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Yorodumi- PDB-4lns: Crystal structure of Asparagine synthetase A (AsnA) from Trypanos... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lns | ||||||
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Title | Crystal structure of Asparagine synthetase A (AsnA) from Trypanosoma brucei | ||||||
Components | Asparagine synthetase a | ||||||
Keywords | LIGASE / Asparagine synthetase A | ||||||
Function / homology | Function and homology information aspartate-ammonia ligase / aspartate-ammonia ligase activity / asparagine biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | Trypanosoma brucei brucei (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Khan, S. / Madhubala, R. / Sharma, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Identification and functional characterization of a novel bacterial type asparagine synthetase A: a tRNA synthetase paralog from Leishmania donovani. Authors: Manhas, R. / Tripathi, P. / Khan, S. / Sethu Lakshmi, B. / Lal, S.K. / Gowri, V.S. / Sharma, A. / Madhubala, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lns.cif.gz | 75 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lns.ent.gz | 56.5 KB | Display | PDB format |
PDBx/mmJSON format | 4lns.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ln/4lns ftp://data.pdbj.org/pub/pdb/validation_reports/ln/4lns | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 39649.344 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / Gene: Tb927.7.1110 / Production host: Escherichia coli (E. coli) / References: UniProt: Q57WT9, aspartate-ammonia ligase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10% w/v PEG 20000, 20% v/v PEG MME 550, 0.03M of each NPS (sodium nitrate, disodium hydrogen phosphate, ammonium sulfate), 0.1M MOPS/HEPES-Na, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.976 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 7, 2013 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→25 Å / Num. obs: 21721 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.2→2.24 Å / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→24.647 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8257 / SU ML: 0.59 / σ(F): 1.34 / Phase error: 23.06 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.433 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 101.2 Å2 / Biso mean: 40.4514 Å2 / Biso min: 20.11 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→24.647 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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