: Water | ChemComp-HOH / | |
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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: 2.2 Å3/Da / Density % sol: 44 % Description: MOLREP WAS USED WITH MODEL 1GZT TO FIND THE POSITION OF 4 CA ATOMS IN THE A.U. PHASING WAS PERFORMED BY ACORN STARTING FROM THE POSITION OF THESE CA ATOMS |
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Crystal grow | Details: PEG 8000 10%, 0.1M NACL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 15, 2004 / Details: MIRRORS |
Radiation | Monochromator: DIAMOND AND GE DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1→23.24 Å / Num. obs: 114226 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 7.02 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 6.48 |
Reflection shell | Resolution: 1→1.03 Å / Redundancy: 3.04 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.67 / % possible all: 94.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GZT Resolution: 1→46.47 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.464 / SU ML: 0.011 / Cross valid method: THROUGHOUT / ESU R: 0.017 / ESU R Free: 0.018 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 7.02 Å2
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Refinement step | Cycle: LAST / Resolution: 1→46.47 Å
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Refine LS restraints |
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