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

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Basic information

Entry
Database: PDB / ID: 1maw
TitleCrystal Structure of Tryptophanyl-tRNA Synthetase Complexed with ATP in an Open Conformation
ComponentsTRYPTOPHAN-TRNA LIGASETryptophan—tRNA ligase
KeywordsLIGASE / Amino-acyl tRNA synthetase / Rossmann fold / atp binding site
Function / homology
Function and homology information


tryptophan-tRNA ligase / tryptophan-tRNA ligase activity / tryptophanyl-tRNA aminoacylation / 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 / 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 / Tryptophan--tRNA ligase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 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: 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 / 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: TRYPTOPHAN-TRNA LIGASE
B: TRYPTOPHAN-TRNA LIGASE
C: TRYPTOPHAN-TRNA LIGASE
D: TRYPTOPHAN-TRNA LIGASE
E: TRYPTOPHAN-TRNA LIGASE
F: TRYPTOPHAN-TRNA LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,39712
Polymers223,3546
Non-polymers3,0436
Water0
1
A: TRYPTOPHAN-TRNA LIGASE
D: TRYPTOPHAN-TRNA LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,4664
Polymers74,4512
Non-polymers1,0142
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5670 Å2
ΔGint-25 kcal/mol
Surface area27030 Å2
MethodPISA
2
B: TRYPTOPHAN-TRNA LIGASE
E: TRYPTOPHAN-TRNA LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,4664
Polymers74,4512
Non-polymers1,0142
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5530 Å2
ΔGint-26 kcal/mol
Surface area27180 Å2
MethodPISA
3
C: TRYPTOPHAN-TRNA LIGASE
F: TRYPTOPHAN-TRNA LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,4664
Polymers74,4512
Non-polymers1,0142
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint-26 kcal/mol
Surface area27060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)228.550, 91.980, 156.890
Angle α, β, γ (deg.)90.00, 132.34, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
TRYPTOPHAN-TRNA LIGASE / Tryptophan—tRNA ligase / Tryptophanyl-tRNA Synthetase


Mass: 37225.672 Da / Num. of mol.: 6
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-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*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: 2.73 Å3/Da / Density % sol: 54.91 %
Crystal growTemperature: 310 K / Method: microdialysis / pH: 6.6
Details: potassium phosphate, mg-atp, pH 6.6, MICRODIALYSIS, temperature 310K
Crystal grow
*PLUS
Temperature: 42 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
14 mg/mlprotein11
22 Mpotassium phosphate12pH6.6
31 mMATP12
420 mM12MgCl2

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS II / 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: 2.99→15.05 Å / Num. obs: 42607 / % possible obs: 87.1 % / Biso Wilson estimate: 48.3 Å2 / Rsym value: 0.079
Reflection
*PLUS
Highest resolution: 3 Å / % possible obs: 87.3 % / Num. measured all: 102635 / Rmerge(I) obs: 0.079
Reflection shell
*PLUS
Highest resolution: 3 Å / Lowest resolution: 3.11 Å / % possible obs: 70.5 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1D2R

1d2r


Resolution: 3→15 Å / Rfactor Rfree error: 0.004 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.253 4285 -RANDOM
Rwork0.218 ---
all-42607 --
obs-42471 88.4 %-
Displacement parametersBiso mean: 41.1 Å2
Baniso -1Baniso -2Baniso -3
1-5.85 Å20 Å211.88 Å2
2---4.63 Å20 Å2
3----1.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.59 Å0.58 Å
Refinement stepCycle: LAST / Resolution: 3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15378 0 186 0 15564
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d1.05
X-RAY DIFFRACTIONc_mcbond_it1.71.5
X-RAY DIFFRACTIONc_mcangle_it3.012
X-RAY DIFFRACTIONc_scbond_it2.412
X-RAY DIFFRACTIONc_scangle_it3.782.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.328 591 9.8 %
Rwork0.324 5435 -
obs-5435 75.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2atp_xplor.paramatp_xplor_top
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 15 Å / Num. reflection obs: 38186 / % reflection Rfree: 10 % / Rfactor Rfree: 0.239 / Rfactor Rwork: 0.154
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.36
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.05

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