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Open data
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Basic information
Entry | Database: PDB / ID: 2dv5 | ||||||
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Title | Crystal structure of Leu65 to Ala mutant of Diphthine synthase | ||||||
![]() | 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 | ![]() ![]() ![]() | ||||||
![]() | Mizutani, H. / Matsuura, Y. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() Title: Crystal structure of diphthine synthase from Pyrococcus horikoshii OT3 Authors: Mizutani, H. / 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 | ![]() | 129.9 KB | Display | ![]() |
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PDB format | ![]() | 99.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 803.7 KB | Display | ![]() |
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Full document | ![]() | 809.7 KB | Display | |
Data in XML | ![]() | 26.7 KB | Display | |
Data in CIF | ![]() | 38.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1vceC ![]() 2dsgC ![]() 2dshC ![]() 2dsiC ![]() 2dv3C ![]() 2dv4C ![]() 2dv7C ![]() 2dxvC ![]() 2dxwC ![]() 2dxxC ![]() 2e07C ![]() 2e08C ![]() 2e15C ![]() 2e16C ![]() 2e17C ![]() 2e7rC ![]() 2egbC ![]() 2eglC ![]() 2egsC ![]() 2ehcC ![]() 2ehlC ![]() 2z6rC ![]() 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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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 29571.287 Da / Num. of mol.: 2 / Mutation: L65A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 449 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: 3.21 Å3/Da / Density % sol: 61.71 % |
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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 JUPITER 210 / Detector: CCD / Date: Apr 18, 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: 2.2→30 Å / Num. all: 39886 / Num. obs: 39886 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.7 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.081 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 12 % / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 5.08 / Num. unique all: 3905 / Rsym value: 0.333 / % 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→30 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2368295.67 / 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: 50.1396 Å2 / ksol: 0.3478 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→30 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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