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Yorodumi- PDB-2dzs: Structure of mutant tryptophan synthase alpha-subunit (E103A) fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dzs | ||||||
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Title | Structure of mutant tryptophan synthase alpha-subunit (E103A) from a hyperthermophile, Pyrococcus furiosus | ||||||
Components | Tryptophan synthase alpha chain | ||||||
Keywords | 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 | Function and homology information | ||||||
Biological species | Pyrococcus furiosus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.4 Å | ||||||
Authors | Ogasahara, K. / Yamagata, Y. / Yutani, K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Structures of mutant tryptophan synthase alpha-subunits from a hyperthermophile, Pyrococcus furiosus Authors: Ogasahara, K. / Yamagata, Y. / Yutani, K. #1: Journal: J.Biol.Chem. / Year: 2001 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dzs.cif.gz | 112.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dzs.ent.gz | 87.7 KB | Display | PDB format |
PDBx/mmJSON format | 2dzs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2dzs_validation.pdf.gz | 369.1 KB | Display | wwPDB validaton report |
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Full document | 2dzs_full_validation.pdf.gz | 376.1 KB | Display | |
Data in XML | 2dzs_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | 2dzs_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dz/2dzs ftp://data.pdbj.org/pub/pdb/validation_reports/dz/2dzs | HTTPS FTP |
-Related structure data
Related structure data | 2dzpC 2dztC 2dzuC 2dzvC 2dzwC 2dzxC 2e09C 1geqS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-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: E103A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: trpA / Plasmid: pa1974 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q8U094, tryptophan synthase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M MES-NAOH, 10-15% 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: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
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→99 Å / Num. all: 23093 / Num. obs: 23093 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.05 % / Biso Wilson estimate: 33.7 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 46.9 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 6.05 % / Rmerge(I) obs: 0.185 / Mean I/σ(I) obs: 6.7 / Num. unique all: 1687 / % possible all: 69.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1GEQ Resolution: 2.4→19.7 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1827339.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 34.4235 Å2 / ksol: 0.317249 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→19.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
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Xplor file |
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