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Yorodumi- PDB-1lc8: Crystal Structure of L-Threonine-O-3-phosphate Decarboxylase from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lc8 | ||||||
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Title | Crystal Structure of L-Threonine-O-3-phosphate Decarboxylase from S. enterica complexed with its reaction intermediate | ||||||
Components | L-Threonine-O-3-Phosphate Decarboxylase | ||||||
Keywords | LYASE / CobD / L-threonine-O-3-phosphate / PLP-dependent decarboxylase / cobalamin | ||||||
Function / homology | Function and homology information threonine-phosphate decarboxylase / threonine-phosphate decarboxylase activity / cobalamin biosynthetic process / pyridoxal phosphate binding / protein homodimerization activity / identical protein binding Similarity search - Function | ||||||
Biological species | Salmonella enterica (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Cheong, C.-G. / Escalante-Semerena, J. / Rayment, I. | ||||||
Citation | Journal: Biochemistry / Year: 2002 Title: Structural studies of the L-threonine-O-3-phosphate decarboxylase (CobD) enzyme from Salmonella enterica: the apo, substrate, and product-aldimine complexes. Authors: Cheong, C.G. / Escalante-Semerena, J.C. / Rayment, I. | ||||||
History |
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Remark 999 | SEQUENCE According to the authors, the GenBank entry is in error because the original DNA sequence ... SEQUENCE According to the authors, the GenBank entry is in error because the original DNA sequence had some errors. The electron density also supports it. The new sequence is Gln25, Ser30, Val42, Arg44 and Ala45. Arg44 lacks side chain density. The organism name in this GenBank entry is Salmonella typhimurium. Salmonella typhimurium has been changed to Salmonella enterica. Therefore, the two names are same. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lc8.cif.gz | 88.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lc8.ent.gz | 65.4 KB | Display | PDB format |
PDBx/mmJSON format | 1lc8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lc8_validation.pdf.gz | 750.2 KB | Display | wwPDB validaton report |
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Full document | 1lc8_full_validation.pdf.gz | 754.5 KB | Display | |
Data in XML | 1lc8_validation.xml.gz | 18.2 KB | Display | |
Data in CIF | 1lc8_validation.cif.gz | 26.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lc/1lc8 ftp://data.pdbj.org/pub/pdb/validation_reports/lc/1lc8 | HTTPS FTP |
-Related structure data
Related structure data | 1l4nC 1l5fC 1l5kC 1l5lC 1l5mC 1l5nC 1lc5C 1lc7C 1kus C: citing same article (ref.) 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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Details | the second subunit of biological dimer can be generated by the operation of crystallographic two-fold symmetry axis |
-Components
#1: Protein | Mass: 40849.848 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica (bacteria) / Gene: cobD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(JE4094) / References: UniProt: P97084 |
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#2: Chemical | ChemComp-33P / { |
#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: 2.47 Å3/Da / Density % sol: 50.12 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / pH: 6 Details: PEG methyl ether 2000, pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS 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: APS / Beamline: 19-BM / Wavelength: 0.9763 Å |
Detector | Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→500 Å / Num. obs: 37471 / % possible obs: 99.4 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 31.9 |
Reflection shell | Resolution: 1.8→1.86 Å / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 5.8 / % possible all: 99.2 |
Reflection | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 500 Å / Rmerge(I) obs: 0.078 |
Reflection shell | *PLUS % possible obs: 99.2 % / Rmerge(I) obs: 0.331 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1KUS 1kus Resolution: 1.8→500 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.8→500 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 500 Å / Num. reflection obs: 35608 / Rfactor Rfree: 0.229 / Rfactor Rwork: 0.196 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |