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Open data
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Basic information
Entry | Database: PDB / ID: 2drv | ||||||
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Title | Structure of PH1069 protein from Pyrococcus horikoshii OT3 | ||||||
![]() | 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. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() Title: Structure of PH1069 protein from Pyrococcus horikoshii OT3 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 | ![]() | 95.7 KB | Display | ![]() |
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PDB format | ![]() | 77.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452.2 KB | Display | ![]() |
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Full document | ![]() | 464 KB | Display | |
Data in XML | ![]() | 21.6 KB | Display | |
Data in CIF | ![]() | 31.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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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: Chemical | ChemComp-SO4 / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43.1 % |
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Crystal grow | Temperature: 295 K / Method: microbatch / pH: 4.6 Details: Sodium acetate, Ammonium sulfate, pH 4.6, MICROBATCH, temperature 295.0K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Mar 16, 2006 | ||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.6→40 Å / Num. all: 43824 / Num. obs: 43824 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 22.5 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 14.7 | ||||||||||||
Reflection shell | Resolution: 1.6→1.66 Å / % possible all: 90.2 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 74.2634 Å2 / ksol: 0.430583 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→36.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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