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Yorodumi- PDB-2efy: Crystal Structure of T.th. HB8 O-acetylserine sulfhydrylase Compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2efy | ||||||
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Title | Crystal Structure of T.th. HB8 O-acetylserine sulfhydrylase Complexed with 4-Acetylbutyric acid | ||||||
Components | O-acetylserine (Thiol)-lyase | ||||||
Keywords | TRANSFERASE / PLP-dependent enzyme | ||||||
Function / homology | Function and homology information cysteine synthase / cysteine synthase activity / cysteine biosynthetic process from serine Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Goto, M. | ||||||
Citation | Journal: to be published Title: Crystal Structure of T.th. HB8 O-acetylserine sulfhydrylase Complexed with 4-Acetylbutyric acid Authors: Goto, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2efy.cif.gz | 127.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2efy.ent.gz | 98.9 KB | Display | PDB format |
PDBx/mmJSON format | 2efy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ef/2efy ftp://data.pdbj.org/pub/pdb/validation_reports/ef/2efy | HTTPS FTP |
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-Related structure data
Related structure data | 1ve1S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33065.094 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET-20b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RP / References: UniProt: Q5SLE6, cysteine synthase #2: Chemical | #3: Chemical | #4: 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: 2.5 Å3/Da / Density % sol: 50.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: tri-sodium citrate, CHES, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 14, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. all: 27420 / Num. obs: 26941 / % possible obs: 98.2 % / Biso Wilson estimate: 26.5 Å2 |
Reflection shell | Resolution: 2.35→2.43 Å / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1VE1 Resolution: 2.35→48.11 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1773193.79 / 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: 32.5266 Å2 / ksol: 0.333373 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.35→48.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.5 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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