+Open data
-Basic information
Entry | Database: PDB / ID: 1zgr | ||||||
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Title | Crystal structure of the Parkia platycephala seed lectin | ||||||
Components | Mannose/glucose-specific lectin | ||||||
Keywords | SUGAR BINDING PROTEIN / beta-prism / lectin | ||||||
Function / homology | Function and homology information glucose binding / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / mannose binding Similarity search - Function | ||||||
Biological species | Parkia platycephala (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Gallego del Sol, F. / Cavada, B.S. / Calvete, J.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: The first crystal structure of a mimosoideae lectin reveals a novel quaternary arrangement of a widespread domain. Authors: Gallego Del Sol, F. / Nagano, C. / Cavada, B.S. / Calvete, J.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zgr.cif.gz | 177.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zgr.ent.gz | 142 KB | Display | PDB format |
PDBx/mmJSON format | 1zgr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zg/1zgr ftp://data.pdbj.org/pub/pdb/validation_reports/zg/1zgr | HTTPS FTP |
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-Related 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: 47566.824 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Parkia platycephala (plant) / Tissue: seedsSeed / References: UniProt: P83304 #2: 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: 2.3 Å3/Da / Density % sol: 46.5 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 4000, isopropanol, hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.93 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 16, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 2→104 Å / Num. obs: 31543 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Rmerge(I) obs: 0.059 / Rsym value: 0.055 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 2.002→2.11 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.101 / Mean I/σ(I) obs: 4.4 / Num. unique all: 2060 / Rsym value: 0.101 / % possible all: 65.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.913 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.775 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 32.576 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 20
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