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Yorodumi- PDB-2r9k: Crystal Structure of Misteltoe Lectin I in Complex with Phloretamide -
+Open data
-Basic information
Entry | Database: PDB / ID: 2r9k | ||||||||||||
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Title | Crystal Structure of Misteltoe Lectin I in Complex with Phloretamide | ||||||||||||
Components | (Beta-galactoside-specific lectin ...) x 2 | ||||||||||||
Keywords | HYDROLASE / ML-I / phloretamide / Viscum album / Glycoprotein / Lectin / Plant defense / Protein synthesis inhibitor / Toxin | ||||||||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||||||||
Authors | Meyer, A. / Rypniewski, W. / Celewicz, L. / Erdmann, V.A. / Voelter, W. / Betzel, C. | ||||||||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2007 Title: The mistletoe lectin I--phloretamide structure reveals a new function of plant lectins. Authors: Meyer, A. / Rypniewski, W. / Celewicz, L. / Erdmann, V.A. / Voelter, W. / Singh, T.P. / Genov, N. / Barciszewski, J. / Betzel, C.h. | ||||||||||||
History |
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Remark 999 | The authors stae that the plant proteins can differ in some codons depending on the season and on ...The authors stae that the plant proteins can differ in some codons depending on the season and on the host where the mistletoe has grown. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2r9k.cif.gz | 119.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2r9k.ent.gz | 91 KB | Display | PDB format |
PDBx/mmJSON format | 2r9k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r9/2r9k ftp://data.pdbj.org/pub/pdb/validation_reports/r9/2r9k | HTTPS FTP |
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-Related structure data
Related structure data | 1m2tS 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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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Dom-ID: 1 / Component-ID: 1 / Refine code: 1
NCS ensembles :
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-Components
-Beta-galactoside-specific lectin ... , 2 types, 2 molecules AB
#1: Protein | Mass: 27820.066 Da / Num. of mol.: 1 Fragment: Beta-galactoside-specific lectin 1 chain A isoform 1, UNP residues 34-287 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Viscum album (European mistletoe) / References: UniProt: P81446*PLUS |
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#2: Protein | Mass: 28568.939 Da / Num. of mol.: 1 Fragment: Beta-galactoside-specific lectin 1 chain B, UNP residues 302-564 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Viscum album (European mistletoe) / References: UniProt: P81446 |
-Sugars , 2 types, 5 molecules
#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(4-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
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#4: Sugar | ChemComp-NAG / |
-Non-polymers , 5 types, 82 molecules
#5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-GOL / #7: Chemical | ChemComp-CL / | #8: Chemical | ChemComp-SGI / | #9: 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: 4.58 Å3/Da / Density % sol: 73.16 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 2.5 Details: pH 2.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.81 |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 23, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.81 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→91.29 Å / Num. obs: 30327 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rmerge(I) obs: 0.6 / Rsym value: 0.473 / Net I/σ(I): 3.6 |
Reflection shell | Resolution: 2.7→2.75 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.06 / Mean I/σ(I) obs: 3.6 / Rsym value: 0.47 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1M2T Resolution: 2.7→19.74 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.896 / SU B: 9.263 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R: 0.363 / ESU R Free: 0.278 / 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: 46.964 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→19.74 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION / Rms dev position: 0 Å
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LS refinement shell | Resolution: 2.696→2.765 Å / Total num. of bins used: 20
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