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Open data
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Basic information
Entry | Database: PDB / ID: 2z6r | ||||||
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Title | Crystal structure of Lys49 to Arg mutant of Diphthine synthase | ||||||
![]() | diphthine synthase | ||||||
![]() | TRANSFERASE / Methyltransferase / S-adenosyl-L-methionine | ||||||
Function / homology | ![]() diphthine synthase / diphthine synthase activity / protein histidyl modification to diphthamide / methylation Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mizutani, H. / Matsuura, Y. / Krishna Swamy, B.S. / Simanshu, D.K. / Murthy, M.R.N. / Kunishima, N. | ||||||
![]() | ![]() Title: Crystal structure of diphthine synthase from Pyrococcus horikoshii OT3 Authors: Mizutani, H. / Matsuura, Y. / Krishna Swamy, B.S. / Simanshu, D.K. / Murthy, M.R.N. / 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 | ![]() | 139.9 KB | Display | ![]() |
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PDB format | ![]() | 107.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1vceC ![]() 2dsgC ![]() 2dshC ![]() 2dsiC ![]() 2dv3C ![]() 2dv4C ![]() 2dv5C ![]() 2dv7C ![]() 2dxvC ![]() 2dxwC ![]() 2dxxC ![]() 2e07C ![]() 2e08C ![]() 2e15C ![]() 2e16C ![]() 2e17C ![]() 2e7rC ![]() 2egbC ![]() 2eglC ![]() 2egsC ![]() 2ehcC ![]() 2ehlC ![]() 1wngS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 29641.381 Da / Num. of mol.: 2 / Mutation: K49R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 827 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/SAH.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SAH.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-SAH / | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.16 % |
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Crystal grow | Temperature: 295 K / Method: microbatch / pH: 6.5 Details: 1.8M AMMONIUM SULFATE, 0.1M MES, 0.01M Co CHLORIDE , pH 6.5, microbatch, 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: Oct 5, 2006 |
Radiation | Monochromator: bending magnet / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→30 Å / Num. all: 121413 / Num. obs: 121413 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 10.7 % / Biso Wilson estimate: 22.4 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.08 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 5.65 / Num. unique all: 12000 / Rsym value: 0.38 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1WNG Resolution: 1.5→30 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2182780.03 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.1267 Å2 / ksol: 0.371901 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.59 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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