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Yorodumi- PDB-8d3z: Crystal structure of GalS1 in complex with Manganese from Populus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8d3z | ||||||
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Title | Crystal structure of GalS1 in complex with Manganese from Populus trichocarpas | ||||||
Components | Galactan synthase | ||||||
Keywords | TRANSFERASE / glycosyltransferase galactan synthase | ||||||
Function / homology | Glycosyltransferase family 92 / Glycosyltransferase family 92 / Transferases; Glycosyltransferases; Hexosyltransferases / glycosyltransferase activity / membrane / : / Glycosyltransferase family 92 protein Function and homology information | ||||||
Biological species | Populus trichocarpa (black cottonwood) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å | ||||||
Authors | Pereira, J.H. / Prabhakar, P.K. / Urbanowicz, B.R. / Adams, P.D. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat.Plants / Year: 2023 Title: Structural and biochemical insight into a modular beta-1,4-galactan synthase in plants. Authors: Prabhakar, P.K. / Pereira, J.H. / Taujale, R. / Shao, W. / Bharadwaj, V.S. / Chapla, D. / Yang, J.Y. / Bomble, Y.J. / Moremen, K.W. / Kannan, N. / Hammel, M. / Adams, P.D. / Scheller, H.V. / Urbanowicz, B.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8d3z.cif.gz | 369.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8d3z.ent.gz | 293.1 KB | Display | PDB format |
PDBx/mmJSON format | 8d3z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d3/8d3z ftp://data.pdbj.org/pub/pdb/validation_reports/d3/8d3z | HTTPS FTP |
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-Related structure data
Related structure data | 8d3tSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 48845.289 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Populus trichocarpa (black cottonwood) / Production host: Escherichia coli (E. coli) References: UniProt: A0A2K2AMS7, Transferases; Glycosyltransferases; Hexosyltransferases |
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-Sugars , 3 types, 12 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / |
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-Non-polymers , 2 types, 39 molecules
#4: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 3.16 Å3/Da / Density % sol: 61.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M sodium citrate tribasic dihydrate pH 5.0 10 % PEG 6,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 24, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.56→49.07 Å / Num. obs: 79592 / % possible obs: 99.9 % / Redundancy: 2 % / Biso Wilson estimate: 68.99 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.018 / Net I/σ(I): 20.3 |
Reflection shell | Resolution: 2.56→2.65 Å / Rmerge(I) obs: 0.35 / Num. unique obs: 7908 / CC1/2: 0.755 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 8D3T Resolution: 2.56→49.07 Å / SU ML: 0.4108 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.2787 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 107.46 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.56→49.07 Å
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Refine LS restraints |
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LS refinement shell |
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