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Yorodumi- PDB-6wyz: Crystal structure of Pseudomonas 7A Glutaminase-Asparaginase (mut... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wyz | ||||||
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Title | Crystal structure of Pseudomonas 7A Glutaminase-Asparaginase (mutant K173M) in complex with D-Glu at pH 5.5 | ||||||
Components | Glutaminase-asparaginase | ||||||
Keywords | HYDROLASE / Amidohydrolase / Glutaminase-Asparaginase / L-Asn/L-Gln-Hydrolase | ||||||
Function / homology | Function and homology information glutamin-(asparagin-)ase / glutamin-(asparagin-)ase activity / asparagine metabolic process / asparaginase activity / glutaminase activity / periplasmic space / cytosol Similarity search - Function | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Strzelczyk, P. / Zhang, D. / Wlodawer, A. / Lubkowski, J. | ||||||
Funding support | United States, 1items
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Citation | Journal: Sci Rep / Year: 2020 Title: Generalized enzymatic mechanism of catalysis by tetrameric L-asparaginases from mesophilic bacteria. Authors: Strzelczyk, P. / Zhang, D. / Dyba, M. / 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 | 6wyz.cif.gz | 277.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wyz.ent.gz | 222.3 KB | Display | PDB format |
PDBx/mmJSON format | 6wyz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6wyz_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 6wyz_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6wyz_validation.xml.gz | 60.4 KB | Display | |
Data in CIF | 6wyz_validation.cif.gz | 90.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wy/6wyz ftp://data.pdbj.org/pub/pdb/validation_reports/wy/6wyz | HTTPS FTP |
-Related structure data
Related structure data | 6wywC 6wyxC 6wyyC 6wz4C 6wz6C 6wz8C 4pgaS 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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Unit cell |
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-Components
#1: Protein | Mass: 36198.008 Da / Num. of mol.: 4 / Fragment: UNP residues 26-362 / Mutation: K173M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (strain ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440) (bacteria) Strain: ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440 / Gene: ansB, PP_2453 / Plasmid: pET22b(+) / Cell (production host): Bacteria / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIPL / References: UniProt: Q88K39, glutamin-(asparagin-)ase #2: Chemical | ChemComp-DGL / #3: 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: 2.22 Å3/Da / Density % sol: 44.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1 M magnesium chloride, 50 mM Bis-Tris, pH 5.5, 20% w/v PEG3350 |
-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: Nov 3, 2019 |
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: 1.7→39.61 Å / Num. obs: 142831 / % possible obs: 99.6 % / Redundancy: 9.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.03 / Net I/σ(I): 27.4 |
Reflection shell | Resolution: 1.7→1.75 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.092 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 7101 / CC1/2: 0.66 / Rpim(I) all: 0.452 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4PGA Resolution: 1.7→39.61 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.503 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.104 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 115.53 Å2 / Biso mean: 17.784 Å2 / Biso min: 4.43 Å2
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Refinement step | Cycle: final / Resolution: 1.7→39.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.701→1.745 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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