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Yorodumi- PDB-7r6a: Crystal structure of mutant L124D/R125A/C273S of L-Asparaginase I... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7r6a | ||||||
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Title | Crystal structure of mutant L124D/R125A/C273S of L-Asparaginase I from Yersinia pestis | ||||||
Components | L-asparaginase IAsparaginase | ||||||
Keywords | HYDROLASE / L-ASPARAGINASE | ||||||
Function / homology | Function and homology information asparaginase / asparaginase activity / amino acid metabolic process / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Yersinia pestis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.89 Å | ||||||
Authors | Strzelczyk, P. / Wlodawer, A. / Lubkowski, J. | ||||||
Funding support | United States, 1items
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Citation | Journal: Febs J. / Year: 2023 Title: The dimeric form of bacterial l-asparaginase YpAI is fully active. Authors: Strzelczyk, P. / Zhang, D. / Alexandratos, J. / Piszczek, G. / Wlodawer, A. / Lubkowski, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7r6a.cif.gz | 288.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7r6a.ent.gz | 230.5 KB | Display | PDB format |
PDBx/mmJSON format | 7r6a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r6/7r6a ftp://data.pdbj.org/pub/pdb/validation_reports/r6/7r6a | HTTPS FTP |
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-Related structure data
Related structure data | 7r69C 7r6bC 3ntxS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Refine code: 0
NCS ensembles :
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-Components
#1: Protein | Mass: 36732.418 Da / Num. of mol.: 4 / Mutation: L124D, R125A, C273S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: ansA, YPO2161 / Plasmid: pET22b(+) / Cell (production host): Bacteria / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIPL / References: UniProt: A0A3N4B0Q2, asparaginase #2: Chemical | ChemComp-FMT / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.4 Å3/Da / Density % sol: 48.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7 / Details: 3.5 M Sodium formate, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 19, 2020 |
Radiation | Monochromator: Double crystal - liquid nitrogen cooled Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→50 Å / Num. obs: 113101 / % possible obs: 99.1 % / Redundancy: 7.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.035 / Net I/σ(I): 22.8 |
Reflection shell | Resolution: 1.89→1.92 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.718 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 5625 / CC1/2: 0.783 / Rpim(I) all: 0.311 / % possible all: 99.9 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3NTX Resolution: 1.89→40.88 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.11 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.13 / 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: 126.51 Å2 / Biso mean: 23.776 Å2 / Biso min: 9.31 Å2
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Refinement step | Cycle: final / Resolution: 1.89→40.88 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 1.89→1.936 Å / Rfactor Rfree error: 0
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