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- PDB-2htb: Crystal Structure of a putative mutarotase (YeaD) from Salmonella... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2htb | ||||||
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Title | Crystal Structure of a putative mutarotase (YeaD) from Salmonella typhimurium in monoclinic form | ||||||
![]() | Putative enzyme related to aldose 1-epimerase | ||||||
![]() | ISOMERASE / Salmonella typhimurium / carbohydrate / aldose 1-epimerase / mutarotase / YeaD / GalM / sugar phosphate | ||||||
Function / homology | ![]() glucose-6-phosphate 1-epimerase / glucose-6-phosphate 1-epimerase activity / carbohydrate binding / carbohydrate metabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Chittori, S. / Simanshu, D.K. / Savithri, H.S. / Murthy, M.R.N. | ||||||
![]() | ![]() Title: Structure of the putative mutarotase YeaD from Salmonella typhimurium: structural comparison with galactose mutarotases. Authors: Chittori, S. / Simanshu, D.K. / Savithri, H.S. / Murthy, M.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 239.8 KB | Display | ![]() |
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PDB format | ![]() | 193.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 464.9 KB | Display | ![]() |
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Full document | ![]() | 499.4 KB | Display | |
Data in XML | ![]() | 48.4 KB | Display | |
Data in CIF | ![]() | 67.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2htaSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 34343.867 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q8ZPV9, Isomerases; Racemases and epimerases; Acting on carbohydrates and derivatives #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.19 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 15-25% PEG8K, 0.1M citrate pH 5.5, 0.2-0.5mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 13, 2005 / Details: osmic mirrors |
Radiation | Monochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. obs: 50200 / % possible obs: 0.99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 22.22 % / Biso Wilson estimate: 54.5 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 2.3 / Num. unique all: 4503 / % possible all: 0.919 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: monomer of orthorhombic form of stYeaD (PDB code 2HTA) Resolution: 2.5→27.8 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.921 / SU B: 8.525 / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.479 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.472 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→27.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.499→2.563 Å / Total num. of bins used: 20
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