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Yorodumi- PDB-1ixl: Crystal structure of uncharacterized protein PH1136 from Pyrococc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ixl | ||||||
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Title | Crystal structure of uncharacterized protein PH1136 from Pyrococcus horikoshii | ||||||
Components | hypothetical protein PH1136Hypothesis | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha+beta / hot-dog-fold | ||||||
Function / homology | Thioesterase domain / Thioesterase superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta / 4HBT domain-containing protein Function and homology information | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.94 Å | ||||||
Authors | Tajika, Y. / Sakai, N. / Tanaka, Y. / Yao, M. / Watanabe, N. / Tanaka, I. | ||||||
Citation | Journal: Proteins / Year: 2004 Title: Crystal structure of conserved protein PH1136 from Pyrococcus horikoshii. Authors: Tajika, Y. / Sakai, N. / Tanaka, Y. / Yao, M. / Watanabe, N. / Tanaka, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ixl.cif.gz | 39.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ixl.ent.gz | 27.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ixl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ix/1ixl ftp://data.pdbj.org/pub/pdb/validation_reports/ix/1ixl | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 14893.058 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Plasmid: pET-22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: O58863 |
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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: 2.58 Å3/Da / Density % sol: 52.3 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: Tris-HCl, Ammonium Sulfate, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8.5 / Method: vapor diffusion | ||||||||||||||||||||||||||||||
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: BL45PX / Wavelength: 0.9000, 0.9785, 0.9791 | ||||||||||||
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Mar 4, 2002 | ||||||||||||
Radiation | Monochromator: MIRRORS + Si (111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.94→31 Å / Num. obs: 11527 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 8.23 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 8.1 | ||||||||||||
Reflection shell | Resolution: 1.94→2.01 Å / Redundancy: 8.39 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.4 / Num. unique all: 1174 / % possible all: 100 | ||||||||||||
Reflection | *PLUS Lowest resolution: 50 Å | ||||||||||||
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.332 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.94→10 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: throughput / Bsol: 49.8 Å2 / ksol: 0.462 e/Å3 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.94→10 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: 10
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Xplor file | Serial no: 1 / Param file: protein_rep.param / Topol file: protein.top | ||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 50 Å | ||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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