+Open data
-Basic information
Entry | Database: PDB / ID: 1ehd | |||||||||
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Title | CRYSTAL STRUCTURE OF URTICA DIOICA AGGLUTININ ISOLECTIN VI | |||||||||
Components | AGGLUTININ ISOLECTIN VI | |||||||||
Keywords | PLANT PROTEIN / Two homologous hevein-like domains | |||||||||
Function / homology | Chitin-binding, type 1, conserved site / Chitin recognition protein / Chitin recognition or binding domain signature. / Chitin-binding type-1 domain profile. / Chitin binding domain / Chitin-binding, type 1 / Endochitinase-like superfamily / chitin binding / Agglutinin isolectin V Function and homology information | |||||||||
Biological species | Urtica dioica (great nettle) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 1.5 Å | |||||||||
Authors | Harata, K. / Muraki, M. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Crystal structures of Urtica dioica agglutinin and its complex with tri-N-acetylchitotriose. Authors: Harata, K. / Muraki, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ehd.cif.gz | 24.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ehd.ent.gz | 18.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ehd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ehd_validation.pdf.gz | 417.8 KB | Display | wwPDB validaton report |
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Full document | 1ehd_full_validation.pdf.gz | 419.8 KB | Display | |
Data in XML | 1ehd_validation.xml.gz | 6.6 KB | Display | |
Data in CIF | 1ehd_validation.cif.gz | 8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eh/1ehd ftp://data.pdbj.org/pub/pdb/validation_reports/eh/1ehd | HTTPS FTP |
-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: 9349.346 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Urtica dioica (great nettle) / References: UniProt: Q9S7B3 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.33 % | ||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: PEG1000, sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 286 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 |
Detector | Type: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: May 7, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→24.5 Å / Num. all: 19125 / Num. obs: 19125 / % possible obs: 89 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.3 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.031 / Net I/σ(I): 7.98 |
Reflection shell | Resolution: 1.4→1.427 Å / Rmerge(I) obs: 0.323 / Num. unique all: 859 / % possible all: 76.1 |
Reflection | *PLUS |
-Processing
Software |
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Refinement | Resolution: 1.5→8 Å / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 1.5→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 8 Å / σ(F): 2 / Rfactor obs: 0.229 | ||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||
Refine LS restraints | *PLUS
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