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- PDB-4lns: Crystal structure of Asparagine synthetase A (AsnA) from Trypanos... -

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Basic information

Entry
Database: PDB / ID: 4lns
TitleCrystal structure of Asparagine synthetase A (AsnA) from Trypanosoma brucei
ComponentsAsparagine synthetase a
KeywordsLIGASE / Asparagine synthetase A
Function / homology
Function and homology information


aspartate-ammonia ligase / aspartate-ammonia ligase activity / : / ATP binding / cytosol
Similarity search - Function
Aspartate--ammonia ligase / Aspartate-ammonia ligase / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Asparagine synthetase a, putative
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKhan, S. / Madhubala, R. / Sharma, A.
CitationJournal: 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
DepositionJul 12, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Asparagine synthetase a


Theoretical massNumber of molelcules
Total (without water)39,6491
Polymers39,6491
Non-polymers00
Water2,468137
1
A: Asparagine synthetase a

A: Asparagine synthetase a


Theoretical massNumber of molelcules
Total (without water)79,2992
Polymers79,2992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area4130 Å2
ΔGint-37 kcal/mol
Surface area26450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.550, 71.550, 268.631
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Asparagine synthetase a


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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.86 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.976 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 7, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.2→25 Å / Num. obs: 21721 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.2428 1105 5.1 %Random
Rwork0.2012 ---
obs0.2033 21648 99.63 %-
all-22753 --
Solvent computationShrinkage 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 parametersBiso max: 101.2 Å2 / Biso mean: 40.4514 Å2 / Biso min: 20.11 Å2
Baniso -1Baniso -2Baniso -3
1-2.9975 Å2-0 Å2-0 Å2
2--2.9975 Å2-0 Å2
3----5.995 Å2
Refinement stepCycle: LAST / Resolution: 2.2→24.647 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2382 0 0 137 2519
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082426
X-RAY DIFFRACTIONf_angle_d1.1693281
X-RAY DIFFRACTIONf_dihedral_angle_d16.185893
X-RAY DIFFRACTIONf_chiral_restr0.084375
X-RAY DIFFRACTIONf_plane_restr0.005418
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1997-2.29970.27711190.21762537100
2.2997-2.42090.28061220.21372499100
2.4209-2.57240.31371490.21552508100
2.5724-2.77080.27721490.20622510100
2.7708-3.04920.24091410.19922536100
3.0492-3.48930.2471420.18732573100
3.4893-4.39210.21521500.1834257699
4.3921-24.64820.22811330.2148280499

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