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Yorodumi- PDB-6wyy: Crystal structure of Pseudomonas 7A Glutaminase-Asparaginase in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wyy | ||||||
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Title | Crystal structure of Pseudomonas 7A Glutaminase-Asparaginase in complex with L-Glu at pH 6.5 | ||||||
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: 1.35 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 | 6wyy.cif.gz | 538.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wyy.ent.gz | 443.2 KB | Display | PDB format |
PDBx/mmJSON format | 6wyy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6wyy_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 6wyy_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 6wyy_validation.xml.gz | 59.2 KB | Display | |
Data in CIF | 6wyy_validation.cif.gz | 89.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wy/6wyy ftp://data.pdbj.org/pub/pdb/validation_reports/wy/6wyy | HTTPS FTP |
-Related structure data
Related structure data | 6wywC 6wyxC 6wyzC 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: 36195.992 Da / Num. of mol.: 4 / Fragment: UNP residues 26-362 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) / References: UniProt: Q88K39, glutamin-(asparagin-)ase #2: Chemical | ChemComp-GLU / #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-GOL / | #5: 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: 2.54 Å3/Da / Density % sol: 51.53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 8% w/v Tacsimate, pH 6.5, 17% 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: Oct 19, 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 twin |
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Reflection | Resolution: 1.35→34.8 Å / Num. obs: 319520 / % possible obs: 96.9 % / Redundancy: 2.7 % / CC1/2: 0.973 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.033 / Net I/σ(I): 16 | |||||||||||||||
Reflection shell | Resolution: 1.35→1.39 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.547 / Mean I/σ(I) obs: 2 / Num. unique obs: 15558 / CC1/2: 0.579 / Rpim(I) all: 0.402 / % possible all: 94.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4PGA Resolution: 1.35→34.76 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.883 / SU ML: 0.018 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.009 / ESU R Free: 0.009 / 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: 76.36 Å2 / Biso mean: 15.081 Å2 / Biso min: 5.77 Å2
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Refinement step | Cycle: final / Resolution: 1.35→34.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.35→1.385 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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