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Yorodumi- PDB-1kko: CRYSTAL STRUCTURE OF CITROBACTER AMALONATICUS METHYLASPARTATE AMM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kko | ||||||
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Title | CRYSTAL STRUCTURE OF CITROBACTER AMALONATICUS METHYLASPARTATE AMMONIA LYASE | ||||||
Components | 3-METHYLASPARTATE AMMONIA-LYASE | ||||||
Keywords | LYASE / Methylaspartate ammonia lyase / Enolase superfamily / Tim barrel | ||||||
Function / homology | Function and homology information methylaspartate ammonia-lyase / methylaspartate ammonia-lyase activity / glutamate catabolic process via L-citramalate / metal ion binding Similarity search - Function | ||||||
Biological species | Citrobacter amalonaticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å | ||||||
Authors | Levy, C.W. / Buckley, P.A. / Sedelnikova, S. / Kato, Y. / Asano, Y. / Rice, D.W. / Baker, P.J. | ||||||
Citation | Journal: Structure / Year: 2002 Title: Insights into enzyme evolution revealed by the structure of methylaspartate ammonia lyase. Authors: Levy, C.W. / Buckley, P.A. / Sedelnikova, S. / Kato, Y. / Asano, Y. / Rice, D.W. / Baker, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kko.cif.gz | 400.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kko.ent.gz | 338.1 KB | Display | PDB format |
PDBx/mmJSON format | 1kko.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kko_validation.pdf.gz | 389 KB | Display | wwPDB validaton report |
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Full document | 1kko_full_validation.pdf.gz | 405.1 KB | Display | |
Data in XML | 1kko_validation.xml.gz | 19.6 KB | Display | |
Data in CIF | 1kko_validation.cif.gz | 40.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kk/1kko ftp://data.pdbj.org/pub/pdb/validation_reports/kk/1kko | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 45989.898 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Citrobacter amalonaticus (bacteria) / Gene: MAL / Plasmid: PMAL / Production host: Escherichia coli (E. coli) / Strain (production host): DL41 / References: UniProt: O66145, methylaspartate ammonia-lyase #2: Chemical | ChemComp-SO4 / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.83 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8 Details: potassium phosphate, ammonium sulphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K | ||||||||||||||||||||||||
Crystal grow | *PLUS Details: Levy, C.W., (2001) Acta Crystallogr., D57, 1922. | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97963,0.97946,0.96863 | ||||||||||||
Detector |
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Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.3→119 Å / Num. all: 245233 / Num. obs: 245233 / Redundancy: 3.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.9 | ||||||||||||
Reflection shell | Resolution: 1.33→1.36 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 3.5 / % possible all: 97.2 | ||||||||||||
Reflection | *PLUS Highest resolution: 1.33 Å / Lowest resolution: 20 Å / % possible obs: 95.8 % / Rmerge(I) obs: 0.06 | ||||||||||||
Reflection shell | *PLUS % possible obs: 97.2 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.33→119.52 Å / SU B: 1.849 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.05
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Displacement parameters | Biso mean: 14.87 Å2
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Refinement step | Cycle: LAST / Resolution: 1.33→119.52 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 5 % / Rfactor obs: 0.174 / Rfactor Rfree: 0.198 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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