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Yorodumi- PDB-1i2b: CRYSTAL STRUCTURE OF MUTANT T145A SQD1 PROTEIN COMPLEX WITH NAD A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1i2b | ||||||
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Title | CRYSTAL STRUCTURE OF MUTANT T145A SQD1 PROTEIN COMPLEX WITH NAD AND UDP-SULFOQUINOVOSE/UDP-GLUCOSE | ||||||
Components | SULFOLIPID BIOSYNTHESIS PROTEIN SQD1 | ||||||
Keywords | BIOSYNTHETIC PROTEIN / SDR / short-chain dehydrogenase/reductase / Rossmann fold | ||||||
Function / homology | Function and homology information UDP-sulfoquinovose synthase / UDPsulfoquinovose synthase activity / glycolipid biosynthetic process / sulfotransferase activity / cellular response to phosphate starvation / chloroplast / zinc ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Theisen, M.J. / Sanda, S.L. / Ginell, S.L. / Benning, C. / Garavito, R.M. | ||||||
Citation | Journal: To be Published Title: Characterization of the Active Site of UDP-sulfoquinovose Synthase: Formation of the Sulfonic Acid Product in the Crystalline State Authors: Theisen, M.J. / Sanda, S.L. / Ginell, S.L. / Benning, C. / Garavito, R.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i2b.cif.gz | 106.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i2b.ent.gz | 77.5 KB | Display | PDB format |
PDBx/mmJSON format | 1i2b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i2/1i2b ftp://data.pdbj.org/pub/pdb/validation_reports/i2/1i2b | HTTPS FTP |
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-Related structure data
Related structure data | 1qrrS 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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Unit cell |
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Components on special symmetry positions |
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Details | The solution form is likely a dimer generated by 2-fold rotation of the crystallographic asymmetric unit about the c-axis: -x -y z |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 45479.508 Da / Num. of mol.: 1 / Mutation: T145A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: COLUMBIA (COL-2) / Gene: SQD1 / Plasmid: PSQD1 / Production host: Escherichia coli (E. coli) / References: UniProt: O48917 |
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-Non-polymers , 5 types, 407 molecules
#2: Chemical | #3: Chemical | ChemComp-NAD / | #4: Chemical | ChemComp-UPG / | #5: Chemical | ChemComp-USQ / | #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: 3.5 Å3/Da / Density % sol: 65 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: ammonium sulfate, sodium chloride, MES buffer, NAD+, UDP-glucose, sodium sulfite, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 19, 2000 / Details: Osmic Max-Flux confocal, multilayer mirrors |
Radiation | Monochromator: Osmic Max-Flux confocal, multilayer mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→30 Å / Num. obs: 63698 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 4.96 % / Biso Wilson estimate: 20.04 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.337 / Mean I/σ(I) obs: 2 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QRR Resolution: 1.75→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 62.77 Å2 / ksol: 0.371 e/Å3 | |||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.02 Å2 | |||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.75→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.81 Å / Total num. of bins used: 10
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