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- PDB-1d2r: 2.9 A CRYSTAL STRUCTURE OF LIGAND-FREE TRYPTOPHANYL-TRNA SYNTHETA... -

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Basic information

Entry
Database: PDB / ID: 1d2r
Title2.9 A CRYSTAL STRUCTURE OF LIGAND-FREE TRYPTOPHANYL-TRNA SYNTHETASE: DOMAIN MOVEMENTS FRAGMENT THE ADENINE NUCLEOTIDE BINDING SITE.
ComponentsPROTEIN (TRYPTOPHANYL TRNA SYNTHETASE)
KeywordsLIGASE / CLASS I TRNA SYNTHETASE / AARS / INDUCED FIT / TRPRS
Function / homology
Function and homology information


tryptophan-tRNA ligase / tryptophan-tRNA ligase activity / tryptophanyl-tRNA aminoacylation / ATP binding / cytoplasm
Similarity search - Function
Tryptophan-tRNA ligase, bacterial-type / Tryptophan-tRNA ligase / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / HUPs / Rossmann-like alpha/beta/alpha sandwich fold ...Tryptophan-tRNA ligase, bacterial-type / Tryptophan-tRNA ligase / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Tryptophan--tRNA ligase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.9 Å
AuthorsIlyin, V.A. / Carter Jr., C.W.
CitationJournal: Protein Sci. / Year: 2000
Title: 2.9 A crystal structure of ligand-free tryptophanyl-tRNA synthetase: domain movements fragment the adenine nucleotide binding site.
Authors: Ilyin, V.A. / Temple, B. / Hu, M. / Li, G. / Yin, Y. / Vachette, P. / Carter Jr., C.W.
History
DepositionSep 27, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 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
Revision 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Feb 7, 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: PROTEIN (TRYPTOPHANYL TRNA SYNTHETASE)
B: PROTEIN (TRYPTOPHANYL TRNA SYNTHETASE)
C: PROTEIN (TRYPTOPHANYL TRNA SYNTHETASE)
D: PROTEIN (TRYPTOPHANYL TRNA SYNTHETASE)
E: PROTEIN (TRYPTOPHANYL TRNA SYNTHETASE)
F: PROTEIN (TRYPTOPHANYL TRNA SYNTHETASE)


Theoretical massNumber of molelcules
Total (without water)220,5076
Polymers220,5076
Non-polymers00
Water0
1
A: PROTEIN (TRYPTOPHANYL TRNA SYNTHETASE)
D: PROTEIN (TRYPTOPHANYL TRNA SYNTHETASE)


Theoretical massNumber of molelcules
Total (without water)73,5022
Polymers73,5022
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-23 kcal/mol
Surface area27560 Å2
MethodPISA
2
B: PROTEIN (TRYPTOPHANYL TRNA SYNTHETASE)
E: PROTEIN (TRYPTOPHANYL TRNA SYNTHETASE)


Theoretical massNumber of molelcules
Total (without water)73,5022
Polymers73,5022
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-23 kcal/mol
Surface area27610 Å2
MethodPISA
3
C: PROTEIN (TRYPTOPHANYL TRNA SYNTHETASE)
F: PROTEIN (TRYPTOPHANYL TRNA SYNTHETASE)


Theoretical massNumber of molelcules
Total (without water)73,5022
Polymers73,5022
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-23 kcal/mol
Surface area27610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)226.760, 91.660, 156.970
Angle α, β, γ (deg.)90.00, 132.66, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
PROTEIN (TRYPTOPHANYL TRNA SYNTHETASE) / TRPRS


Mass: 36751.090 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Geobacillus stearothermophilus (bacteria) / References: UniProt: P00953, tryptophan-tRNA ligase

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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: 2.72 Å3/Da / Density % sol: 54.76 %
Crystal growTemperature: 315 K / Method: microdialysis / pH: 6.8
Details: 2.0 M K2HPO4 , pH 6.8, MICRODIALYSIS, temperature 315K
Crystal grow
*PLUS
Components of the solutions
*PLUS
Conc.: 2.0 M / Common name: potassium phosphate

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→18 Å / Num. obs: 38244 / Redundancy: 1.8 % / Biso Wilson estimate: 45.6 Å2 / Rmerge(I) obs: 0.091
Reflection
*PLUS
% possible obs: 75 %
Reflection shell
*PLUS
% possible obs: 55 %

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Processing

Software
NameVersionClassification
RSREFmodel building
MICEmodel building
CNS0.9refinement
DENZOdata reduction
RSREFphasing
MICEphasing
RefinementResolution: 2.9→10 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2395488.35 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1929 5 %RANDOM
Rwork0.237 ---
obs0.237 38244 74.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.32 Å2 / ksol: 0.348 e/Å3
Displacement parametersBiso mean: 49.6 Å2
Baniso -1Baniso -2Baniso -3
1-9.88 Å20 Å214.23 Å2
2---7.04 Å20 Å2
3----2.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.41 Å
Luzzati d res low-10 Å
Luzzati sigma a0.57 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 2.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15480 0 0 0 15480
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_mcbond_it2.11.5
X-RAY DIFFRACTIONc_mcangle_it3.652
X-RAY DIFFRACTIONc_scbond_it2.772
X-RAY DIFFRACTIONc_scangle_it4.572.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.327 201 4.6 %
Rwork0.344 4172 -
obs--51.2 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PA / Topol file: PROTEIN.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.25 / Rfactor Rfree: 0.28
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 49.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.14
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.84
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.327 / % reflection Rfree: 4.6 % / Rfactor Rwork: 0.344

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