+Open data
-Basic information
Entry | Database: PDB / ID: 1ufo | ||||||
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Title | Crystal Structure of TT1662 from Thermus thermophilus | ||||||
Components | hypothetical protein TT1662Hypothesis | ||||||
Keywords | HYDROLASE / alpha-beta fold / structural genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / membrane => GO:0016020 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Hydrolase Function and homology information | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å | ||||||
Authors | Murayama, K. / Shirouzu, M. / Terada, T. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Proteins / Year: 2005 Title: Crystal structure of TT1662 from Thermus thermophilus HB8: a member of the alpha/beta hydrolase fold enzymes. Authors: Murayama, K. / Shirouzu, M. / Terada, T. / Kuramitsu, S. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ufo.cif.gz | 318 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ufo.ent.gz | 260.7 KB | Display | PDB format |
PDBx/mmJSON format | 1ufo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uf/1ufo ftp://data.pdbj.org/pub/pdb/validation_reports/uf/1ufo | 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 26256.873 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: P83821 #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: 2.16 Å3/Da / Density % sol: 43.19 % | ||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 24% PEG3350, 0.2M KF, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.9794 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 14, 2002 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 174213 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 16.2 Å2 / Rsym value: 0.072 |
Reflection shell | Resolution: 1.6→1.66 Å / Mean I/σ(I) obs: 6.5 / Rsym value: 0.321 / % possible all: 99.7 |
Reflection | *PLUS Num. measured all: 1336033 / Rmerge(I) obs: 0.072 |
Reflection shell | *PLUS % possible obs: 99.7 % / Rmerge(I) obs: 0.321 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.6→21.99 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 2514544.48 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 82.0509 Å2 / ksol: 0.465362 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→21.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.005 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 50 Å / Rfactor Rfree: 0.207 / Rfactor Rwork: 0.17 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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