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Yorodumi- PDB-8col: Crystal structure of Rhizobium etli constitutive L-asparaginase R... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8col | ||||||
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Title | Crystal structure of Rhizobium etli constitutive L-asparaginase ReAIV (orthorombic form R4oP-2) | ||||||
Components | Putative L-asparaginase II proteinAsparaginase | ||||||
Keywords | HYDROLASE / L-asparaginase / Rhizobium etli / enzyme / amidohydrolase | ||||||
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 Å | ||||||
Authors | Loch, J.I. / Worsztynowicz, P. / Sliwiak, J. / Imioloczyk, 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 | 8col.cif.gz | 451.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8col.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8col.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/co/8col ftp://data.pdbj.org/pub/pdb/validation_reports/co/8col | HTTPS FTP |
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-Related structure data
Related structure data | 8clyC 8clzC 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules AAABBBCCCDDD
#1: Protein | Mass: 36116.391 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhizobium etli (bacteria) / Gene: RHE_CH01144 / Plasmid: pET151D-topo / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold / References: UniProt: Q2KB35 |
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-Non-polymers , 5 types, 901 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-EDO / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
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: 2.18 Å3/Da / Density % sol: 43.68 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M Tris pH 8.5, 0.2 M MgCl2, 17.5% PEG 8000, 0.3% dodecyl-beta-D-maltoside (DDM) |
-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 EIGER X 16M / Detector: PIXEL / Date: May 5, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2→84.6 Å / Num. obs: 86068 / % possible obs: 99.7 % / Redundancy: 5.94 % / Biso Wilson estimate: 34.76 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.135 / Rrim(I) all: 0.148 / Net I/σ(I): 10.22 |
Reflection shell | Resolution: 2→2.12 Å / Redundancy: 6.11 % / Rmerge(I) obs: 1.115 / Mean I/σ(I) obs: 1.45 / Num. unique obs: 13748 / CC1/2: 0.681 / Rrim(I) all: 1.22 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→84.599 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.944 / SU B: 12.409 / SU ML: 0.141 / Cross valid method: FREE R-VALUE / ESU R: 0.182 / ESU R Free: 0.168
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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: 31.057 Å2
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Refinement step | Cycle: LAST / Resolution: 2→84.599 Å
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Refine LS restraints |
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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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