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- PDB-1g51: ASPARTYL TRNA SYNTHETASE FROM THERMUS THERMOPHILUS AT 2.4 A RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1g51
TitleASPARTYL TRNA SYNTHETASE FROM THERMUS THERMOPHILUS AT 2.4 A RESOLUTION
ComponentsASPARTYL-TRNA SYNTHETASE
KeywordsLIGASE / aminoacyl tRNA synthetase
Function / homology
Function and homology information


aspartate-tRNA ligase / aspartyl-tRNA aminoacylation / aspartate-tRNA ligase activity / nucleic acid binding / ATP binding / cytoplasm
Similarity search - Function
GAD-like domain / : / : / Aspartate-tRNA ligase, type 1 / GAD domain / GAD domain / GAD-like domain superfamily / Aspartyl/Asparaginyl-tRNA synthetase, class IIb / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) ...GAD-like domain / : / : / Aspartate-tRNA ligase, type 1 / GAD domain / GAD domain / GAD-like domain superfamily / 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. / Gyrase A; domain 2 / 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
ASPARTYL-ADENOSINE-5'-MONOPHOSPHATE / ADENOSINE MONOPHOSPHATE / Aspartate--tRNA(Asp) ligase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsPoterzsman, A. / Delarue, M. / Thierry, J.C. / Moras, D.
CitationJournal: J.Mol.Biol. / Year: 1994
Title: Synthesis and recognition of aspartyl-adenylate by Thermus thermophilus aspartyl-tRNA synthetase.
Authors: Poterszman, A. / Delarue, M. / Thierry, J.C. / Moras, D.
History
DepositionOct 30, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: ASPARTYL-TRNA SYNTHETASE
B: ASPARTYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,7147
Polymers132,2502
Non-polymers1,4645
Water12,052669
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13540 Å2
ΔGint-71 kcal/mol
Surface area46480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.135, 155.500, 171.145
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit consists of chains A and B

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Components

#1: Protein ASPARTYL-TRNA SYNTHETASE


Mass: 66124.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P36419, aspartate-tRNA ligase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-AMO / ASPARTYL-ADENOSINE-5'-MONOPHOSPHATE


Mass: 462.309 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H19N6O10P
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 669 / 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: 3.02 Å3/Da / Density % sol: 59.32 %
Crystal growTemperature: 271 K / Method: vapor diffusion, hanging drop / pH: 7
Details: ammonium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 271.0K
Crystal grow
*PLUS
pH: 7.5 / Details: seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
22 Msodium formate1drop
350 mMTris-HCl1drop
450 mMTris-HCl1drop
52 Msodium formate1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.901
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.901 Å / Relative weight: 1
ReflectionResolution: 2.6→11.5 Å / Num. all: 63386 / Num. obs: 60454 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 3.11 % / Biso Wilson estimate: 24.5 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 22.15
Reflection shellResolution: 2.4→2.45 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.285 / Num. unique all: 3736 / % possible all: 87.6
Reflection shell
*PLUS
% possible obs: 87.6 %

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Processing

Software
NameClassification
CNSrefinement
XDSdata reduction
AUTOMARdata reduction
CNSphasing
RefinementResolution: 2.4→14 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1079648.19 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.251 4443 7.7 %RANDOM
Rwork0.194 ---
all0.199 63312 --
obs0.194 57893 91.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.8 Å2 / ksol: 0.364 e/Å3
Displacement parametersBiso mean: 39.8 Å2
Baniso -1Baniso -2Baniso -3
1-10.25 Å20 Å20 Å2
2---9.75 Å20 Å2
3----0.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.4→14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9336 0 95 669 10100
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_improper_angle_d1.2
X-RAY DIFFRACTIONc_mcbond_it1.411.5
X-RAY DIFFRACTIONc_mcangle_it2.42
X-RAY DIFFRACTIONc_scbond_it1.992
X-RAY DIFFRACTIONc_scangle_it3.012.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.299 635 7.5 %
Rwork0.256 7791 -
obs--81.2 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.2

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