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Yorodumi- PDB-3ds8: The crystal structure of the gene lin2722 products from Listeria ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ds8 | ||||||
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Title | The crystal structure of the gene lin2722 products from Listeria innocua | ||||||
Components | Lin2722 protein | ||||||
Keywords | structural genomics / unknown function / Unkonwn function / lin2722 / PSI / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics | ||||||
Function / homology | Protein of unknown function DUF915, hydrolase-like / Alpha/beta hydrolase of unknown function (DUF915) / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Lin2722 protein Function and homology information | ||||||
Biological species | Listeria innocua (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Zhang, R. / Wu, R. / Freeman, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crysatl structure of the gene lin2722 products from Listeria innocua Authors: Zhang, R. / Wu, R. / Freeman, L. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ds8.cif.gz | 67.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ds8.ent.gz | 53.4 KB | Display | PDB format |
PDBx/mmJSON format | 3ds8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ds8_validation.pdf.gz | 440.2 KB | Display | wwPDB validaton report |
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Full document | 3ds8_full_validation.pdf.gz | 441.8 KB | Display | |
Data in XML | 3ds8_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | 3ds8_validation.cif.gz | 23.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ds/3ds8 ftp://data.pdbj.org/pub/pdb/validation_reports/ds/3ds8 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | authors state that the protein does not complexate in solution |
-Components
#1: Protein | Mass: 28718.018 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria innocua (bacteria) / Strain: Clip11262 / Gene: lin2722 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q927R6 | ||
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#2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.63 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 10% Glycerol, 20.5% PEK4000, 0.065M tris_Na Citrate, 0.1M NH4 acetate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9796 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 16, 2008 / Details: mirrors |
Radiation | Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→49.94 Å / Num. all: 29987 / Num. obs: 29792 / % possible obs: 99.35 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 17 % / Biso Wilson estimate: 15.02 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 31.68 |
Reflection shell | Resolution: 1.8→1.847 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2270 / % possible all: 95.29 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→49.94 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.532 / SU ML: 0.058 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.106 / ESU R Free: 0.106 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.844 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→49.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 23.4573 Å / Origin y: 2.6299 Å / Origin z: 55.6975 Å
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Refinement TLS group |
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