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- PDB-2guw: Crystal structure of AMP Nucleosidase from Salmonella typhimurium LT2 -
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Open data
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Basic information
Entry | Database: PDB / ID: 2guw | ||||||
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Title | Crystal structure of AMP Nucleosidase from Salmonella typhimurium LT2 | ||||||
![]() | AMP nucleosidase | ||||||
![]() | HYDROLASE / AMP Nucleosidase / Molecular Replacement / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | ![]() AMP nucleosidase / AMP nucleosidase activity / nucleoside metabolic process / AMP salvage Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rao, K.N. / Swaminathan, S. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
![]() | ![]() Title: Crystal structure of AMP Nucleosidase from Salmonella typhimurium LT2 Authors: Rao, K.N. / 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 | ![]() | 240.7 KB | Display | ![]() |
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PDB format | ![]() | 193.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451.6 KB | Display | ![]() |
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Full document | ![]() | 502.4 KB | Display | |
Data in XML | ![]() | 46.7 KB | Display | |
Data in CIF | ![]() | 63.3 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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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Details | Trimer in the asymmetric unit but forms an hexamer via crystallographic symmetry |
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Components
#1: Protein | Mass: 54067.812 Da / Num. of mol.: 3 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: 3.12 Å3/Da / Density % sol: 60.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20-30% PEG MME550, 0.05M MgCl2, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 12, 2006 / Details: Mirrors |
Radiation | Monochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.64→50 Å / Num. all: 59111 / Num. obs: 59111 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 52.1 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 2.64→2.73 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.538 / Num. unique all: 5227 / % possible all: 98.4 |
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Processing
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Refinement | Method to determine structure: ![]() Details: The residues listed in remark 465 are missing due to lack of electron density. For the atoms listed in remark 470 the relevant residues were modeled as Alanines since side chain density was ...Details: The residues listed in remark 465 are missing due to lack of electron density. For the atoms listed in remark 470 the relevant residues were modeled as Alanines since side chain density was absent. In general, the B factor seems to be high.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 47.1105 Å2 / ksol: 0.324631 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 76.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.64→45.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.64→2.81 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
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Xplor file |
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