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- PDB-2zzf: Crystal structure of alanyl-tRNA synthetase without oligomerizati... -

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Basic information

Entry
Database: PDB / ID: 2zzf
TitleCrystal structure of alanyl-tRNA synthetase without oligomerization domain
ComponentsAlanyl-tRNA synthetase
KeywordsLIGASE / hydrolase
Function / homology
Function and homology information


alanine-tRNA ligase / alanine-tRNA ligase activity / alanyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / tRNA binding / zinc ion binding / ATP binding / cytoplasm
Similarity search - Function
Alanine-tRNA ligase, archaea / Elongation Factor Tu (Ef-tu); domain 3 - #130 / Replication Terminator Protein; Chain A, domain 2 - #20 / Threonyl-trna Synthetase; Chain A, domain 2 / Replication Terminator Protein; Chain A, domain 2 / Alanine-tRNA ligase, class IIc / Alanine-tRNA ligase, class IIc, anti-codon-binding domain superfamily / : / Alanyl-tRNA synthetase, class IIc, N-terminal / Alanyl-tRNA synthetase, class IIc, core domain ...Alanine-tRNA ligase, archaea / Elongation Factor Tu (Ef-tu); domain 3 - #130 / Replication Terminator Protein; Chain A, domain 2 - #20 / Threonyl-trna Synthetase; Chain A, domain 2 / Replication Terminator Protein; Chain A, domain 2 / Alanine-tRNA ligase, class IIc / Alanine-tRNA ligase, class IIc, anti-codon-binding domain superfamily / : / Alanyl-tRNA synthetase, class IIc, N-terminal / Alanyl-tRNA synthetase, class IIc, core domain / tRNA synthetases class II (A) / Alanyl-transfer RNA synthetases family profile. / Threonyl-tRNA Synthetase; Chain A, domain 2 / Threonyl and Alanyl tRNA synthetase second additional domain / Threonyl/alanyl tRNA synthetase, SAD / Threonyl and Alanyl tRNA synthetase second additional domain / DHHA1 domain / DHHA1 domain / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Elongation Factor Tu (Ef-tu); domain 3 / Translation protein, beta-barrel domain superfamily / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Alanine--tRNA ligase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsSokabe, M. / Ose, T. / Tokunaga, K. / Nakamura, A. / Nureki, O. / Yao, M. / Tanaka, I.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: The structure of alanyl-tRNA synthetase with editing domain.
Authors: Sokabe, M. / Ose, T. / Nakamura, A. / Tokunaga, K. / Nureki, O. / Yao, M. / Tanaka, I.
History
DepositionFeb 10, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alanyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9913
Polymers86,8601
Non-polymers1312
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)164.258, 98.840, 72.927
Angle α, β, γ (deg.)90.000, 108.640, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Alanyl-tRNA synthetase / Alanine-tRNA ligase / AlaRS


Mass: 86859.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: alaS, PH0297, PH0297 / Plasmid: pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-codonplus-RIL / References: UniProt: O58035, alanine-tRNA ligase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 3.23 Å3/Da / Density % sol: 61.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.6
Details: PEG6000, MES, succinic acid, glucose, pH 5.6, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 5, 2006 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 5.3 % / Av σ(I) over netI: 44.06 / Rmerge(I) obs: 0.05 / Χ2: 1.88 / D res high: 2.7 Å / D res low: 50 Å / Num. obs: 29921 / % possible obs: 98.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.81509810.0373.5265.3
4.625.8199.910.0382.75.4
4.034.6210010.042.4115.6
3.664.0310010.0492.1065.6
3.43.6610010.0641.8635.6
3.23.410010.0931.4785.7
3.043.210010.1371.2345.6
2.913.0410010.2041.075.5
2.82.9198.510.2611.0284.8
2.72.888.110.2860.9634
ReflectionResolution: 2.7→50 Å / Num. obs: 29921 / % possible obs: 98.5 % / Redundancy: 5.3 % / Biso Wilson estimate: 85.4 Å2 / Rmerge(I) obs: 0.05 / Χ2: 1.881 / Net I/σ(I): 44.059
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.7-2.840.28626670.96388.1
2.8-2.914.80.26129741.02898.5
2.91-3.045.50.20430211.07100
3.04-3.25.60.13730211.234100
3.2-3.45.70.09330291.478100
3.4-3.665.60.06430351.863100
3.66-4.035.60.04930182.106100
4.03-4.625.60.0430422.411100
4.62-5.815.40.03830642.799.9
5.81-505.30.03730503.52698

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.5 Å32.36 Å
Translation3.5 Å32.36 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RIQ, 1V7O

1riq

1v7o


Resolution: 2.7→30.15 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.92 / Occupancy max: 1 / Occupancy min: 1 / SU B: 27.928 / SU ML: 0.264 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.643 / ESU R Free: 0.333 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: Used TLS refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.263 1506 5 %RANDOM
Rwork0.206 ---
obs0.208 29902 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 128.79 Å2 / Biso mean: 75.929 Å2 / Biso min: 54.34 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å2-0.2 Å2
2--0.27 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.7→30.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5926 0 2 14 5942
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0226065
X-RAY DIFFRACTIONr_angle_refined_deg1.4541.978187
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.215725
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.54223.333279
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.599151126
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3011548
X-RAY DIFFRACTIONr_chiral_restr0.1060.2886
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024539
X-RAY DIFFRACTIONr_nbd_refined0.2180.22589
X-RAY DIFFRACTIONr_nbtor_refined0.3130.24116
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2166
X-RAY DIFFRACTIONr_metal_ion_refined0.0020.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1520.217
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1240.26
X-RAY DIFFRACTIONr_mcbond_it0.6741.53725
X-RAY DIFFRACTIONr_mcangle_it1.16225881
X-RAY DIFFRACTIONr_scbond_it1.56632667
X-RAY DIFFRACTIONr_scangle_it2.6314.52306
LS refinement shellResolution: 2.702→2.772 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.455 87 -
Rwork0.336 1807 -
all-1894 -
obs--85.86 %

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