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Yorodumi- PDB-1d6s: CRYSTAL STRUCTURE OF THE K41A MUTANT OF O-ACETYLSERINE SULFHYDRYL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d6s | ||||||
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Title | CRYSTAL STRUCTURE OF THE K41A MUTANT OF O-ACETYLSERINE SULFHYDRYLASE COMPLEXED IN EXTERNAL ALDIMINE LINKAGE WITH METHIONINE | ||||||
Components | O-ACETYLSERINE SULFHYDRYLASE | ||||||
Keywords | LYASE / CYSTEINE BIOSYNTHESIS / BETA REPLACEMENT ENZYME / PLP / K41A | ||||||
Function / homology | Function and homology information cysteine synthase / cysteine synthase activity / L-cysteine desulfhydrase activity / cysteine biosynthetic process from serine / pyridoxal phosphate binding / cytoplasm Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.3 Å | ||||||
Authors | Burkhard, P. / Tai, C.H. / Ristroph, C.M. / Cook, P.F. / Jansonius, J.N. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: Ligand binding induces a large conformational change in O-acetylserine sulfhydrylase from Salmonella typhimurium. Authors: Burkhard, P. / Tai, C.H. / Ristroph, C.M. / Cook, P.F. / Jansonius, J.N. #1: Journal: J.Mol.Biol. / Year: 1998 Title: Three-dimensional Structure of O-Acetylserine Sulfhydrylase from Salmonella typhimurium Authors: Burkhard, P. / Rao, G.S. / Hohenester, E. / Schnackerz, K.D. / Cook, P.F. / Jansonius, J.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d6s.cif.gz | 134.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d6s.ent.gz | 106.7 KB | Display | PDB format |
PDBx/mmJSON format | 1d6s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1d6s_validation.pdf.gz | 463.1 KB | Display | wwPDB validaton report |
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Full document | 1d6s_full_validation.pdf.gz | 468.3 KB | Display | |
Data in XML | 1d6s_validation.xml.gz | 26.5 KB | Display | |
Data in CIF | 1d6s_validation.cif.gz | 37.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d6/1d6s ftp://data.pdbj.org/pub/pdb/validation_reports/d6/1d6s | HTTPS FTP |
-Related structure data
Related structure data | |
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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: 34412.320 Da / Num. of mol.: 2 / Mutation: K41A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: DW378 / Production host: Escherichia coli (E. coli) References: UniProt: P12674, UniProt: P0A1E3*PLUS, EC: 4.2.99.8 #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: 2.83 Å3/Da / Density % sol: 56.55 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 30 % PEG 4000 8 % ETHANOL 100 MM TRIS (PH 7.0) 150 MM LI2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 297K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ELLIOTT GX-20 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 5, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Biso Wilson estimate: 15.3 Å2 / Rmerge(I) obs: 0.105 |
Reflection | *PLUS Num. all: 32531 |
-Processing
Software |
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Refinement | Resolution: 2.3→29.67 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2355706.22 / 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: 58.3 Å2 / ksol: 0.319 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→29.67 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTRAINED | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 33.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.297 / % reflection Rfree: 5.2 % / Rfactor Rwork: 0.268 |