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- PDB-7r6a: Crystal structure of mutant L124D/R125A/C273S of L-Asparaginase I... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7r6a | ||||||
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Title | Crystal structure of mutant L124D/R125A/C273S of L-Asparaginase I from Yersinia pestis | ||||||
![]() | L-asparaginase I | ||||||
![]() | HYDROLASE / L-ASPARAGINASE | ||||||
Function / homology | ![]() asparaginase / asparaginase activity / amino acid metabolic process / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Strzelczyk, P. / Wlodawer, A. / Lubkowski, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The dimeric form of bacterial l-asparaginase YpAI is fully active. Authors: Strzelczyk, P. / Zhang, D. / Alexandratos, J. / Piszczek, G. / Wlodawer, A. / Lubkowski, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 288.9 KB | Display | ![]() |
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PDB format | ![]() | 230.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 461.6 KB | Display | ![]() |
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Full document | ![]() | 474 KB | Display | |
Data in XML | ![]() | 60.2 KB | Display | |
Data in CIF | ![]() | 91.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7r69C ![]() 7r6bC ![]() 3ntxS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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Components
#1: Protein | Mass: 36732.418 Da / Num. of mol.: 4 / Mutation: L124D, R125A, C273S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-FMT / #3: 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: 2.4 Å3/Da / Density % sol: 48.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7 / Details: 3.5 M Sodium formate, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 19, 2020 |
Radiation | Monochromator: Double crystal - liquid nitrogen cooled Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→50 Å / Num. obs: 113101 / % possible obs: 99.1 % / Redundancy: 7.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.035 / Net I/σ(I): 22.8 |
Reflection shell | Resolution: 1.89→1.92 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.718 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 5625 / CC1/2: 0.783 / Rpim(I) all: 0.311 / % possible all: 99.9 |
-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 3NTX Resolution: 1.89→40.88 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.11 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 126.51 Å2 / Biso mean: 23.776 Å2 / Biso min: 9.31 Å2
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Refinement step | Cycle: final / Resolution: 1.89→40.88 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 1.89→1.936 Å / Rfactor Rfree error: 0
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