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Yorodumi- PDB-3t8k: The crystal structure of a functionally unknown protein Lebu_0176... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3t8k | ||||||
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Title | The crystal structure of a functionally unknown protein Lebu_0176 from Leptotrichia buccalis C-1013-b | ||||||
Components | uncharacterized protein | ||||||
Keywords | Structural Genomics / Unknown Function / PSI-Biology / protein structure initiative / midwest center f or structural genomics / MCSG / Midwest Center for Structural Genomics / alpha-hairpin repeat (Ankyrin repeat) fold | ||||||
Function / homology | Domain of unknown function DUF3447 / Ankyrin repeat-containing domain / Ankyrin repeat region circular profile. / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha / ANK_REP_REGION domain-containing protein Function and homology information | ||||||
Biological species | Leptotrichia buccalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.769 Å | ||||||
Authors | Tan, K. / Bigelow, L. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure of a functionally unknown protein Lebu_0176 from Leptotrichia buccalis C-1013-b Authors: Tan, K. / Bigelow, L. / Bearden, J. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3t8k.cif.gz | 163.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3t8k.ent.gz | 136.8 KB | Display | PDB format |
PDBx/mmJSON format | 3t8k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t8/3t8k ftp://data.pdbj.org/pub/pdb/validation_reports/t8/3t8k | HTTPS FTP |
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-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 | Experimentally unknown. It is predicted that the A and B chains form a dimer. |
-Components
#1: Protein | Mass: 21771.219 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leptotrichia buccalis (bacteria) / Strain: C-1013-b / Gene: Lebu_0176 / Plasmid: pMCSG48 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) magic / References: UniProt: C7NDE2 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.84 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.3 Details: 0.2M Ammonium Chloride, 20% (w/v) PEG 3350, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 31, 2011 / Details: Mirror |
Radiation | Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.769→34 Å / Num. all: 38999 / Num. obs: 38999 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 39.6 |
Reflection shell | Resolution: 1.78→1.81 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 4.3 / Num. unique all: 1939 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.769→33.962 Å / SU ML: 0.38 / σ(F): 1.37 / Phase error: 21.6 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.463 Å2 / ksol: 0.321 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.769→33.962 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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