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Yorodumi- PDB-2pq6: Crystal structure of Medicago truncatula UGT85H2- Insights into t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pq6 | ||||||
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Title | Crystal structure of Medicago truncatula UGT85H2- Insights into the structural basis of a multifunctional (Iso) flavonoid glycosyltransferase | ||||||
Components | UDP-glucuronosyl/UDP-glucosyltransferase | ||||||
Keywords | TRANSFERASE / glycosylation / isoflavonoid / uridine diphosphate glycosyltransferase / Structural Genomics | ||||||
Function / homology | Function and homology information quercetin 7-O-glucosyltransferase activity / quercetin 3-O-glucosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases Similarity search - Function | ||||||
Biological species | Medicago truncatula (barrel medic) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Li, L. / Modolo, L.V. / Escamilla-Trevino, L.L. / Wang, X. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Crystal Structure of Medicago truncatula UGT85H2 - Insights into the Structural Basis of a Multifunctional (Iso)flavonoid Glycosyltransferase. Authors: Li, L. / Modolo, L.V. / Escamilla-Trevino, L.L. / Achnine, L. / Dixon, R.A. / Wang, X. | ||||||
History |
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Remark 999 | SEQUENCE Authors state that residue at position 305 is indeed THR. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pq6.cif.gz | 105.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pq6.ent.gz | 79.2 KB | Display | PDB format |
PDBx/mmJSON format | 2pq6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2pq6_validation.pdf.gz | 422.4 KB | Display | wwPDB validaton report |
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Full document | 2pq6_full_validation.pdf.gz | 430.4 KB | Display | |
Data in XML | 2pq6_validation.xml.gz | 20 KB | Display | |
Data in CIF | 2pq6_validation.cif.gz | 29.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pq/2pq6 ftp://data.pdbj.org/pub/pdb/validation_reports/pq/2pq6 | HTTPS FTP |
-Related structure data
Related structure data | 2acvS 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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-Components
#1: Protein | Mass: 54557.543 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Medicago truncatula (barrel medic) / Plasmid: pET28a(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q1RXH4, UniProt: A6XNC5*PLUS |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.9 Details: 20% PEG3350, 0.2M magnesium formate, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 8, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→100 Å / Num. all: 27676 / Num. obs: 27621 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 99.8 % / Biso Wilson estimate: 10.2 Å2 / Rsym value: 0.082 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 99.8 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 2710 / Rsym value: 0.052 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ACV Resolution: 2.1→24.96 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 297161.85 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.6229 Å2 / ksol: 0.335367 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→24.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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