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Yorodumi- PDB-7qyx: Structure of E.coli Class 2 L-asparaginase EcAIII, mutant RDM1-24... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qyx | ||||||
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Title | Structure of E.coli Class 2 L-asparaginase EcAIII, mutant RDM1-24 (R207A, D210S, S211T) | ||||||
Components |
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Keywords | HYDROLASE / L-asparaginase / mutation | ||||||
Function / homology | Function and homology information beta-aspartyl-peptidase / asparagine catabolic process via L-aspartate / asparaginase / asparaginase activity / beta-aspartyl-peptidase activity / protein autoprocessing / hydrolase activity / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Loch, J.I. / Klonecka, A. / Kadziolka, K. / Bonarek, P. / Barciszewski, J. / Imiolczyk, B. / Brzezinski, K. / Jaskolski, M. | ||||||
Funding support | Poland, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2022 Title: Structural and biophysical studies of new L-asparaginase variants: lessons from random mutagenesis of the prototypic Escherichia coli Ntn-amidohydrolase. Authors: Loch, J.I. / Klonecka, A. / Kadziolka, K. / Bonarek, P. / Barciszewski, J. / Imiolczyk, B. / Brzezinski, K. / 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 | 7qyx.cif.gz | 199.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qyx.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7qyx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qyx_validation.pdf.gz | 447.6 KB | Display | wwPDB validaton report |
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Full document | 7qyx_full_validation.pdf.gz | 448.8 KB | Display | |
Data in XML | 7qyx_validation.xml.gz | 22.9 KB | Display | |
Data in CIF | 7qyx_validation.cif.gz | 32.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qy/7qyx ftp://data.pdbj.org/pub/pdb/validation_reports/qy/7qyx | HTTPS FTP |
-Related structure data
Related structure data | 7qq8C 7qsfC 7qtcC 7qvrC 7qy6C 7qymC 7r1gC 7r5cC 2zalS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
Experimental dataset #1 | Data reference: 10.18150/6OXPLO / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Refine code: 1
NCS ensembles :
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-Components
#1: Protein | Mass: 19013.773 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: iaaA, spt, ybiK, b0828, JW0812 / Plasmid: pET11d / Production host: Escherichia coli (E. coli) / Strain (production host): BL 21 Gold / References: UniProt: P37595, beta-aspartyl-peptidase #2: Protein | Mass: 14328.045 Da / Num. of mol.: 2 / Mutation: R207A, D210S, S211T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: iaaA, BG821_004768, BMC79_000629, D3822_09905, FJQ51_03270, GQW68_09230, NCTC9044_04106, NCTC9702_03859 Plasmid: pET11d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold References: UniProt: A0A3A6SJA6, beta-aspartyl-peptidase, asparaginase #3: Chemical | #4: Chemical | #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: 2.06 Å3/Da / Density % sol: 40.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 20% PEG 6K; 15% PEG 400; 0.2M MgCl2 in 0.1 Tris-HCl pH 8.5 |
-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: 0.7749 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 21, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7749 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→52.335 Å / Num. obs: 48066 / % possible obs: 98.4 % / Redundancy: 13.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.119 / Rrim(I) all: 0.118 / Net I/σ(I): 15.16 |
Reflection shell | Resolution: 1.85→1.95 Å / Redundancy: 12.4 % / Rmerge(I) obs: 2.141 / Mean I/σ(I) obs: 1.75 / Num. unique obs: 7553 / CC1/2: 0.789 / Rrim(I) all: 1.852 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ZAL Resolution: 1.85→52.335 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / SU B: 8.13 / SU ML: 0.112 / Cross valid method: FREE R-VALUE / ESU R: 0.14 / ESU R Free: 0.134 Details: Hydrogens have been added in their 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: 32.827 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→52.335 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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