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- PDB-2dzw: Structure of mutant tryptophan synthase alpha-subunit (E244A) fro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2dzw | ||||||
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Title | Structure of mutant tryptophan synthase alpha-subunit (E244A) from a hyperthermophile, Pyrococcus furiosus | ||||||
![]() | Tryptophan synthase alpha chain | ||||||
![]() | LYASE / tryptophan synthase alpha-subunit / hyperthermophile / pyrococcus furiosus / x-ray analysis / stability / calorimetry / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ogasahara, K. / Yamagata, Y. / Yutani, K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() Title: Structures of mutant tryptophan synthase alpha-subunits from a hyperthermophile, Pyrococcus furiosus Authors: Ogasahara, K. / Yamagata, Y. / Yutani, K. #1: ![]() Title: Entropic stabilization of the tryptophan synthase alpha-subunit from a hyperthermophile, Pyrococcus furiosus. X-ray analysis and calorimetry Authors: Yamagata, Y. / Ogasahara, K. / Hioki, Y. / Lee, S.J. / Nakagawa, A. / Nakamura, H. / Ishida, M. / Kuramitsu, S. / Yutani, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 113.6 KB | Display | ![]() |
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PDB format | ![]() | 88.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 372.4 KB | Display | ![]() |
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Full document | ![]() | 380.5 KB | Display | |
Data in XML | ![]() | 11.5 KB | Display | |
Data in CIF | ![]() | 19.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2dzpC ![]() 2dzsC ![]() 2dztC ![]() 2dzuC ![]() 2dzvC ![]() 2dzxC ![]() 2e09C ![]() 1geqS 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: 27477.809 Da / Num. of mol.: 2 / Mutation: E244A 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: 2.15 Å3/Da / Density % sol: 42.79 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M MES-NAOH, 12% PEG 20000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: May 16, 2001 / Details: mirror |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. obs: 20436 / % possible obs: 81.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.41 % / Biso Wilson estimate: 34.5 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 2.2→2.28 Å / Rmerge(I) obs: 0.429 / Mean I/σ(I) obs: 2.7 / Num. unique all: 1507 / % possible all: 60.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1GEQ Resolution: 2.4→19.68 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2261830.59 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.6528 Å2 / ksol: 0.332847 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→19.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
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Xplor file |
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