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Yorodumi- PDB-1pc8: Crystal Structure of a novel form of mistletoe lectin from Himala... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pc8 | |||||||||
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Title | Crystal Structure of a novel form of mistletoe lectin from Himalayan Viscum album L. at 3.8A resolution | |||||||||
Components | (Himalayan mistletoe ribosome-inactivating ...) x 2 | |||||||||
Keywords | HYDROLASE / Novel form / mistletoe lectin | |||||||||
Function / homology | Function and homology information rRNA N-glycosylase / rRNA N-glycosylase activity / defense response / toxin activity / carbohydrate binding / negative regulation of translation Similarity search - Function | |||||||||
Biological species | Viscum album (European mistletoe) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.8 Å | |||||||||
Authors | Mishra, V. / Ethayathulla, A.S. / Paramasivam, M. / Singh, G. / Yadav, S. / Kaur, P. / Sharma, R.S. / Babu, C.R. / Singh, T.P. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: Structure of a novel ribosome-inactivating protein from a hemi-parasitic plant inhabiting the northwestern Himalayas. Authors: Mishra, V. / Ethayathulla, A.S. / Sharma, R.S. / Yadav, S. / Krauspenhaar, R. / Betzel, C. / Babu, C.R. / Singh, T.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pc8.cif.gz | 113.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pc8.ent.gz | 86.7 KB | Display | PDB format |
PDBx/mmJSON format | 1pc8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pc/1pc8 ftp://data.pdbj.org/pub/pdb/validation_reports/pc/1pc8 | HTTPS FTP |
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-Related structure data
Related structure data | 1ce7S 1mqc 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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Details | The biological Unit is Heterodimer |
-Components
-Himalayan mistletoe ribosome-inactivating ... , 2 types, 2 molecules AB
#1: Protein | Mass: 26566.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Viscum album (European mistletoe) / Strain: Himalayan V.album References: GenBank: 47716663, UniProt: Q6ITZ3*PLUS, rRNA N-glycosylase |
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#2: Protein | Mass: 27633.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Viscum album (European mistletoe) / Strain: Himalayan V.album References: GenBank: 47716663, UniProt: Q6ITZ3*PLUS, rRNA N-glycosylase |
-Sugars , 3 types, 4 molecules
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / | |
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-Non-polymers , 1 types, 13 molecules
#6: 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: 4.91 Å3/Da / Density % sol: 74.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: Ammonium Sulphate, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 290 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 8, 2001 / Details: mirrors |
Radiation | Monochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.8→32.44 Å / Num. all: 11420 / Num. obs: 11420 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Rsym value: 0.179 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 3.8→3.94 Å / Mean I/σ(I) obs: 2.1 / Rsym value: 0.517 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1CE7 Resolution: 3.8→20 Å / Cor.coef. Fo:Fc: 0.886 / Cor.coef. Fo:Fc free: 0.838 / SU B: 39.946 / SU ML: 0.6 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.634 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.322 Å2
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Refine analyze | Luzzati d res low obs: 0.53 Å / Luzzati sigma a obs: 0.5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.8→3.897 Å / Total num. of bins used: 20 /
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