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- PDB-1m83: Crystal Structure of Tryptophanyl-tRNA Synthetase Complexed with ... -

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Basic information

Entry
Database: PDB / ID: 1m83
TitleCrystal Structure of Tryptophanyl-tRNA Synthetase Complexed with ATP in a Closed, Pre-transition State Conformation
ComponentsTryptophan-tRNA ligase
KeywordsLIGASE / Aminoacyl-tRNA Synthetase / ATP binding site / Rossmann Fold
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-5'-TRIPHOSPHATE / Tryptophan--tRNA ligase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SIR / Resolution: 2.2 Å
AuthorsRetailleau, P. / Huang, X. / Yin, Y. / Hu, M. / Weinreb, V. / Vachette, P. / Vonrhein, C. / Bricogne, G. / Roversi, P. / Ilyin, V. / Carter Jr., C.W.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Interconversion of ATP binding and conformational free energies by tryptophanyl-tRNA synthetase: structures of ATP bound to open and closed, pre-transition-state conformations.
Authors: Retailleau, P. / Huang, X. / Yin, Y. / Hu, M. / Weinreb, V. / Vachette, P. / Vonrhein, C. / Bricogne, G. / Roversi, P. / Ilyin, V. / Carter, C.W.
History
DepositionJul 24, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Tryptophan-tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0336
Polymers37,2261
Non-polymers8085
Water3,027168
1
A: Tryptophan-tRNA ligase
hetero molecules

A: Tryptophan-tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,06712
Polymers74,4512
Non-polymers1,61610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area7930 Å2
ΔGint-35 kcal/mol
Surface area25660 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)62.133, 62.133, 217.807
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Tryptophan-tRNA ligase / Tryptophanyl-tRNA Synthetase


Mass: 37225.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: P00953, tryptophan-tRNA ligase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 310 K / Method: microdialysis / pH: 7.5
Details: sodium citrate, sodium atp, magnesium chloride, pH 7.5, MICRODIALYSIS, temperature 310K
Crystal grow
*PLUS
Temperature: 35 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14 mg/mlprotein11
20.6 Mpotassium phosphate11
350 %(v/v)glycerol11
41 Msodium citrate12
510 mMATP12
610 mM12MgCl2
750000 mMtryptophanamide12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 1, 1999
RadiationMonochromator: GRAPHITE / Protocol: SIR / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→45 Å / Num. all: 24329 / Num. obs: 19650 / % possible obs: 80.8 % / Observed criterion σ(I): -3 / Redundancy: 8.2 % / Biso Wilson estimate: 32.1 Å2 / Rsym value: 0.08 / Net I/σ(I): 10.2
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 285 / Rsym value: 0.31 / % possible all: 12.1
Reflection
*PLUS
Lowest resolution: 45 Å / Num. obs: 24329 / % possible obs: 97.5 % / Num. measured all: 303099 / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
% possible obs: 12.1 % / Rmerge(I) obs: 0.31

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
BUSTER-TNTrefinement
RefinementMethod to determine structure: SIR / Resolution: 2.2→20 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1986 -RANDOM
Rwork0.21 ---
all0.214 20306 --
obs0.214 17449 90 %-
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2613 0 50 168 2831
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg0.986
X-RAY DIFFRACTIONt_bond_d0.006
LS refinement shell
Resolution (Å)Rfactor RfreeRfactor RworkRefine-ID
2.2-2.2620.3950.251X-RAY DIFFRACTION
2.262-2.3280.3310.233X-RAY DIFFRACTION
2.328-2.4080.2490.181X-RAY DIFFRACTION
2.408-2.5870.2550.196X-RAY DIFFRACTION
2.587-2.8120.2450.194X-RAY DIFFRACTION
2.812-3.1090.2260.194X-RAY DIFFRACTION
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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