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Open data
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Basic information
Entry | Database: PDB / ID: 4y0n | ||||||
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Title | SAV1875 | ||||||
![]() | Uncharacterized protein SAV1875 | ||||||
![]() | HYDROLASE / DJ-1/PFPI/THIJ FAMILY | ||||||
Function / homology | ![]() Deglycase PfpI / PfpI endopeptidase domain profile. / DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kim, H.J. / Kwon, A.R. / Lee, B.J. | ||||||
![]() | ![]() Title: Structural and functional insight into the different oxidation states of SAV1875 from Staphylococcus aureus Authors: Kim, H.J. / Kwon, A.R. / Lee, B.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 144.1 KB | Display | ![]() |
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PDB format | ![]() | 114.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.5 KB | Display | ![]() |
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Full document | ![]() | 449 KB | Display | |
Data in XML | ![]() | 14.8 KB | Display | |
Data in CIF | ![]() | 19.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4y1eC ![]() 4y1fC ![]() 4y1gC ![]() 4y1rC ![]() 1oi4S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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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: 19755.914 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: Mu50 / Gene: SAV1875 / Plasmid: pET21a / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 29% PEG mme2000, 100mM Bis-Tris |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 27, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.23986 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→40 Å / Num. obs: 19995 / % possible obs: 99.5 % / Redundancy: 6.5 % / Net I/σ(I): 39.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1OI4 Resolution: 2.1→37.78 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.924 / SU B: 10.12 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.244 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.35 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→37.78 Å
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Refine LS restraints |
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