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Yorodumi- PDB-5h1w: Crystal Structure of Hyperthermophilic Thermotoga maritima L-Keto... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5h1w | |||||||||
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Title | Crystal Structure of Hyperthermophilic Thermotoga maritima L-Ketose-3-Epimerase with Mn2+ and L(+)-Erythrulose | |||||||||
Components | Uncharacterized protein TM_0416 | |||||||||
Keywords | ISOMERASE / epimerase / Mn2+ / hyperthermophilic / eubacterium / Erythrulose | |||||||||
Function / homology | Function and homology information Isomerases; Intramolecular oxidoreductases; Interconverting aldoses and ketoses, and related compounds / Isomerases; Racemases and epimerases; Acting on carbohydrates and derivatives / inositol metabolic process / isomerase activity / carbohydrate metabolic process / metal ion binding Similarity search - Function | |||||||||
Biological species | Thermotoga maritima MSB8 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.631 Å | |||||||||
Authors | Cao, T.P. / Shin, S.M. / Lee, D.W. / Lee, S.H. | |||||||||
Funding support | Korea, Republic Of, 2items
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Citation | Journal: Appl. Environ. Microbiol. / Year: 2017 Title: TM0416, a Hyperthermophilic Promiscuous Nonphosphorylated Sugar Isomerase, Catalyzes Various C5and C6Epimerization Reactions Authors: Shin, S.M. / Cao, T.P. / Choi, J.M. / Kim, S.B. / Lee, S.J. / Lee, S.H. / Lee, D.W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5h1w.cif.gz | 136.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5h1w.ent.gz | 103.9 KB | Display | PDB format |
PDBx/mmJSON format | 5h1w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h1/5h1w ftp://data.pdbj.org/pub/pdb/validation_reports/h1/5h1w | HTTPS FTP |
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-Related structure data
Related structure data | 5b7yC 5b7zC 5b80C 5h6hC 5jtx 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 32677.482 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Strain: MSB8 / Gene: TM_0416 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9WYP7 #2: Sugar | #3: Chemical | #4: Chemical | #5: 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: 2.32 Å3/Da / Density % sol: 47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 100 mM MES, 5%(w/w) PEG1000, 20%(v/v) PEG200 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 10, 2016 |
Radiation | Monochromator: DCM Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97933 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 70454 / % possible obs: 95.6 % / Redundancy: 3.9 % / Net I/σ(I): 37.01 |
Reflection shell | Resolution: 1.63→1.66 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 7.46 / % possible all: 74.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5JTX 5jtx Resolution: 1.631→24.51 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 17.68 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.631→24.51 Å
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Refine LS restraints |
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LS refinement shell |
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