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Yorodumi- PDB-4ioh: Crystal Structure of the Tll1086 protein from Thermosynechococcus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ioh | ||||||
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Title | Crystal Structure of the Tll1086 protein from Thermosynechococcus elongatus, Northeast Structural Genomics Consortium Target TeR258 | ||||||
Components | Tll1086 protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Protein of unknown function DUF2237 / Protein of unknown function DUF2237 / Uncharacterized protein conserved in bacteria (DUF2237) / Phenylalanyl-tRNA Synthetase; Chain B, domain 1 / 2-Layer Sandwich / Alpha Beta / Tll1086 protein Function and homology information | ||||||
Biological species | Thermosynechococcus elongatus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.53 Å | ||||||
Authors | Vorobiev, S. / Su, M. / Seetharaman, J. / Maglaqui, M. / Xiao, X. / Kohan, E. / Wang, D. / Everett, J.K. / Acton, T.B. / Montelione, G.T. ...Vorobiev, S. / Su, M. / Seetharaman, J. / Maglaqui, M. / Xiao, X. / Kohan, E. / Wang, D. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the Tll1086 protein from Thermosynechococcus elongatus. Authors: Vorobiev, S. / Su, M. / Seetharaman, J. / Maglaqui, M. / Xiao, X. / Kohan, E. / Wang, D. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ioh.cif.gz | 55.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ioh.ent.gz | 44.8 KB | Display | PDB format |
PDBx/mmJSON format | 4ioh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ioh_validation.pdf.gz | 425.2 KB | Display | wwPDB validaton report |
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Full document | 4ioh_full_validation.pdf.gz | 428.8 KB | Display | |
Data in XML | 4ioh_validation.xml.gz | 7.1 KB | Display | |
Data in CIF | 4ioh_validation.cif.gz | 8.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/io/4ioh ftp://data.pdbj.org/pub/pdb/validation_reports/io/4ioh | 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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Components on special symmetry positions |
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Details | dimer,35.35 kD,91.5%, heptamer,109.8 kD,4.5% |
-Components
#1: Protein | Mass: 14908.289 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermosynechococcus elongatus (bacteria) Strain: BP-1 / Gene: tll1086 / Plasmid: TeR258-21.4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q8DJY4 |
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#2: 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: 56.64 % |
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Crystal grow | Temperature: 291 K / Method: microbatch crystallization under oil / pH: 8 Details: 1.11M sodium phosphate, 0.1M Tris-HCl, pH 8.0, Microbatch crystallization under oil, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97923 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 19, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97923 Å / Relative weight: 1 |
Reflection | Resolution: 2.53→50 Å / Num. all: 10991 / Num. obs: 10905 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.6 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 30.5 |
Reflection shell | Resolution: 2.53→2.65 Å / Redundancy: 14.3 % / Rmerge(I) obs: 0.0127 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1422 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.53→33.999 Å / Occupancy max: 1 / Occupancy min: 0.47 / SU ML: 0.69 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.51 / Stereochemistry target values: ML Details: Cys15 makes a disulfide bond with Cys42 form symmetry-related mate (x,x-y,-z+1/6 + (0 0 0))
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Solvent computation | Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 71.871 Å2 / ksol: 0.332 e/Å3 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 155.41 Å2 / Biso mean: 91.813 Å2 / Biso min: 39.61 Å2
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Refinement step | Cycle: LAST / Resolution: 2.53→33.999 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3
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