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Yorodumi- PDB-1xd5: Crystal structures of novel monomeric monocot mannose-binding lec... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xd5 | ||||||
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Title | Crystal structures of novel monomeric monocot mannose-binding lectins from Gastrodia elata | ||||||
Components | antifungal protein GAFP-1 | ||||||
Keywords | ANTIFUNGAL PROTEIN / monocot mannose binding lectin / monomer / homogeneous beta-sheet | ||||||
Function / homology | Agglutinin, subunit A / Bulb-type lectin domain / Bulb-type lectin domain / Bulb-type lectin domain superfamily / Bulb-type lectin domain profile. / Bulb-type mannose-specific lectin / Orthogonal Prism / Mainly Beta / Antifungal protein Function and homology information | ||||||
Biological species | Gastrodia elata (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Liu, W. / Yang, N. / Wang, M. / Huang, R.H. / Hu, Z. / Wang, D.C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Structural Mechanism Governing the Quaternary Organization of Monocot Mannose-binding Lectin Revealed by the Novel Monomeric Structure of an Orchid Lectin Authors: Liu, W. / Yang, N. / Ding, J. / Huang, R.H. / Hu, Z. / Wang, D.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xd5.cif.gz | 96.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xd5.ent.gz | 79.6 KB | Display | PDB format |
PDBx/mmJSON format | 1xd5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xd/1xd5 ftp://data.pdbj.org/pub/pdb/validation_reports/xd/1xd5 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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5 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 12307.442 Da / Num. of mol.: 4 / Fragment: residues 1-112 / Source method: isolated from a natural source / Source: (natural) Gastrodia elata (plant) / Tissue: corms / References: UniProt: Q9AXZ2 #2: Chemical | #3: 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: 2.35 Å3/Da / Density % sol: 47.15 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: ammonium sulfate, dioxane, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 15, 2002 |
Radiation | Monochromator: Fixed-exit double-crystal monochromator with silicon (111) and germanium (220) crystals Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→24.7 Å / Num. all: 31377 / Num. obs: 31341 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rsym value: 0.097 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 2→2.11 Å / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 2.5 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→24.69 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.088 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.168 / ESU R Free: 0.148 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.265 Å2
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Refinement step | Cycle: LAST / Resolution: 2→24.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20 /
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