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- PDB-7qym: Structure of E.coli Class 2 L-asparaginase EcAIII, mutant RDM1-18... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7qym | ||||||
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Title | Structure of E.coli Class 2 L-asparaginase EcAIII, mutant RDM1-18 (R207V, D210P, S211W) | ||||||
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![]() | HYDROLASE / L-asparaginase / mutation | ||||||
Function / homology | ![]() beta-aspartyl-peptidase / asparagine catabolic process via L-aspartate / asparaginase activity / beta-aspartyl-peptidase activity / protein autoprocessing / hydrolase activity / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Loch, J.I. / Klonecka, A. / Kadziolka, K. / Bonarek, P. / Barciszewski, J. / Imiolczyk, B. / Brzezinski, K. / Jaskolski, M. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 245.5 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452.1 KB | Display | ![]() |
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Full document | ![]() | 456.7 KB | Display | |
Data in XML | ![]() | 29.7 KB | Display | |
Data in CIF | ![]() | 44.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7qq8C ![]() 7qsfC ![]() 7qtcC ![]() 7qvrC ![]() 7qy6C ![]() 7qyxC ![]() 7r1gC ![]() 7r5cC ![]() 2zalS C: citing same article ( S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
Experimental dataset #1 | Data reference: ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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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.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 14451.242 Da / Num. of mol.: 2 / Mutation: R207V, D210P, S211W Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: iaaA, BH692_00390, EA435_03160, ELT72_09480, ELV13_05050, ELV22_03305, ELX56_08605, ELX68_03450, ELX70_05465, ELX79_08565, ELX83_03275, ELY23_01235, ELY24_20545, ELY50_10250, EPS76_07410, FNJ67_ ...Gene: iaaA, BH692_00390, EA435_03160, ELT72_09480, ELV13_05050, ELV22_03305, ELX56_08605, ELX68_03450, ELX70_05465, ELX79_08565, ELX83_03275, ELY23_01235, ELY24_20545, ELY50_10250, EPS76_07410, FNJ67_18185, G3565_10375, G6P89_17140, GRC73_03160, GUI33_12170, HIE29_000291 Plasmid: pET11d / Production host: ![]() ![]() #3: Chemical | #4: Chemical | ChemComp-CL / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.22 % |
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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: ![]() ![]() ![]() |
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: 1.2→66.896 Å / Num. obs: 167749 / % possible obs: 98.1 % / Redundancy: 13.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.085 / Rrim(I) all: 0.088 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 1.2→1.22 Å / Redundancy: 13.2 % / Rmerge(I) obs: 1.786 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 8018 / CC1/2: 0.556 / Rrim(I) all: 1.857 / % possible all: 95.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2ZAL Resolution: 1.2→66.896 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.978 / SU B: 1.638 / SU ML: 0.03 / Cross valid method: FREE R-VALUE / ESU R: 0.032 / ESU R Free: 0.032
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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: 19.234 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→66.896 Å
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Refine LS restraints |
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LS refinement shell |
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