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Open data
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Basic information
Entry | Database: PDB / ID: 6pa8 | ||||||
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Title | ECAII(T89V,K162T) MUTANT IN COMPLEX WITH L-ASN AT PH 7.0 | ||||||
![]() | L-asparaginase 2 | ||||||
![]() | HYDROLASE / inactive mutant / hydrolysis of L-asparagine | ||||||
Function / homology | ![]() asparagine catabolic process / asparaginase / asparaginase activity / outer membrane-bounded periplasmic space / protein homotetramerization / periplasmic space / protein-containing complex / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lubkowski, J. / Wlodawer, A. | ||||||
![]() | ![]() Title: Geometric considerations support the double-displacement catalytic mechanism of l-asparaginase. Authors: Lubkowski, J. / Wlodawer, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 273.3 KB | Display | ![]() |
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PDB format | ![]() | 226.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 57.6 KB | Display | |
Data in CIF | ![]() | 86.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6pa2C ![]() 6pa3C ![]() 6pa4C ![]() 6pa5C ![]() 6pa6C ![]() 6pa9C ![]() 6paaC ![]() 6pabC ![]() 6pacC ![]() 6paeC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 35671.914 Da / Num. of mol.: 4 / Mutation: T89V, K162T Source method: isolated from a genetically manipulated source Details: Expressed variant contains 8 additional N-terminal residues MDHHHHHH (affinity tag) and two mutations (T89V and K162T) in mature protein Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: ansB, b2957, JW2924 / Plasmid: pET22b(+) Details (production host): contains secretion sequence pelB leader Cell (production host): bacteria / Production host: ![]() ![]() |
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-Non-polymers , 6 types, 1108 molecules ![](data/chem/img/ASN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/FLC.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/FLC.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ASN / #3: Chemical | ChemComp-MG / | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-FLC / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.94 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Crystals were grown from 0.17 M NH4-citrate, pH 7.0, 17-18% PEG3350, then soaked in equivalent solution containing L-Asn at concentration 0.5 mM |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Sep 12, 2018 / Details: X-ray mirrors VariMax HF | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Multilayer X-ray mirrors VariMax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→40 Å / Num. obs: 88385 / % possible obs: 95.3 % / Redundancy: 3 % / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.029 / Rrim(I) all: 0.053 / Χ2: 0.854 / Net I/σ(I): 13.6 / Num. measured all: 262551 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() 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: 92.48 Å2 / Biso mean: 22.727 Å2 / Biso min: 10.58 Å2
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Refinement step | Cycle: final / Resolution: 1.9→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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