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- PDB-3fhj: Independent saturation of three TrpRS subsites generates a partia... -

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Basic information

Entry
Database: PDB / ID: 3fhj
TitleIndependent saturation of three TrpRS subsites generates a partially-assembled state similar to those observed in molecular simulations
ComponentsTryptophanyl-tRNA synthetase
KeywordsTRANSLATION / ligand-dependent domain rearrangement / mechanistic pathway / molecular simulations / Aminoacyl-tRNA synthetase / ATP-binding / Cytoplasm / Ligase / Nucleotide-binding / Protein biosynthesis
Function / homology
Function and homology information


tryptophan-tRNA ligase / tryptophanyl-tRNA aminoacylation / tryptophan-tRNA ligase activity / ATP binding / cytosol
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 ...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
ADENOSINE MONOPHOSPHATE / PHOSPHATE ION / TRYPTOPHAN / Tryptophan--tRNA ligase
Similarity search - Component
Biological speciesBacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsLaowanapiban, P. / Kapustina, M. / Vonrhein, C. / Delarue, M. / Koehl, P. / Carter Jr., C.W.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2009
Title: Independent saturation of three TrpRS subsites generates a partially assembled state similar to those observed in molecular simulations.
Authors: Laowanapiban, P. / Kapustina, M. / Vonrhein, C. / Delarue, M. / Koehl, P. / Carter, C.W.
History
DepositionDec 9, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 22, 2017Group: Database references / Category: pdbx_database_related
Revision 1.3Jan 22, 2020Group: Database references / Derived calculations
Category: pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_ref_seq_dif
Item: _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _struct_ref_seq_dif.details
Revision 1.4Sep 6, 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: Tryptophanyl-tRNA synthetase
D: Tryptophanyl-tRNA synthetase
B: Tryptophanyl-tRNA synthetase
C: Tryptophanyl-tRNA synthetase
E: Tryptophanyl-tRNA synthetase
F: Tryptophanyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,23324
Polymers223,3546
Non-polymers3,87918
Water00
1
A: Tryptophanyl-tRNA synthetase
B: Tryptophanyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7448
Polymers74,4512
Non-polymers1,2936
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6040 Å2
ΔGint-40 kcal/mol
Surface area26420 Å2
MethodPISA
2
D: Tryptophanyl-tRNA synthetase
C: Tryptophanyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7448
Polymers74,4512
Non-polymers1,2936
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6030 Å2
ΔGint-37 kcal/mol
Surface area24800 Å2
MethodPISA
3
E: Tryptophanyl-tRNA synthetase
F: Tryptophanyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7448
Polymers74,4512
Non-polymers1,2936
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-38 kcal/mol
Surface area25750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)223.606, 91.989, 158.322
Angle α, β, γ (deg.)90.00, 134.01, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Tryptophanyl-tRNA synthetase / Tryptophan--tRNA ligase / TrpRS


Mass: 37225.672 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus stearothermophilus (bacteria) / Strain: NC1500 / Gene: trpS / Plasmid: PET42 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P00953, tryptophan-tRNA ligase
#2: Chemical
ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C11H12N2O2
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM

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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: 2.63 Å3/Da / Density % sol: 53.22 %
Crystal growTemperature: 315 K / pH: 6.58
Details: 2.28M K2HPO4, 0.6% (v/v) PEG 400, pH 6.58, dialysis, temperature 315K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Sep 1, 2006
RadiationMonochromator: APS SERCAT 22ID BEAMLINE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→25 Å / Num. obs: 161648 / % possible obs: 97.6 % / Observed criterion σ(I): 3 / Redundancy: 3.48 % / Biso Wilson estimate: 52.66 Å2 / Rmerge(I) obs: 0.081
Reflection shellResolution: 2.65→2.85 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 4.22 / % possible all: 77.5

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.006data extraction
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FI0

3fi0


Resolution: 2.65→25 Å / Occupancy max: 1 / Occupancy min: 0.33
Isotropic thermal model: We alternated the use of TLS refinement in REFMAC5 and mapping these parameters to individual isotropic B-values, which were fixed in coordinate refinements with Buster 2.0.
Cross valid method: THROUGHOUT / σ(F): 1.5 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.27 3680 -RANDOM
Rwork0.2 ---
obs0.21 157769 92.5 %-
all-70313 --
Displacement parametersBiso mean: 63.5 Å2
Refinement stepCycle: LAST / Resolution: 2.65→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14035 0 168 0 14203
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.039
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg3.132
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.893
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.585
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.206
X-RAY DIFFRACTIONr_gen_planes_refined
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.56 Å
RfactorNum. reflection% reflection
Rfree0.435 152 -
Rwork0.331 --
obs--52.65 %

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