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Yorodumi- PDB-8cly: Crystal structure of Rhizobium etli constitutive L-asparaginase R... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8cly | ||||||
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Title | Crystal structure of Rhizobium etli constitutive L-asparaginase ReAIV (tetragonal form R4tP) | ||||||
Components | Putative L-asparaginase II proteinAsparaginase | ||||||
Keywords | HYDROLASE / amidohydrolase / zinc binding protein / structural homology / enzymatic mechanism / enzyme kinetics / occluded water molecules | ||||||
Function / homology | L-asparaginase II / L-asparaginase II / metal ion binding / L-asparaginase II protein Function and homology information | ||||||
Biological species | Rhizobium etli (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.503 Å | ||||||
Authors | Loch, J.I. / Worsztynowicz, P. / Sliwiak, J. / Imiolczyk, B. / Grzechowiak, M. / Gilski, M. / Jaskolski, M. | ||||||
Funding support | Poland, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2023 Title: Rhizobium etli has two L-asparaginases with low sequence identity but similar structure and catalytic center. Authors: Loch, J.I. / Worsztynowicz, P. / Sliwiak, J. / Grzechowiak, M. / Imiolczyk, B. / Pokrywka, K. / Chwastyk, M. / Gilski, M. / Jaskolski, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cly.cif.gz | 233 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cly.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8cly.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cl/8cly ftp://data.pdbj.org/pub/pdb/validation_reports/cl/8cly | HTTPS FTP |
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-Related structure data
Related structure data | 8clzC 8colC 8oriC 8oswC 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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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ALA / End label comp-ID: ALA / Auth seq-ID: 2 - 335 / Label seq-ID: 8 - 341
NCS ensembles : (Details: Local NCS retraints between domains: 1 2) |
-Components
#1: Protein | Mass: 36100.387 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhizobium etli (bacteria) / Gene: RHE_CH01144 / Plasmid: pET-151D-topo / Production host: Escherichia coli (E. coli) / Strain (production host): BL 21 Gold / References: UniProt: Q2KB35 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / | #5: 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: 3.19 Å3/Da / Density % sol: 61.44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M ammonium formate, 20 % (w/v) PEG 3350, and 0.2% lauryldimethylamine oxide (LDAO) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97 Å |
Detector | Type: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Nov 23, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→88.63 Å / Num. obs: 32235 / % possible obs: 99.9 % / Redundancy: 8.82 % / Biso Wilson estimate: 44.99 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.176 / Rrim(I) all: 0.187 / Net I/σ(I): 11.41 |
Reflection shell | Resolution: 2.5→2.65 Å / Rmerge(I) obs: 1.016 / Mean I/σ(I) obs: 2.16 / Num. unique obs: 5074 / CC1/2: 0.739 / Rrim(I) all: 1.079 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.503→88.63 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.917 / SU B: 15.712 / SU ML: 0.168 / Cross valid method: FREE R-VALUE / ESU R: 0.3 / ESU R Free: 0.222
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.493 Å2
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Refinement step | Cycle: LAST / Resolution: 2.503→88.63 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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