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- PDB-1mb2: Crystal Structure of Tryptophanyl-tRNA Synthetase Complexed with ... -

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Basic information

Entry
Database: PDB / ID: 1mb2
TitleCrystal Structure of Tryptophanyl-tRNA Synthetase Complexed with Tryptophan in an Open Conformation
ComponentsTRYPTOPHAN-TRNA LIGASE
KeywordsLIGASE / Aminoacyl-tRNA Synthetase / Rossmann fold / amino acid binding site
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
TRYPTOPHAN / Tryptophan--tRNA ligase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 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)224,57912
Polymers223,3546
Non-polymers1,2256
Water00
1
A: TRYPTOPHAN-TRNA LIGASE
D: TRYPTOPHAN-TRNA LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8604
Polymers74,4512
Non-polymers4082
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-25 kcal/mol
Surface area27020 Å2
MethodPISA
2
B: TRYPTOPHAN-TRNA LIGASE
E: TRYPTOPHAN-TRNA LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8604
Polymers74,4512
Non-polymers4082
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-33 kcal/mol
Surface area28400 Å2
MethodPISA
3
C: TRYPTOPHAN-TRNA LIGASE
F: TRYPTOPHAN-TRNA LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8604
Polymers74,4512
Non-polymers4082
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-24 kcal/mol
Surface area27030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)228.730, 92.240, 157.590
Angle α, β, γ (deg.)90.00, 132.71, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
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-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C11H12N2O2

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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: 55 %
Crystal growTemperature: 310 K / Method: microdialysis / pH: 6.6
Details: potassium phosphate, l-tryptophan, pH 6.6, MICRODIALYSIS, temperature 310K
Crystal grow
*PLUS
Temperature: 42 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
14 mg/mlprotein11
22 Mpotassium phosphate12pH6.6
32 mMTrp12

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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: 2.585→15.024 Å / Num. obs: 55705 / % possible obs: 83.1 % / Rsym value: 0.071
Reflection shellResolution: 2.7→2.8 Å / % possible all: 50.4
Reflection
*PLUS
Highest resolution: 2.7 Å / Num. measured all: 120955 / Rmerge(I) obs: 0.079
Reflection shell
*PLUS
% possible obs: 50.4 %

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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: 2.7→14.98 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.254 5594 10.1 %RANDOM
Rwork0.22 ---
all-58869 --
obs-55411 83.9 %-
Displacement parametersBiso mean: 49.4 Å2
Baniso -1Baniso -2Baniso -3
1-7.2 Å20 Å210.2 Å2
2---5.4 Å20 Å2
3----1.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.6 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 2.7→14.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15378 0 90 0 15468
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_mcbond_it1.791.5
X-RAY DIFFRACTIONc_mcangle_it3.192
X-RAY DIFFRACTIONc_scbond_it2.262
X-RAY DIFFRACTIONc_scangle_it3.772.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.365 647 10 %
Rwork0.341 5837 -
obs-5837 59.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ltr_xplor.paramltr_xplor.top
Refinement
*PLUS
Lowest resolution: 15 Å / Num. reflection obs: 49817 / % reflection Rfree: 10 % / Rfactor Rfree: 0.243 / Rfactor Rwork: 0.173
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.02
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.94

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