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- PDB-3u5r: Crystal structure of a hypothetical protein SMc02350 from Sinorhi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3u5r | ||||||
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Title | Crystal structure of a hypothetical protein SMc02350 from Sinorhizobium meliloti 1021 | ||||||
![]() | uncharacterized protein | ||||||
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Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Agarwal, R. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC) | ||||||
![]() | ![]() Title: Crystal structure of a hypothetical protein SMc02350 from Sinorhizobium meliloti 1021 Authors: Agarwal, R. / Almo, S.C. / 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 | ![]() | 156.4 KB | Display | ![]() |
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PDB format | ![]() | 123.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2ywiS S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 23515.324 Da / Num. of mol.: 4 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: 2.68 Å3/Da / Density % sol: 54.17 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.2M Ammonium acetate, 0.1M tri sodium citrate pH 5.6, 30% PEG 4000, 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: Oct 10, 2011 / Details: mirrors |
Radiation | Monochromator: SI-III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.05→50 Å / Num. all: 59768 / Num. obs: 59768 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 5 / Num. unique all: 5911 / % possible all: 96.5 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: pdb entry 2YWI Resolution: 2.05→34.02 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.925 / SU B: 3.724 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R Free: 0.159 / 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: 26.28 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→34.02 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.053→2.106 Å / Total num. of bins used: 20
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