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- PDB-1t3m: Structure of the isoaspartyl peptidase with L-asparaginase activi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1t3m | ||||||
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Title | Structure of the isoaspartyl peptidase with L-asparaginase activity from E. coli | ||||||
![]() | (Putative L-asparaginase) x 2 | ||||||
![]() | HYDROLASE / TYPE III L-ASPARAGINASE / PLANT-TYPE ASPARAGINASE / ISOASPARTYL PEPTIDASE | ||||||
Function / homology | ![]() beta-aspartyl-peptidase / asparagine catabolic process via L-aspartate / asparaginase activity / beta-aspartyl-peptidase activity / protein autoprocessing / hydrolase activity / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Prahl, A. / Pazgier, M. / Hejazi, M. / Lockau, W. / Lubkowski, J. | ||||||
![]() | ![]() Title: Structure of the isoaspartyl peptidase with L-asparaginase activity from Escherichia coli. Authors: Prahl, A. / Pazgier, M. / Hejazi, M. / Lockau, W. / 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 | ![]() | 140.3 KB | Display | ![]() |
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PDB format | ![]() | 106.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 458.3 KB | Display | ![]() |
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Full document | ![]() | 464 KB | Display | |
Data in XML | ![]() | 31.7 KB | Display | |
Data in CIF | ![]() | 46.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ayyS 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
#1: Protein | Mass: 18882.576 Da / Num. of mol.: 2 / Fragment: N-TERMINAL RESIDUES 1-177 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 14895.645 Da / Num. of mol.: 2 / Fragment: C-TERMINAL RESIDUES 178-320 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.21 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 15% PEG4000, 15% GLYCEROL, 0.3 M MAGNESIUM NITRATE, 0.1 M BIS-TRIS-HCL, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→30 Å / Num. obs: 84176 / % possible obs: 98.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.01 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 1.97 / % possible all: 97.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1AYY Resolution: 1.65→10 Å / Num. parameters: 20273 / Num. restraintsaints: 17952 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56. ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.024.
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Refine analyze | Num. disordered residues: 21 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 4852.6 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→10 Å
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Refine LS restraints |
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