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Open data
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Basic information
Entry | Database: PDB / ID: 2pca | ||||||
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Title | Crystal structure of PH0725 from Pyrococcus horikoshii OT3 | ||||||
![]() | Probable diphthine synthase | ||||||
![]() | TRANSFERASE / Pyrococcus horikoshii OT3 / Methyltransferase / S-adenosyl-L-methionine / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | ![]() diphthine synthase / diphthine synthase activity / protein histidyl modification to diphthamide / methylation Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sugahara, M. / Taketa, M. / Morikawa, Y. / Matsuura, Y. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() Title: Crystal structure of PH0725 from Pyrococcus horikoshii OT3 Authors: Sugahara, M. / Taketa, M. / Morikawa, Y. / Matsuura, Y. / 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 | ![]() | 126.7 KB | Display | ![]() |
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PDB format | ![]() | 97.1 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 ![]() 2hr8C ![]() 2huqC ![]() 2hutC ![]() 2huvC ![]() 2huxC ![]() 2owfC ![]() 2owgC ![]() 2owkC ![]() 2owuC ![]() 2owvC ![]() 2p2xC ![]() 2p5cC ![]() 2p5fC ![]() 2p6dC ![]() 2p6iC ![]() 2p6kC ![]() 2p6lC ![]() 2p9dC ![]() 2pb4C ![]() 2pb5C ![]() 2pb6C ![]() 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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Unit cell |
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Components
#1: Protein | Mass: 29631.404 Da / Num. of mol.: 2 / Mutation: L83M Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-NA / | #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: 3.26 Å3/Da / Density % sol: 62.3 % |
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Crystal grow | Temperature: 295 K / Method: oil microbatch / pH: 5.5 Details: 3.86M Sodium formate, 0.1M Acetate, pH5.5, oil microbatch, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU JUPITER / Detector: CCD / Date: Nov 20, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 53695 / Num. obs: 53695 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.1 % / Biso Wilson estimate: 30.037 Å2 / Rmerge(I) obs: 0.099 / Rsym value: 0.097 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 3.3 / Num. unique all: 5275 / Rsym value: 0.483 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1wng Resolution: 2→29.15 Å / Isotropic thermal model: Anisotrop / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 33 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→29.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å / Rfactor Rfree error: 0.017
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