[English] 日本語
Yorodumi- PDB-1kkr: CRYSTAL STRUCTURE OF CITROBACTER AMALONATICUS METHYLASPARTATE AMM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kkr | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF CITROBACTER AMALONATICUS METHYLASPARTATE AMMONIA LYASE CONTAINING (2S,3S)-3-METHYLASPARTIC ACID | ||||||
Components | 3-METHYLASPARTATE AMMONIA-LYASE | ||||||
Keywords | LYASE / Methylaspartate ammonia lyase / Enolase superfamily / TIM barrel / substrate complex | ||||||
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 / Resolution: 2.1 Å | ||||||
Authors | Levy, C.W. / Buckley, P.A. / Sedelnikova, S. / Kato, K. / 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1kkr.cif.gz | 179.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1kkr.ent.gz | 148.1 KB | Display | PDB format |
PDBx/mmJSON format | 1kkr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kkr_validation.pdf.gz | 396.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1kkr_full_validation.pdf.gz | 418.9 KB | Display | |
Data in XML | 1kkr_validation.xml.gz | 20.5 KB | Display | |
Data in CIF | 1kkr_validation.cif.gz | 34.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kk/1kkr ftp://data.pdbj.org/pub/pdb/validation_reports/kk/1kkr | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-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 | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.85 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54179 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 20, 2001 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→18 Å / Num. all: 60480 / Num. obs: 60480 / Redundancy: 3 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 2.1→2.15 Å / Rmerge(I) obs: 0.218 / Mean I/σ(I) obs: 5.1 / % possible all: 91.6 |
Reflection | *PLUS Lowest resolution: 18 Å / % possible obs: 93.4 % |
Reflection shell | *PLUS % possible obs: 91.6 % |
-Processing
Software | Name: REFMAC / Classification: refinement | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.1→18 Å / SU B: 5.805 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.176
| ||||||||||||||||||||
Displacement parameters | Biso mean: 25.34 Å2
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→18 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
LS refinement shell | Highest resolution: 2.1 Å / Rfactor Rfree: 0.254 / Rfactor Rwork: 0.184 / Total num. of bins used: 20 | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.1 Å / % reflection Rfree: 5.1 % / Rfactor obs: 0.167 / Rfactor Rfree: 0.227 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
|