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- PDB-1mau: Crystal structure of Tryptophanyl-tRNA Synthetase Complexed with ... -

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Basic information

Entry
Database: PDB / ID: 1mau
TitleCrystal structure of Tryptophanyl-tRNA Synthetase Complexed with ATP and Tryptophanamide in a Pre-Transition state Conformation
Componentstryptophan-tRNA ligaseTryptophan—tRNA ligase
KeywordsLIGASE / Amino-acyl tRNA synthetase / Rossmann fold / atp binding site / pre-transition state
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
ADENOSINE-5'-TRIPHOSPHATE / CITRIC ACID / L-TRYPTOPHANAMIDE / Tryptophan--tRNA ligase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SIR / Resolution: 2.15 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
DepositionAug 2, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Feb 14, 2024Group: 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 / 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.ptnr1_label_seq_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.ptnr3_label_seq_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.ptnr1_label_seq_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_conn.ptnr2_label_seq_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)38,4529
Polymers37,2261
Non-polymers1,2268
Water2,144119
1
A: tryptophan-tRNA ligase
hetero molecules

A: tryptophan-tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,90418
Polymers74,4512
Non-polymers2,45216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area9150 Å2
ΔGint-69 kcal/mol
Surface area26170 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

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Protein , 1 types, 1 molecules A

#1: Protein tryptophan-tRNA ligase / 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

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Non-polymers , 7 types, 127 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-LTN / L-TRYPTOPHANAMIDE


Mass: 203.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H13N3O
#6: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.82 Å3/Da / Density % sol: 56.42 %
Crystal growTemperature: 310 K / Method: microdialysis / pH: 7.5
Details: sodium citrate, magnesium chloride, sodium ATP , l-tryptophanamide, 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 RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. all: 25809 / Num. obs: 23318 / % possible obs: 90.5 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 35.5 Å2 / Rsym value: 0.079 / Net I/σ(I): 16
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.75 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 1933 / Rsym value: 0.32 / % possible all: 77.5
Reflection
*PLUS
Lowest resolution: 25 Å / Num. measured all: 335452 / Rmerge(I) obs: 0.079
Reflection shell
*PLUS
% possible obs: 77.5 % / Rmerge(I) obs: 0.32

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
BUSTER-TNTrefinement
RefinementMethod to determine structure: SIR
Starting model: PDB ENTRY 1M83

1m83


Resolution: 2.15→20 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.243 2254 10 %random
Rwork0.208 ---
all0.212 24050 --
obs0.212 22227 --
Refinement stepCycle: LAST / Resolution: 2.15→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2605 0 79 119 2803
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.00627452
X-RAY DIFFRACTIONt_angle_deg0.97436982
X-RAY DIFFRACTIONt_dihedral_angle_d17.04816110
X-RAY DIFFRACTIONt_trig_c_planes0.009902
X-RAY DIFFRACTIONt_gen_planes0.0154535
X-RAY DIFFRACTIONt_it1.363274620
X-RAY DIFFRACTIONt_nbd1.1761305
X-RAY DIFFRACTIONt_incorr_chiral_ct0
Refinement
*PLUS
Num. reflection obs: 19973 / % reflection Rfree: 10 % / Rfactor Rfree: 0.244 / Rfactor Rwork: 0.209
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_angle_deg0.975
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg17.0480

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