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Yorodumi- PDB-7ou1: Crystal structure of Rhizobium etli inducible L-asparaginase ReAV... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ou1 | ||||||
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Title | Crystal structure of Rhizobium etli inducible L-asparaginase ReAV (monoclinic form MP2) | ||||||
Components | L-asparaginaseAsparaginase | ||||||
Keywords | HYDROLASE / L-asparaginase / amidohydrolase / Rhizobium etli | ||||||
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: 1.65 Å | ||||||
Authors | Imiolczyk, B. / Loch, J.I. / Gilski, M. / Jaskolski, M. | ||||||
Funding support | Poland, 1items
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Citation | Journal: Nat Commun / Year: 2021 Title: Crystal structures of the elusive Rhizobium etli L-asparaginase reveal a peculiar active site. Authors: Loch, J.I. / Imiolczyk, B. / Sliwiak, J. / Wantuch, A. / Bejger, M. / Gilski, M. / Jaskolski, M. #1: Journal: Acta Biochim Pol / Year: 2001 Title: Sequence analysis of enzymes with asparaginase activity Authors: Borek, D. / Jaskolski, M. #2: Journal: IUCrJ / Year: 2021 Title: Structural and biophysical aspects of L-asparaginases - a growing family with amazing diversity Authors: Loch, J.I. / Jaskolski, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ou1.cif.gz | 498.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ou1.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7ou1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ou/7ou1 ftp://data.pdbj.org/pub/pdb/validation_reports/ou/7ou1 | HTTPS FTP |
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-Related structure data
Related structure data | 7os3SC 7os5C 7os6C 7oz6C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.18150/VQQIHQ / Data set type: diffraction image data / Metadata reference: 10.18150/VQQIHQ |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 1 / Auth seq-ID: 3 - 352 / Label seq-ID: 9 - 358
NCS ensembles :
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-Components
#1: Protein | Mass: 39570.867 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Class 3 (R. etli) type L-asparaginase Source: (gene. exp.) Rhizobium etli (strain CFN 42 / ATCC 51251) (bacteria) Strain: CFN 42 / ATCC 51251 / Gene: ansA, RHE_PE00350 / Plasmid: pET-151D-TOPO / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Magic / References: UniProt: Q2K0Z2 #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-EDO / | #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: 2.55 Å3/Da / Density % sol: 51.69 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 2% PEG8000, 20% PEG400, 5 mM Mg(CH3COO)2, 6 mM 3.0 mM sucrose monolaureate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.895 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 7, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.895 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→45.65 Å / Num. obs: 189888 / % possible obs: 99 % / Redundancy: 4 % / Biso Wilson estimate: 21.54 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.134 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.65→1.75 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.622 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 30255 / CC1/2: 0.795 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7OS3 Resolution: 1.65→45.65 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.928 / SU B: 5.22 / SU ML: 0.077 / Cross valid method: FREE R-VALUE / ESU R: 0.091 / ESU R Free: 0.092 / Details: Hydrogen atoms were added at riding positions
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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: 16.259 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→45.65 Å
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Refine LS restraints |
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