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- PDB-1o7j: Atomic resolution structure of Erwinia chrysanthemi L-asparaginase -
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Open data
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Basic information
Entry | Database: PDB / ID: 1o7j | ||||||
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Title | Atomic resolution structure of Erwinia chrysanthemi L-asparaginase | ||||||
![]() | L-ASPARAGINASE | ||||||
![]() | HYDROLASE / L-ASPARAGINASE / ATOMIC RESOLUTION | ||||||
Function / homology | ![]() asparagine metabolic process / asparaginase / asparaginase activity / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lubkowski, J. / Dauter, M. / Aghaiypour, K. / Wlodawer, A. / Dauter, Z. | ||||||
![]() | ![]() Title: Atomic Resolution Structure of Erwinia Chrysanthemi L-Asparaginase Authors: Lubkowski, J. / Dauter, M. / Aghaiypour, K. / Wlodawer, A. / Dauter, Z. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 752.6 KB | Display | ![]() |
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PDB format | ![]() | 636 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 485.9 KB | Display | ![]() |
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Full document | ![]() | 512.7 KB | Display | |
Data in XML | ![]() | 63.7 KB | Display | |
Data in CIF | ![]() | 95.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1jslS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 35123.020 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | Compound details | CONVERTS L-ASPARAGINE TO L-ASPARATE WITH THE RELEASE OF AMMONIA. AVAILABLE UNDER THE NAME ERWINASE ...CONVERTS L-ASPARAGINE | Sequence details | THE PROTEIN SEQUENCE FOLLOWS THE SEQUENCE DERIVED FROM A VARIANT STRAIN NCPPB 1125 OF ERWINIA ...THE PROTEIN SEQUENCE FOLLOWS THE SEQUENCE DERIVED FROM A VARIANT STRAIN NCPPB 1125 OF ERWINIA CHRYSANTHE | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44 % | ||||||||||||||||||||||||
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Crystal grow | pH: 8.5 / Details: AMMONIUM SULFATE, PEG 400, TRIS BUFFER PH 8.5 | ||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: vapor diffusion, hanging drop / Details: Miller, M., (1993) FEBS Lett., 328, 275. | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 10, 2000 / Details: FOCUSSING MIRROR |
Radiation | Monochromator: DOUBLE CRYSTAL SI(111) SAGITALLY FOCUSSING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1→25 Å / Num. obs: 559626 / % possible obs: 87.6 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 24.2 |
Reflection shell | Resolution: 1→1.04 Å / Redundancy: 3 % / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 3 / % possible all: 75.1 |
Reflection | *PLUS Num. measured all: 1780326 / Rmerge(I) obs: 0.05 |
Reflection shell | *PLUS Highest resolution: 1 Å / % possible obs: 75.1 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1JSL Resolution: 1→10 Å / Num. parameters: 104166 / Num. restraintsaints: 128707 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: MOEWS & KRETSINGER | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 76 / Occupancy sum hydrogen: 9277 / Occupancy sum non hydrogen: 11164.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1→10 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 25 Å / Num. reflection obs: 553402 / Rfactor Rwork: 0.1098 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: s_chiral_restr / Dev ideal: 0.099 |