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- PDB-6pa4: E. coli L-asparaginase II double mutant (T89V,K162T) in complex w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6pa4 | ||||||
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Title | E. coli L-asparaginase II double mutant (T89V,K162T) in complex with L-Asp at pH 7.0 | ||||||
![]() | 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: Geometric considerations support the double-displacement catalytic mechanism of l-asparaginase. Authors: Lubkowski, J. / Wlodawer, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 264.3 KB | Display | ![]() |
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PDB format | ![]() | 219 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 56.5 KB | Display | |
Data in CIF | ![]() | 82.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6pa2C ![]() 6pa3C ![]() 6pa5C ![]() 6pa6C ![]() 6pa8C ![]() 6pa9C ![]() 6paaC ![]() 6pabC ![]() 6pacC ![]() 6paeC 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: 35671.914 Da / Num. of mol.: 4 / Mutation: T89V,K162T Source method: isolated from a genetically manipulated source Details: Expressed variant contains 8 additional N-terminal residues MDHHHHHH (affinity tag) and two engineered mutations (T89V and K162T) in the sequence of mature protein. Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: ansB, b2957, JW2924 / Plasmid: pet22b(+) Details (production host): contains secretion sequence pelB leader Cell (production host): bacteria / Production host: ![]() ![]() #2: Chemical | ChemComp-ASP / #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.9 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Crystals were grown in 0.17 M NH4-citrate, pH 7.0, 17-18% PEG3350, 5 mM L-Asp |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Jun 22, 2018 / Details: Multilayer X-ray mirrors VariMax HF | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.85→40 Å / Num. obs: 95807 / % possible obs: 95.2 % / Redundancy: 3 % / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.028 / Rrim(I) all: 0.051 / Χ2: 0.822 / Net I/σ(I): 14 / Num. measured all: 289815 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 105.25 Å2 / Biso mean: 23.189 Å2 / Biso min: 8.21 Å2
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Refinement step | Cycle: final / Resolution: 1.85→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.846→1.894 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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