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- PDB-2afa: Crystal Structure of putative NAG isomerase from Salmonella typhi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2afa | ||||||
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Title | Crystal Structure of putative NAG isomerase from Salmonella typhimurium | ||||||
![]() | NAG isomerase | ||||||
![]() | ISOMERASE / NAG isomerase / Dimer-of-Trimers / renin-binding protein / alpha/alpha-fold / T1489 / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | ![]() sulfoquinovose isomerase / N-acylglucosamine 2-epimerase activity / sulfoquinovose isomerase activity / 6-sulfoquinovose(1-) catabolic process to glycerone phosphate and 3-sulfolactaldehyde / N-acetylmannosamine metabolic process / N-acetylglucosamine metabolic process / peptidase inhibitor activity / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kumaran, D. / Swaminathan, S. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
![]() | ![]() Title: Crystal Structure of putative NAG isomerase from Salmonella typhimurium Authors: Kumaran, D. / Swaminathan, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 490.6 KB | Display | ![]() |
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PDB format | ![]() | 421.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 480.8 KB | Display | ![]() |
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Full document | ![]() | 523.2 KB | Display | |
Data in XML | ![]() | 89.7 KB | Display | |
Data in CIF | ![]() | 124.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 49413.785 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43 % |
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, sitting drop / pH: 6 Details: PEG, sodium cacodylate, sodium acetate , pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 273K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 19, 2004 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→50 Å / Num. all: 132272 / Num. obs: 132272 / % possible obs: 100 % / Observed criterion σ(F): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 22.5 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.75 / Num. unique all: 13231 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Details: In all the chains, residue 416 and residues 376 to 379 were not modelled due to lack of electron density.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.3409 Å2 / ksol: 0.334343 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 34 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.15→45.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.28 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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