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Yorodumi- PDB-6v2b: Complex of double mutant (T89V,K162T) of E. coli L-asparaginase I... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6v2b | ||||||
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Title | Complex of double mutant (T89V,K162T) of E. coli L-asparaginase II with L-Asn | ||||||
Components | L-asparaginase 2 | ||||||
Keywords | HYDROLASE / L-asparagine hydrolase / anti-cancer drug / inactive mutant | ||||||
Function / homology | Function and homology information asparagine catabolic process / asparaginase / asparaginase activity / outer membrane-bounded periplasmic space / protein homotetramerization / protein-containing complex / identical protein binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Lubkowski, J. / Wlodawer, A. | ||||||
Citation | Journal: Biochemistry / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6v2b.cif.gz | 263.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6v2b.ent.gz | 210.1 KB | Display | PDB format |
PDBx/mmJSON format | 6v2b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v2/6v2b ftp://data.pdbj.org/pub/pdb/validation_reports/v2/6v2b | HTTPS FTP |
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-Related structure data
Related structure data | 6v23C 6v24C 6v25C 6v26C 6v27C 6v28C 6v29C 6v2aC 6v2cC 6v2gC 3ecaS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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: 35556.828 Da / Num. of mol.: 4 / Mutation: T89V, K162T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: ansB, b2957, JW2924 / Plasmid: pET22b(+) 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: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): JC2 / References: UniProt: P00805, asparaginase #2: Chemical | ChemComp-ASN / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.74 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: Crystals grown at 0.17 M sodium citrate (pH 6) and 17-18% (w/v) PEG3350. Soaked for 1-2 minutes (empirically determined for each crystal) in equivalent solution with 0.025% (w/v) ...Details: Crystals grown at 0.17 M sodium citrate (pH 6) and 17-18% (w/v) PEG3350. Soaked for 1-2 minutes (empirically determined for each crystal) in equivalent solution with 0.025% (w/v) glutaraldehyde. Finally transferred and soaked for 10-20 sec in solution containing 40% (w/v) PEG3350, 5 mM L-Asn, and 0.17 M sodium citrate (pH 5.5) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 16, 2017 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: 1.5418 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.05→40 Å / Num. obs: 70596 / % possible obs: 95.7 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.033 / Rrim(I) all: 0.057 / Χ2: 0.863 / Net I/σ(I): 12.5 / Num. measured all: 199695 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3eca Resolution: 2.05→26.55 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.196 / SU ML: 0.111 / SU R Cruickshank DPI: 0.2147 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.215 / ESU R Free: 0.171 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: 104.25 Å2 / Biso mean: 28.11 Å2 / Biso min: 12.89 Å2
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Refinement step | Cycle: final / Resolution: 2.05→26.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.103 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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