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- PDB-2ywa: Crystal structure of uncharacterized conserved protein from Therm... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ywa | ||||||
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Title | Crystal structure of uncharacterized conserved protein from Thermus thermophilus HB8 | ||||||
![]() | Hypothetical protein TTHA0048![]() | ||||||
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Function / homology | Probable ribonuclease HepT / Nucleotidyltransferase substrate binding protein like / Nucleotidyltransferases domain 2 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / ![]() ![]() | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kitamura, Y. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() Title: Crystal structure of uncharacterized conserved protein from Thermus thermophilus HB8 Authors: Kitamura, Y. / Yokoyama, S. / Kuramitsu, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 101.3 KB | Display | ![]() |
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PDB format | ![]() | 80.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2yzyC ![]() 2z07C ![]() 2z08C ![]() 2z09C ![]() 2z0jC ![]() 2z3vC ![]() 1wtyS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 14045.812 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 6.14 Å3/Da / Density % sol: 79.97 % / Description: the file contains Friedel pairs |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.7 Details: 1.5M NaFormate 0.1M Tris-HCl pH8.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Feb 6, 2004 |
Radiation | Monochromator: Fixed exit Si double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 3.2→44.28 Å / Num. obs: 44105 / % possible obs: 100 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 3.2→3.31 Å / Redundancy: 19.37 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 6.2 / Num. unique all: 2340 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1WTY Resolution: 3.2→44.13 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 216963.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: the file contains Friedel pairs
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 30.7125 Å2 / ksol: 0.383684 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.2→44.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.4 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file | Serial no: 1 / Param file: protein_rep.param / Topol file: protein.top |