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- PDB-6v25: Complex of mutant (K162M) of E. coli L-asparaginase II with L-Asp -
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Open data
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Basic information
Entry | Database: PDB / ID: 6v25 | ||||||
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Title | Complex of mutant (K162M) of E. coli L-asparaginase II with L-Asp | ||||||
![]() | (L-asparaginase 2) x 2 | ||||||
![]() | HYDROLASE / L-asparagine hydrolase / anti-cancer drug / inactive mutant | ||||||
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: Mechanism of Catalysis by l-Asparaginase. Authors: Lubkowski, J. / Vanegas, J. / Chan, W.K. / Lorenzi, P.L. / Weinstein, J.N. / Sukharev, S. / Fushman, D. / Rempe, S. / Anishkin, A. / 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 | ![]() | 286.1 KB | Display | ![]() |
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PDB format | ![]() | 226 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 992.7 KB | Display | ![]() |
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Full document | ![]() | 1004.7 KB | Display | |
Data in XML | ![]() | 62 KB | Display | |
Data in CIF | ![]() | 94.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6v23C ![]() 6v24C ![]() 6v26C ![]() 6v27C ![]() 6v28C ![]() 6v29C ![]() 6v2aC ![]() 6v2bC ![]() 6v2cC ![]() 6v2gC ![]() 3ecaS S: Starting model for refinement 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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Unit cell |
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Components
#1: Protein | Mass: 35588.895 Da / Num. of mol.: 2 / Mutation: K162M 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 / Production host: ![]() ![]() #2: Protein | Mass: 35703.980 Da / Num. of mol.: 2 / Mutation: K162M 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 / Production host: ![]() ![]() #3: Chemical | #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: 2.02 Å3/Da / Density % sol: 39.03 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: 0.1 M sodium acetate, pH 5.2, 5 mM L-Asp, and 18-20% (w/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 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: 1.78→40 Å / Num. obs: 102698 / % possible obs: 94.3 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.024 / Rpim(I) all: 0.017 / Rrim(I) all: 0.029 / Χ2: 0.736 / Net I/σ(I): 21.3 / Num. measured all: 288124 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3eca Resolution: 1.78→24.61 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.179 / WRfactor Rwork: 0.1263 / FOM work R set: 0.8695 / SU B: 2.699 / SU ML: 0.083 / SU R Cruickshank DPI: 0.114 / SU Rfree: 0.1194 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.114 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 120.4 Å2 / Biso mean: 29.504 Å2 / Biso min: 8 Å2
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Refinement step | Cycle: final / Resolution: 1.78→24.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.78→1.826 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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