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- PDB-2cwq: Crystal structure of conserved protein TTHA0727 from Thermus ther... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2cwq | ||||||
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Title | Crystal structure of conserved protein TTHA0727 from Thermus thermophilus HB8 | ||||||
![]() | hypothetical protein TTHA0727 | ||||||
![]() | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Conserved Hypothetical Protein / All Alpha / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | AhpD-like / AhpD-like / Carboxymuconolactone decarboxylase-like / Carboxymuconolactone decarboxylase family / AhpD-like / peroxiredoxin activity / Up-down Bundle / Mainly Alpha / CMD domain-containing protein![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ito, K. / Arai, R. / Fusatomi, E. / Kamo-Uchikubo, T. / Kawaguchi, S. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() Title: Crystal structure of the conserved protein TTHA0727 from Thermus thermophilus HB8 at 1.9 A resolution: A CMD family member distinct from carboxymuconolactone decarboxylase (CMD) and AhpD Authors: Ito, K. / Arai, R. / Fusatomi, E. / Kamo-Uchikubo, T. / Kawaguchi, S. / Akasaka, R. / Terada, T. / Kuramitsu, S. / Shirouzu, M. / Yokoyama, 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 | ![]() | 81.5 KB | Display | ![]() |
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PDB format | ![]() | 66.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-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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1 | ![]()
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Unit cell |
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Details | The biological assembly is a hexamer consist of A, B, C and A', B', C' generated by the operation: y, x, -z. |
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Components
#1: Protein | Mass: 15005.659 Da / Num. of mol.: 3 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: 2.08 Å3/Da / Density % sol: 40.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1M potassium formate, 21% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Apr 15, 2005 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.9→50 Å / Num. obs: 29204 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 10.8 % / Biso Wilson estimate: 20.6 Å2 / Rsym value: 0.103 / Net I/σ(I): 17.54 | ||||||||||||
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 10.6 % / Mean I/σ(I) obs: 8.8 / Num. unique all: 2883 / Rsym value: 0.293 / % possible all: 100 |
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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: 41.719 Å2 / ksol: 0.323284 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→47.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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