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Yorodumi- PDB-2eco: Crystal Structure of T.th. HB8 O-acetylserine sulfhydrylase Compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2eco | ||||||
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Title | Crystal Structure of T.th. HB8 O-acetylserine sulfhydrylase Complexed with 4-methylvalerate | ||||||
Components | O-acetylserine (Thiol)-lyase | ||||||
Keywords | TRANSFERASE / PLP-dependent | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Goto, M. | ||||||
Citation | Journal: to be published Title: Crystal Structure of T.th. HB8 O-acetylserine sulfhydrylase Complexed with 4-methylvalerate 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 | 2eco.cif.gz | 78.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2eco.ent.gz | 57.3 KB | Display | PDB format |
PDBx/mmJSON format | 2eco.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ec/2eco ftp://data.pdbj.org/pub/pdb/validation_reports/ec/2eco | 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.: 1 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 |
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#2: Chemical | ChemComp-PLP / |
#3: Chemical | ChemComp-4MV / |
#4: 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: 3.81 Å3/Da / Density % sol: 67.75 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: Ammonium Sulfate, Tris-HCl, Glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 24, 2002 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→45.29 Å / Num. all: 40094 / Num. obs: 39346 / % possible obs: 98.1 % / Biso Wilson estimate: 17.8 Å2 |
Reflection shell | Resolution: 1.9→1.97 Å / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1VE1 Resolution: 1.9→43.76 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1706618.66 / 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: 55.9472 Å2 / ksol: 0.37673 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→43.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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