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- PDB-1ixl: Crystal structure of uncharacterized protein PH1136 from Pyrococc... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ixl | ||||||
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Title | Crystal structure of uncharacterized protein PH1136 from Pyrococcus horikoshii | ||||||
![]() | hypothetical protein PH1136 | ||||||
![]() | 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![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tajika, Y. / Sakai, N. / Tanaka, Y. / Yao, M. / Watanabe, N. / Tanaka, I. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 39.1 KB | Display | ![]() |
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PDB format | ![]() | 27.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() | ||||||||||||
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 |
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Processing
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Refinement | Method to determine structure: ![]()
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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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