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Open data
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Basic information
Entry | Database: PDB / ID: 2e4r | ||||||
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Title | Mutant I253M 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 | ![]() ![]() | ||||||
![]() | Shimizu, K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() Title: Mutant I253M structure of PH0725 from Pyrococcus horikoshii OT3 Authors: Shimizu, K. / Matsuura, Y. / Tanaka, Y. / Shimada, H. / 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 | ![]() | 125.3 KB | Display | ![]() |
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PDB format | ![]() | 96 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1wngS S: Starting model for refinement |
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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: I253M 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: 3.24 Å3/Da / Density % sol: 62.08 % |
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Crystal grow | Temperature: 295 K / Method: microbach / pH: 5.5 Details: 3.85M Na Formate, 0.1M Acetate, 1mM DTT, pH 5.5, Microbach, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Sep 6, 2006 / Details: Mirror |
Radiation | Monochromator: Mirror / 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: 40184 / Num. obs: 40184 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.8 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.069 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 4.6 / Rsym value: 0.488 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1WNG Resolution: 2.2→19.75 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2266584.12 / 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: 44.5587 Å2 / ksol: 0.358108 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.1 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 / Total num. of bins used: 6
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Xplor file |
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