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- PDB-6nxd: TYPE I L-ASPARAGINASE FROM ESCHERICHIA COLI IN COMPLEX WITH CITRA... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6nxd | ||||||
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Title | TYPE I L-ASPARAGINASE FROM ESCHERICHIA COLI IN COMPLEX WITH CITRATE AT PH 4 | ||||||
![]() | L-asparaginase 1 | ||||||
![]() | HYDROLASE / hydrolysis of L-asparagine | ||||||
Function / homology | ![]() asparagine catabolic process via L-aspartate / asparaginase / asparaginase activity / protein homotetramerization / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Lubkowski, J. / Wlodawer, A. | ||||||
![]() | ![]() Title: Crystal structure and allosteric regulation of the cytoplasmic Escherichia coli L-asparaginase I. Authors: Yun, M.K. / Nourse, A. / White, S.W. / Rock, C.O. / Heath, R.J. | ||||||
History |
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Remark 0 | THIS ENTRY 1ZET REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 2P2N, DETERMINED BY YUN, M. ...THIS ENTRY 1ZET REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 2P2N, DETERMINED BY YUN, M.K., NOURSE, A., WHITE, S.W., ROCK, C.O., HEATH, R.J. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 264 KB | Display | ![]() |
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PDB format | ![]() | 217.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 515.6 KB | Display | ![]() |
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Full document | ![]() | 537.4 KB | Display | |
Data in XML | ![]() | 53 KB | Display | |
Data in CIF | ![]() | 74.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6nx6C ![]() 6nx7C ![]() 6nx8C ![]() 6nx9C ![]() 6nxaC ![]() 6nxbC ![]() 6nxcC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 39335.461 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: ansA, b1767, JW1756 / Plasmid: pET-15b / Cell (production host): mesophilic bacteria / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 595 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/CIT.gif)
![](data/chem/img/ASN.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CIT.gif)
![](data/chem/img/ASN.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-CIT / #4: Chemical | ChemComp-ASN / #5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.41 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 2P2N. |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: citric acid, sodium chloride, pH 4.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 6, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.01259 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 95017 / % possible obs: 90.6 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 1.9→1.97 Å |
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Processing
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Refinement | Resolution: 1.9→45.17 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.913 / SU B: 3.663 / SU ML: 0.109 / SU R Cruickshank DPI: 0.1885 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.189 / ESU R Free: 0.166 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 103.22 Å2 / Biso mean: 21.296 Å2 / Biso min: 6.53 Å2
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Refinement step | Cycle: final / Resolution: 1.9→45.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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