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- PDB-5zg8: Crystal Structure of TtNRS -

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Basic information

Entry
Database: PDB / ID: 5zg8
TitleCrystal Structure of TtNRS
ComponentsAsparagine--tRNA ligase
KeywordsLIGASE / GlnRS / QRS / Synthetase
Function / homology
Function and homology information


asparagine-tRNA ligase / asparagine-tRNA ligase activity / asparaginyl-tRNA aminoacylation / nucleic acid binding / ATP binding / cytoplasm
Similarity search - Function
Asparagine-tRNA ligase / Aspartyl/Asparaginyl-tRNA synthetase, class IIb / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. ...Asparagine-tRNA ligase / Aspartyl/Asparaginyl-tRNA synthetase, class IIb / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / 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) / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Asparagine--tRNA ligase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsMutharasappan, N. / Jain, V. / Sharma, A. / Manickam, Y. / Jeyaraman, J.
CitationJournal: To be published
Title: Crystal Structure of TtNRS
Authors: Mutharasappan, N. / Jain, V. / Sharma, A. / Manickam, Y. / Jeyaraman, J.
History
DepositionMar 8, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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--tRNA ligase


Theoretical massNumber of molelcules
Total (without water)50,8591
Polymers50,8591
Non-polymers00
Water2,774154
1
A: Asparagine--tRNA ligase

A: Asparagine--tRNA ligase


Theoretical massNumber of molelcules
Total (without water)101,7182
Polymers101,7182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area7390 Å2
ΔGint-48 kcal/mol
Surface area32910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.294, 67.294, 189.117
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Asparagine--tRNA ligase


Mass: 50858.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P54263, asparagine-tRNA ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Source detailsAuthors state that the source of the protein is "Thermus thermophilus". Meanwhile, according to the ...Authors state that the source of the protein is "Thermus thermophilus". Meanwhile, according to the reference sequence, the source is "Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)".

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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: 2.43 Å3/Da / Density % sol: 49.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M Ammonium sulfate, 0.1M Sodium cacodylate trihydrate pH 6.5, 30%(w/v) Polyethylene glycol 8,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.976 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.399→36.761 Å / Num. obs: 19150 / % possible obs: 94.7 % / Redundancy: 11.1 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 7.48
Reflection shellResolution: 2.399→2.44 Å / Rmerge(I) obs: 0.571 / Num. unique obs: 993

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
AMoREphasing
REFMAC1.8.4_1496refinement
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1X54

1x54


Resolution: 2.4→2.44 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.21
RfactorNum. reflection% reflection
Rfree0.2086 976 5.1 %
Rwork0.1551 --
obs0.1579 19150 94.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 130.61 Å2 / Biso mean: 34.1817 Å2 / Biso min: 16.35 Å2
Refinement stepCycle: final / Resolution: 2.4→2.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3420 0 0 154 3574
Biso mean---36.68 -
Num. residues----422
LS refinement shellResolution: 2.399→2.5255 Å /
RfactorNum. reflection
Rfree0.267 103
Rwork0.1821 1748
Refinement TLS params.Method: refined / Origin x: 27.1372 Å / Origin y: -12.2581 Å / Origin z: -28.443 Å
111213212223313233
T0.1785 Å20.0045 Å20.0165 Å2-0.2149 Å20.0277 Å2--0.2373 Å2
L0.2335 °20.1327 °20.1288 °2-0.4417 °20.2236 °2--1.2587 °2
S0.0211 Å °-0.0053 Å °-0.0262 Å °0.046 Å °-0.0339 Å °0.0092 Å °0.0641 Å °-0.1098 Å °0.0024 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 438
2X-RAY DIFFRACTION1allA501 - 654

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