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- PDB-2dp9: Crystal Structure of Conserved Hypothetical Protein TTHA0113 from... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2dp9 | ||||||
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Title | Crystal Structure of Conserved Hypothetical Protein TTHA0113 from Thermus thermophilus HB8 | ||||||
![]() | Hypothetical protein TTHA0113 | ||||||
![]() | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / jellyroll / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Hypothetical protein. / ASCH / ASCH domain / ASCH domain / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / PUA-like superfamily / Roll / Mainly Beta / ASCH domain-containing protein![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Agari, Y. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() Title: Crystal Structure of Conserved Hypothetical Protein TTHA0113 from Thermus thermophilus HB8 Authors: Agari, 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 | ![]() | 39.6 KB | Display | ![]() |
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PDB format | ![]() | 26.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 422.6 KB | Display | ![]() |
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Full document | ![]() | 425.2 KB | Display | |
Data in XML | ![]() | 7.8 KB | Display | |
Data in CIF | ![]() | 10 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1wk2S 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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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 14460.768 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-121 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.3 Details: 0.2M Calcium Acetate, 20% w/v Polyethylene Glycol 3350 , pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction |
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Sep 28, 2004 | ||||||||||||||||||
Radiation |
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Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 1.9→50 Å / Num. all: 9486 / Num. obs: 9411 / % possible obs: 99.7 % / Observed criterion σ(I): 5 / Redundancy: 5.3 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 32.28 | ||||||||||||||||||
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 4.1 / % possible all: 97.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1WK2 Resolution: 1.9→29.57 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 254955.91 / 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: 36.1682 Å2 / ksol: 0.31367 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→29.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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