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Yorodumi- PDB-7os6: Crystal structure of Rhizobium etli inducible L-asparaginase ReAV... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7os6 | ||||||
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Title | Crystal structure of Rhizobium etli inducible L-asparaginase ReAV (monoclinic form MP1) | ||||||
Components | L-asparaginase | ||||||
Keywords | HYDROLASE / L-asparaginase / amidohydrolase / Rhizobium etli | ||||||
Function / homology | L-asparaginase II / L-asparaginase II / metal ion binding / ETHANOL / L-asparaginase II protein Function and homology information | ||||||
Biological species | Rhizobium etli (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å | ||||||
Authors | Loch, J.I. / Imiolczyk, B. / 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7os6.cif.gz | 518.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7os6.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7os6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7os6_validation.pdf.gz | 2.7 MB | Display | wwPDB validaton report |
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Full document | 7os6_full_validation.pdf.gz | 2.7 MB | Display | |
Data in XML | 7os6_validation.xml.gz | 64 KB | Display | |
Data in CIF | 7os6_validation.cif.gz | 98.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/os/7os6 ftp://data.pdbj.org/pub/pdb/validation_reports/os/7os6 | HTTPS FTP |
-Related structure data
Related structure data | 7os3C 7os5C 7ou1C 7oz6C C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.18150/XBX6JE / Data set type: diffraction image data / Metadata reference: 10.18150/XBX6JE |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
-Protein , 1 types, 4 molecules AAADDDBBBCCC
#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: pET151D-TOPO / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Magic / References: UniProt: Q2K0Z2 |
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-Non-polymers , 6 types, 1560 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-EDO / #5: Chemical | #6: Chemical | ChemComp-EOH / | #7: Water | ChemComp-HOH / | |
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-Details
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: 2.6 Å3/Da / Density % sol: 52.1 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 25% PEG3350, 0.2 M Li2SO4, 0.1 M Tris pH 8.0, 20 mM n-octyl-beta-D-thioglucoside |
-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: 0.9763 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 7, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.43→77.22 Å / Num. obs: 287575 / % possible obs: 99.3 % / Redundancy: 4.1 % / Biso Wilson estimate: 22.93 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.073 / Rrim(I) all: 0.084 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 1.43→1.52 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.818 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 45258 / CC1/2: 0.671 / Rrim(I) all: 0.952 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: XXXX Resolution: 1.43→77.22 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.439 / SU ML: 0.04 / Cross valid method: FREE R-VALUE / ESU R: 0.051 / ESU R Free: 0.053 / 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: 18.944 Å2
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Refinement step | Cycle: LAST / Resolution: 1.43→77.22 Å
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Refine LS restraints |
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