+Open data
-Basic information
Entry | Database: PDB / ID: 6jak | ||||||
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Title | OtsA apo structure | ||||||
Components | Trehalose-6-phosphate synthase | ||||||
Keywords | TRANSFERASE / Trehalose-6-phosphate synthase | ||||||
Function / homology | Function and homology information trehalose metabolism in response to cold stress / alpha,alpha-trehalose-phosphate synthase (UDP-forming) / alpha,alpha-trehalose-phosphate synthase (UDP-forming) activity / trehalose biosynthetic process / response to osmotic stress / DNA damage response Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å | ||||||
Authors | Wang, S. / Zhao, Y. / Wang, D. / Liu, J. | ||||||
Funding support | China, 1items
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Citation | Journal: Biochem.J. / Year: 2019 Title: Crystal structures of Magnaporthe oryzae trehalose-6-phosphate synthase (MoTps1) suggest a model for catalytic process of Tps1. Authors: Wang, S. / Zhao, Y. / Yi, L. / Shen, M. / Wang, C. / Zhang, X. / Yang, J. / Peng, Y.L. / Wang, D. / Liu, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jak.cif.gz | 359.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jak.ent.gz | 294.7 KB | Display | PDB format |
PDBx/mmJSON format | 6jak.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ja/6jak ftp://data.pdbj.org/pub/pdb/validation_reports/ja/6jak | HTTPS FTP |
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-Related structure data
Related structure data | 6jbiC 6jbrC 6jbwC 1uquS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 51526.496 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: otsA, NCTC9077_02568 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: A0A376VH75, UniProt: P31677*PLUS, alpha,alpha-trehalose-phosphate synthase (UDP-forming) #2: 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: 2.55 Å3/Da / Density % sol: 51.75 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M Tris pH 8.5, 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 27, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.41→87.42 Å / Num. obs: 75262 / % possible obs: 95.3 % / Redundancy: 7.2 % / CC1/2: 0.993 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.08 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 2.41→2.47 Å / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 7695 / CC1/2: 0.685 / Rpim(I) all: 0.521 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1UQU Resolution: 2.41→29.687 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.64
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.41→29.687 Å
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Refine LS restraints |
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LS refinement shell |
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