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Open data
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Basic information
Entry | Database: PDB / ID: 2hr8 | ||||||
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Title | Crystal structure of PH0725 from Pyrococcus horikoshii OT3 | ||||||
![]() | diphthine synthase![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yamamoto, H. / Taketa, M. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() Title: Crystal structure of PH0725 from Pyrococcus horikoshii OT3 Authors: Yamamoto, H. / Taketa, M. / Kunishima, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 117.4 KB | Display | ![]() |
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PDB format | ![]() | 90.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2e8hC ![]() 2huqC ![]() 2hutC ![]() 2huvC ![]() 2huxC ![]() 2owfC ![]() 2owgC ![]() 2owkC ![]() 2owuC ![]() 2owvC ![]() 2p2xC ![]() 2p5cC ![]() 2p5fC ![]() 2p6dC ![]() 2p6iC ![]() 2p6kC ![]() 2p6lC ![]() 2p9dC ![]() 2pb4C ![]() 2pb5C ![]() 2pb6C ![]() 2pcaC ![]() 2pcgC ![]() 2pchC ![]() 2pciC ![]() 2pckC ![]() 2pcmC ![]() 1wngS S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Other databases |
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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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Details | Biological assembly is dimer in the asymmetric unit. |
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Components
#1: Protein | ![]() Mass: 29581.389 Da / Num. of mol.: 2 / Mutation: Y220M Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-PT / #3: Chemical | ChemComp-SAH / | ![]() #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.21 Å3/Da / Density % sol: 61.72 % |
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Crystal grow![]() | Temperature: 291 K / Method: microbatch / pH: 5.5 Details: 3.85M Sodium Formate, 0.1M Sodium Acetate, pH 5.5, MICROBATCH, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Dec 18, 2005 / Details: MIRRORS |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.8→40 Å / Num. obs: 19573 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.6 % / Biso Wilson estimate: 66.5 Å2 / Rmerge(I) obs: 0.148 / Rsym value: 0.122 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 3.6 / Num. unique all: 1917 / Rsym value: 0.406 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1WNG Resolution: 2.8→39.29 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1653079.07 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.2343 Å2 / ksol: 0.350656 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→39.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
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Xplor file |
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