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Yorodumi- PDB-4zrm: Crystal Structure of UDP-Glucose 4-Epimerase (TM0509) from Hypert... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zrm | ||||||
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Title | Crystal Structure of UDP-Glucose 4-Epimerase (TM0509) from Hyperthermophilic Eubacterium Thermotoga maritima | ||||||
Components | UDP-glucose 4-epimerase | ||||||
Keywords | ISOMERASE / Thermotoga maritima / Hyperthermophiles / epimerization | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Choi, J.M. / Lee, D.W. / Lee, S.H. | ||||||
Citation | Journal: Arch.Biochem.Biophys. / Year: 2015 Title: The structural basis of substrate promiscuity in UDP-hexose 4-epimerase from the hyperthermophilic Eubacterium Thermotoga maritima. Authors: Shin, S.M. / Choi, J.M. / di Luccio, E. / Lee, Y.J. / Lee, S.J. / 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 | 4zrm.cif.gz | 143.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zrm.ent.gz | 110.7 KB | Display | PDB format |
PDBx/mmJSON format | 4zrm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zr/4zrm ftp://data.pdbj.org/pub/pdb/validation_reports/zr/4zrm | HTTPS FTP |
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-Related structure data
Related structure data | 4zrnC 2p5yS C: citing same article (ref.) 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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Unit cell |
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-Components
#1: Protein | Mass: 35226.094 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria) Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_0509, THEMA_02130, Tmari_0505 / Plasmid: pET28a(+) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9WYX9, UDP-glucose 4-epimerase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.16 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 8% Tascimate pH 5.0, 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 14, 2013 |
Radiation | Monochromator: Si(111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 60368 / % possible obs: 99 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 29.9 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 13.2 % / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 8.3 / % possible all: 96.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2P5Y Resolution: 1.9→34.972 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 16.59 / 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: 1.9→34.972 Å
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Refine LS restraints |
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LS refinement shell |
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