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Yorodumi- PDB-1tua: 1.5 A Crystal Structure of a Protein of Unknown Function APE0754 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tua | ||||||
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Title | 1.5 A Crystal Structure of a Protein of Unknown Function APE0754 from Aeropyrum pernix | ||||||
Components | Hypothetical protein APE0754Hypothesis | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / protein structure initiative / MCSG / Aeropyrum pernix / Four layers alpha-beta sandwich / PSI / Midwest Center for Structural Genomics | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aeropyrum pernix (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å | ||||||
Authors | Zhang, R. / Skarina, T. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: 1.5A crystal structure of a hypothetical protein APE0754 from Aeropyrum pernix Authors: Zhang, R. / Skarina, T. / Savchenko, A. / Edwards, A. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tua.cif.gz | 52.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tua.ent.gz | 37.7 KB | Display | PDB format |
PDBx/mmJSON format | 1tua.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tu/1tua ftp://data.pdbj.org/pub/pdb/validation_reports/tu/1tua | 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 | This protein existed as monomer. The deposited coords. represents the monomer in the asymmtric unit |
-Components
#1: Protein | Mass: 21770.502 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aeropyrum pernix (archaea) / Gene: GI:14600942 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9YE16 |
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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: 2.412 Å3/Da / Density % sol: 47 % |
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Crystal grow | Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9797 Å |
Detector | Type: SBC-2 / Detector: CCD / Date: Jun 21, 2004 / Details: mirrors |
Radiation | Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. all: 63292 / Num. obs: 61520 / % possible obs: 97.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 1.9 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 17.61 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 2.15 / Num. unique all: 6292 / % possible all: 95.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.5→20.88 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 439793.35 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 61.2203 Å2 / ksol: 0.443564 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→20.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.59 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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