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Open data
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Basic information
Entry | Database: PDB / ID: 2it2 | ||||||
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Title | Structure of PH1069 protein from Pyrococcus horikoshii | ||||||
![]() | UPF0130 protein PH1069 | ||||||
![]() | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Hypothetical protein / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | ![]() tRNAPhe 7-[(3-amino-3-carboxypropyl)-4-demethylwyosine37-N4]-methyltransferase / tRNA methyltransferase activity / wybutosine biosynthetic process / tRNA methylation Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lokanath, N.K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() Title: Structure of PH1069 protein from Pyrococcus horikoshii Authors: Lokanath, N.K. / 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 | ![]() | 96.9 KB | Display | ![]() |
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PDB format | ![]() | 73.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439.7 KB | Display | ![]() |
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Full document | ![]() | 452.5 KB | Display | |
Data in XML | ![]() | 20.4 KB | Display | |
Data in CIF | ![]() | 29.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2it3C ![]() 2drvS C: citing same article ( 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: 23544.447 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.28 % |
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Crystal grow | Temperature: 295 K / Method: microbatch / pH: 7.5 Details: HEPES, KH2PO4, pH 7.5, microbatch, temperature 295K |
-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
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Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Apr 6, 2006 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. all: 53425 / Num. obs: 53423 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 24.1 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 21.9 |
Reflection shell | Resolution: 1.5→1.55 Å / % possible all: 99 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2DRV Resolution: 1.5→17.55 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 499042.2 / 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: 90.8646 Å2 / ksol: 0.453612 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→17.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.59 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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