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- PDB-7r1g: Structure of E.coli Class 2 L-asparaginase EcAIII, mutant RDM1-38... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7r1g | ||||||
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Title | Structure of E.coli Class 2 L-asparaginase EcAIII, mutant RDM1-38 (R207C, D210S, S211V) | ||||||
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![]() | HYDROLASE / L-asparaginase / Ntn-hydrolase / EcAIII | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Loch, J.I. / Kadziolka, 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 | ![]() | 198.3 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 410.1 KB | Display | ![]() |
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Full document | ![]() | 414.3 KB | Display | |
Data in XML | ![]() | 12.8 KB | Display | |
Data in CIF | ![]() | 19.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7qq8C ![]() 7qsfC ![]() 7qtcC ![]() 7qvrC ![]() 7qy6C ![]() 7qymC ![]() 7qyxC ![]() 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: 14358.139 Da / Num. of mol.: 2 / Mutation: R207C, D210S, S211V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: iaaA, iaaA_1, A6583_11900, A9819_04170, AM340_25825, AT845_002782, B6R12_001137, B6R15_002170, B7C15_001855, B9T59_03785, BHS87_04410, BJJ90_17725, BK272_22150, BON86_21650, BON92_22175, BUE82_ ...Gene: iaaA, iaaA_1, A6583_11900, A9819_04170, AM340_25825, AT845_002782, B6R12_001137, B6R15_002170, B7C15_001855, B9T59_03785, BHS87_04410, BJJ90_17725, BK272_22150, BON86_21650, BON92_22175, BUE82_16375, BvCmsKSP076_04930, C2M16_01470, C2U48_05880, C3F40_08425, CDL37_06080, CG831_000717, CIG67_24035, CQP61_18640, CR539_08595, D3Y67_16925, D9J11_12335, D9K17_05660, DNQ45_21365, E2123_17525, E2135_02495, ELT49_19670, ELT58_16270, ExPECSC038_02859, F3N40_09450, F6U69_05970, F9400_10180, F9V07_02875, F9X20_012640, F9X20_12740, FDM60_08630, FGG80_18755, FQ021_11565, FQE77_03270, G4A38_09815, G7635_000303, GBE29_09760, GF699_09605, GJ11_04600, GKF52_09360, GKG12_09800, GQE42_02190, GQE87_02220, GQM13_17755, GRQ19_05905, H0O72_02540, HH795_002282, HIN64_003880, HJO75_000955, HJS37_002784, HMJ82_04325, HNC36_00665, HNC38_00260, HNC59_02050, HNC99_06385, HND24_01780, HNO08_00970, HNY50_16000, HNY54_13200, HV109_15925, HZ71_000057, NCTC10429_05732, NCTC8621_03538, NCTC9706_00685, NCTC9969_03483, SAMEA3472064_00385, SAMEA3752557_02250 Plasmid: pET11d / Production host: ![]() ![]() References: UniProt: A0A0K4KR53, beta-aspartyl-peptidase, asparaginase #3: Chemical | #4: 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: 2.05 Å3/Da / Density % sol: 40.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 30% PEG 4000, 0.2 M MgCl2 in 0.1M Tris-HCl pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: Agilent SuperNova / Wavelength: 1.54056 Å |
Detector | Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: May 28, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54056 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→21.131 Å / Num. obs: 38942 / % possible obs: 95.3 % / Redundancy: 2.7 % / CC1/2: 0.991 / Rmerge(I) obs: 0.099 / Rrim(I) all: 0.121 / Net I/σ(I): 7 |
Reflection shell | Resolution: 1.95→2 Å / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2596 / CC1/2: 0.741 / Rrim(I) all: 0.464 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2ZAL Resolution: 1.95→21.131 Å / Cor.coef. Fo:Fc: 0.886 / Cor.coef. Fo:Fc free: 0.848 / SU B: 11.353 / SU ML: 0.158 / Cross valid method: FREE R-VALUE / ESU R: 0.231 / ESU R Free: 0.193
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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: 15.092 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→21.131 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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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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