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- PDB-1x56: Crystal structure of asparaginyl-tRNA synthetase from Pyrococcus ... -

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Basic information

Entry
Database: PDB / ID: 1x56
TitleCrystal structure of asparaginyl-tRNA synthetase from Pyrococcus horikoshii
ComponentsAsparaginyl-tRNA synthetase
KeywordsLIGASE / aminoacyl-trna synthetase / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
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 speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsIwasaki, W. / Sekine, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structural Basis of the Water-assisted Asparagine Recognition by Asparaginyl-tRNA Synthetase.
Authors: Iwasaki, W. / Sekine, S. / Kuroishi, C. / Kuramitsu, S. / Shirouzu, M. / Yokoyama, S.
History
DepositionMay 15, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 23, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 25, 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: Asparaginyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)50,2291
Polymers50,2291
Non-polymers00
Water3,819212
1
A: Asparaginyl-tRNA synthetase

A: Asparaginyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)100,4572
Polymers100,4572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area8180 Å2
ΔGint-49 kcal/mol
Surface area33620 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)126.122, 68.597, 75.641
Angle α, β, γ (deg.)90.00, 117.05, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1053-

HOH

21A-1462-

HOH

DetailsThe second part of the biological assembly is generated by the two fold axis: -x, y, -z.

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Components

#1: Protein Asparaginyl-tRNA synthetase / Asparagine-tRNA ligase / AsnRS


Mass: 50228.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: O57980, asparagine-tRNA ligase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Nov 30, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. all: 39880 / Num. obs: 39362 / % possible obs: 98.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4 %
Reflection shellResolution: 1.98→2.05 Å / Redundancy: 3.4 % / % possible all: 91.6

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Processing

Software
NameVersionClassification
REFMAC5.1.9999refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1B8A

1b8a


Resolution: 1.98→34.3 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.739 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21158 1970 5 %RANDOM
Rwork0.1769 ---
obs0.17865 37391 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.684 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å2-0.06 Å2
2--0.15 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.98→34.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3444 0 0 212 3656
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223532
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5781.9544780
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.425415
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.12623.81168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.97515633
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3981524
X-RAY DIFFRACTIONr_chiral_restr0.1080.2511
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022665
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.21505
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2241
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1510.283
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1250.230
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1321.52177
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.77523389
X-RAY DIFFRACTIONr_scbond_it2.82331602
X-RAY DIFFRACTIONr_scangle_it4.234.51391
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.975→2.027 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.29 102
Rwork0.265 2069

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