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Yorodumi- PDB-1ujp: Crystal Structure of Tryptophan Synthase A-Subunit From Thermus t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ujp | ||||||
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Title | Crystal Structure of Tryptophan Synthase A-Subunit From Thermus thermophilus HB8 | ||||||
Components | Tryptophan synthase alpha chain | ||||||
Keywords | LYASE / Tryptophan Synthase / Tryptophan / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å | ||||||
Authors | Asada, Y. / Yokoyama, S. / Kuramitsu, S. / Miyano, M. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: J.Biochem.(Tokyo) / Year: 2005 Title: Stabilization mechanism of the tryptophan synthase alpha-subunit from Thermus thermophilus HB8: X-ray crystallographic analysis and calorimetry. Authors: Asada, Y. / Sawano, M. / Ogasahara, K. / Nakamura, J. / Ota, M. / Kuroishi, C. / Sugahara, M. / Yutani, K. / Kunishima, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ujp.cif.gz | 66.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ujp.ent.gz | 47.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ujp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ujp_validation.pdf.gz | 445.1 KB | Display | wwPDB validaton report |
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Full document | 1ujp_full_validation.pdf.gz | 447.2 KB | Display | |
Data in XML | 1ujp_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | 1ujp_validation.cif.gz | 21.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uj/1ujp ftp://data.pdbj.org/pub/pdb/validation_reports/uj/1ujp | HTTPS FTP |
-Related structure data
Related structure data | 1geqS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28977.525 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: P16608, tryptophan synthase |
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#2: Chemical | ChemComp-CIT / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.18 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: microbatch / pH: 5.6 Details: Ammonium Acetate, tri-Sodium Citrate dihydrate, PEG 4000, Glycerol anhydrous, pH 5.6, MICROBATCH, temperature 291K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 291 K / pH: 8 / Method: batch method | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.8 Å |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Jun 5, 2003 / Details: mirrors |
Radiation | Monochromator: Bending Magnet / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.34→30 Å / Num. all: 55454 / Num. obs: 55454 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.042 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 1.34→1.39 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 3.6 / Num. unique all: 5551 / Rsym value: 0.304 / % possible all: 100 |
Reflection | *PLUS Num. measured all: 201760 |
Reflection shell | *PLUS % possible obs: 100 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GEQ Resolution: 1.34→27.3 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 17.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.34→27.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.34→1.4 Å / Rfactor Rfree error: 0.015
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Refinement | *PLUS Lowest resolution: 30 Å / % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
LS refinement shell | *PLUS Lowest resolution: 1.39 Å |