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Open data
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Basic information
Entry | Database: PDB / ID: 2p6i | ||||||
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Title | Crystal structure of PH0725 from Pyrococcus horikoshii OT3 | ||||||
![]() | diphthine synthase | ||||||
![]() | TRANSFERASE / 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 | ![]() | ||||||
![]() | Yamamoto, H. / Matsuura, Y. / Morikawa, Y. / Shimada, H. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() Title: Crystal structure of PH0725 from Pyrococcus horikoshii OT3 Authors: Sugahara, 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 | ![]() | 123.3 KB | Display | ![]() |
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PDB format | ![]() | 95.3 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 ![]() 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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1 |
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Unit cell |
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Details | Biological assembly is a dimer in the asymmetric unit. |
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Components
#1: Protein | Mass: 29615.447 Da / Num. of mol.: 2 / Mutation: E259M Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-SAH / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.22 Å3/Da / Density % sol: 61.81 % |
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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 RAXIS IV / Detector: IMAGE PLATE / Date: Sep 6, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. all: 39981 / Num. obs: 39981 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.3 % / Biso Wilson estimate: 41.918 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.044 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.592 / Mean I/σ(I) obs: 3.95 / Num. unique all: 3914 / Rsym value: 0.509 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: DIFFERENCE FOURIER Starting model: PDB ENTRY 1WNG Resolution: 2.2→19.75 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 39.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→19.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.016
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