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Yorodumi- PDB-2zq5: Crystal structure of sulfotransferase STF1 from Mycobacterium tub... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zq5 | ||||||
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Title | Crystal structure of sulfotransferase STF1 from Mycobacterium tuberculosis H37Rv (type1 form) | ||||||
Components | Putative uncharacterized protein | ||||||
Keywords | TRANSFERASE / sulfotransferase fold | ||||||
Function / homology | P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Uncharacterized protein Function and homology information | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2 Å | ||||||
Authors | Tanaka, S. / Kimura, M. / Kakuta, Y. | ||||||
Citation | Journal: To be Published Title: Crystal structure of sulfotransferase STF1 from Mycobacterium tuberculosis H37Rv Authors: Tanaka, S. / Kimura, M. / Kakuta, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zq5.cif.gz | 101.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zq5.ent.gz | 75.2 KB | Display | PDB format |
PDBx/mmJSON format | 2zq5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zq/2zq5 ftp://data.pdbj.org/pub/pdb/validation_reports/zq/2zq5 | HTTPS FTP |
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-Related structure data
Related structure data | 2zq6 |
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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: 43388.711 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: MT3632, Rv3529c / Plasmid: pGEX4T3 / Production host: Escherichia coli (E. coli) / References: UniProt: P71872 |
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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: 2.08 Å3/Da / Density % sol: 40.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.1 Details: 20% PEG 3350, 0.1M bis-tris pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. all: 56164 / Num. obs: 56164 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 5.8 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 26.1 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.125 / Mean I/σ(I) obs: 10 / Num. unique all: 5474 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2→46.08 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 481773.12 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.1825 Å2 / ksol: 0.365925 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→46.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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