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Open data
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Basic information
Entry | Database: PDB / ID: 6nxa | ||||||
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Title | ECAII(D90T,K162T) MUTANT AT PH 7 | ||||||
![]() | L-asparaginase 2 | ||||||
![]() | HYDROLASE / inactive mutant / hydrolysis of L-asparagine | ||||||
Function / homology | ![]() asparagine catabolic process / asparaginase / asparaginase activity / outer membrane-bounded periplasmic space / protein homotetramerization / periplasmic space / protein-containing complex / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Lubkowski, J. / Wlodawer, A. | ||||||
![]() | ![]() Title: Opportunistic complexes of E. coli L-asparaginases with citrate anions. Authors: Lubkowski, J. / Chan, W. / Wlodawer, A. #1: ![]() 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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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 267.9 KB | Display | ![]() |
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PDB format | ![]() | 222.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.1 MB | Display | ![]() |
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Full document | ![]() | 2.1 MB | Display | |
Data in XML | ![]() | 58.8 KB | Display | |
Data in CIF | ![]() | 87.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6nx6C ![]() 6nx7C ![]() 6nx8C ![]() 6nx9C ![]() 6nxbC ![]() 6nxcC ![]() 6nxdC 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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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 35544.820 Da / Num. of mol.: 4 / Mutation: K162T Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: ansB, b2957, JW2924 / Plasmid: pET-22b Details (production host): ORF contains a secretion sequence, 'HHHHHH' affinity tag and sequence of doubly mutated mature EcAII Cell (production host): mesophilic bacteria / Cell line (production host): JC2 / Production host: ![]() ![]() #2: Chemical | ChemComp-ACY / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Protein, at the concentration 15 mg/ml in 50 mM HEPES buffer pH 7 and 150 mM sodium chloride was mixed with equivolume solution of precipitant that contained, 17% (w/v) PEG3350 and 0.17 M ...Details: Protein, at the concentration 15 mg/ml in 50 mM HEPES buffer pH 7 and 150 mM sodium chloride was mixed with equivolume solution of precipitant that contained, 17% (w/v) PEG3350 and 0.17 M ammonium citrate pH 7. Resulting droplets were equilibrated against the precipitant. For the data collection, crystal was briefly transferred to cryo-protecting solution, which had the same composition as precipitant, except concentration of PEG3350 was increased to 35 % (v/w/) and 10% (v/v), and also contained 15% of glycerol Temp details: incubator-controlled |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Stream of liquid nitrogen / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Jul 2, 2018 / Details: Multilayer X-ray mirrors VariMax HF | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Multilayer X-ray mirrors VariMax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.93→40 Å / Num. obs: 86035 / % possible obs: 96.1 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.064 / Rrim(I) all: 0.119 / Χ2: 0.923 / Net I/σ(I): 7.8 / Num. measured all: 284693 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() 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: 114.3 Å2 / Biso mean: 33.522 Å2 / Biso min: 15.22 Å2
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Refinement step | Cycle: final / Resolution: 1.93→26.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.93→1.98 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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