+Open data
-Basic information
Entry | Database: PDB / ID: 6pac | ||||||
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Title | E. coli L-asparaginase II in complex with L-Asp at pH 5.6 | ||||||
Components | L-asparaginase 2 | ||||||
Keywords | HYDROLASE / inactive mutant / hydrolysis of L-asparagine | ||||||
Function / homology | Function and homology information 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 | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å | ||||||
Authors | Lubkowski, J. / Wlodawer, A. | ||||||
Citation | Journal: Protein Sci. / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6pac.cif.gz | 286.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6pac.ent.gz | 236.3 KB | Display | PDB format |
PDBx/mmJSON format | 6pac.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6pac_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 6pac_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 6pac_validation.xml.gz | 63.2 KB | Display | |
Data in CIF | 6pac_validation.cif.gz | 98.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pa/6pac ftp://data.pdbj.org/pub/pdb/validation_reports/pa/6pac | HTTPS FTP |
-Related structure data
Related structure data | 6pa2C 6pa3C 6pa4C 6pa5C 6pa6C 6pa8C 6pa9C 6paaC 6pabC 6paeC C: citing same article (ref.) |
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Similar structure data |
-Links
-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
#1: Protein | Mass: 35701.965 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Expressed variant contains 8 additional N-terminal residues MDHHHHHH (affinity tag) Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: ansB, b2957, JW2924 / Plasmid: pET22b(+) Details (production host): contains secretion sequence pelB leader Cell (production host): bacteria / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): JC2 strain lacking in ansA / References: UniProt: P00805, asparaginase #2: Chemical | ChemComp-ASP / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.27 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: Crystals were grown in 0.17 M NH4-citrate, pH 5.6, 17-18% PEG3350, then soaked for 1 min in solution with 5 mM L-Asp |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Jun 24, 2018 / Details: Multilayer 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 |
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Reflection | Resolution: 1.6→40 Å / Num. obs: 135099 / % possible obs: 88 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.019 / Rpim(I) all: 0.013 / Rrim(I) all: 0.024 / Χ2: 0.712 / Net I/σ(I): 21 / Num. measured all: 337531 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→40 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.962 / WRfactor Rfree: 0.1582 / WRfactor Rwork: 0.1205 / FOM work R set: 0.8932 / SU B: 1.588 / SU ML: 0.054 / SU R Cruickshank DPI: 0.0807 / SU Rfree: 0.0856 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.086 / 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: 104.77 Å2 / Biso mean: 20.616 Å2 / Biso min: 5.78 Å2
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Refinement step | Cycle: final / Resolution: 1.6→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.641 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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