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- PDB-7r6b: Crystal structure of mutant R43D/L124D/R125A/C273S of L-Asparagin... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7r6b | ||||||
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Title | Crystal structure of mutant R43D/L124D/R125A/C273S of L-Asparaginase I from Yersinia pestis | ||||||
![]() | L-asparaginase I![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() 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 | ![]() | 140.9 KB | Display | ![]() |
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PDB format | ![]() | 107.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7r69C ![]() 7r6aC ![]() 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: 0 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 0 / Auth seq-ID: 3 - 336 / Label seq-ID: 3 - 336
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Components
#1: Protein | ![]() Mass: 36690.309 Da / Num. of mol.: 2 / Mutation: R43D, L124D, R125A, C273S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-EDO / ![]() #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: 2.52 Å3/Da / Density % sol: 51.28 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion / pH: 8 Details: 0.2 M Calcium acetate, 10% (w/v) PEG 8000, 0.1 M Imidazole/ Hydrochloric acid, pH 8.0 |
-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: Mar 6, 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![]() |
Reflection | Resolution: 2.03→50 Å / Num. obs: 47794 / % possible obs: 98.7 % / Redundancy: 5.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.042 / Net I/σ(I): 22 |
Reflection shell | Resolution: 2.03→2.07 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2370 / CC1/2: 0.719 / Rpim(I) all: 0.47 / % possible all: 99.5 |
-Phasing
Phasing![]() | Method: ![]() |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3NTX Resolution: 2.03→48.85 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.234 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.164 / ESU R Free: 0.155 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 113.19 Å2 / Biso mean: 31.099 Å2 / Biso min: 11.55 Å2
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Refinement step | Cycle: final / Resolution: 2.03→48.85 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 8892 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.03→2.08 Å / Rfactor Rfree error: 0
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