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- PDB-1i6m: 1.7 HIGH RESOLUTION EXPERIMENTAL PHASES FOR TRYPTOPHANYL-TRNA SYN... -

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Basic information

Entry
Database: PDB / ID: 1i6m
Title1.7 HIGH RESOLUTION EXPERIMENTAL PHASES FOR TRYPTOPHANYL-TRNA SYNTHETASE COMPLEXED WITH TRYPTOPHANYL-5'AMP
ComponentsTRYPTOPHANYL- ...
KeywordsLIGASE / CLASS I TRNA SYNTHETASE / AARS / INDUCED FIT / TRPRS
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
AMMONIUM ION / TRYPTOPHANYL-5'AMP / Tryptophan--tRNA ligase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.72 Å
AuthorsRetailleau, P. / Carter, C.W.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2001
Title: High-resolution experimental phases for tryptophanyl-tRNA synthetase (TrpRS) complexed with tryptophanyl-5'AMP.
Authors: Retailleau, P. / Yin, Y. / Hu, M. / Roach, J. / Bricogne, G. / Vonrhein, C. / Roversi, P. / Blanc, E. / Sweet, R.M. / Carter, C.W.
History
DepositionMar 2, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: TRYPTOPHANYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,81814
Polymers37,2261
Non-polymers1,59213
Water5,675315
1
A: TRYPTOPHANYL-TRNA SYNTHETASE
hetero molecules

A: TRYPTOPHANYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,63628
Polymers74,4512
Non-polymers3,18526
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area10810 Å2
ΔGint-192 kcal/mol
Surface area25460 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)59.770, 59.770, 232.650
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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TRYPTOPHANYL- ... , 1 types, 1 molecules A

#1: Protein TRYPTOPHANYL-TRNA SYNTHETASE / TRPRS


Mass: 37225.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Geobacillus stearothermophilus (bacteria) / References: UniProt: P00953, tryptophan-tRNA ligase

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Non-polymers , 5 types, 328 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NH4 / AMMONIUM ION / Ammonium


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#4: Chemical ChemComp-TYM / TRYPTOPHANYL-5'AMP


Mass: 533.431 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H24N7O8P
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 315 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.47 %
Crystal growTemperature: 310 K / Method: microdialysis / pH: 7.6
Details: POTASSIUM PHOSPHATE, AMMONIUM SULFATE, MAGNESIUM SULFATE, pH 7.60, MICRODIALYSIS, temperature 310.0K
Crystal grow
*PLUS
Temperature: 310 K / pH: 7.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12 mMtryptophan11
210 mMATP11
310 mMmagnesium11
42.0 Mpotassium phosphate12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.0, 0.978, 0.979, 0.985
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Jun 1, 1998
RadiationProtocol: MULTIPLE WAVELENGTHS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.9781
30.9791
40.9851
ReflectionResolution: 1.72→25 Å / Num. obs: 45713 / % possible obs: 83.4 % / Redundancy: 4.9 % / Rsym value: 0.042 / Net I/σ(I): 15.9
Reflection shellResolution: 1.72→1.78 Å / Mean I/σ(I) obs: 3.1 / Rsym value: 0.315 / % possible all: 75.7
Reflection
*PLUS
Num. measured all: 332053 / Rmerge(I) obs: 0.042
Reflection shell
*PLUS
% possible obs: 75.7 % / Rmerge(I) obs: 0.315

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Processing

Software
NameClassification
SHARPphasing
BUSTER-TNTrefinement
DENZOdata reduction
SCALEPACKdata scaling
BUSTER-TNTphasing
RefinementMethod to determine structure: MIRAS / Resolution: 1.72→13 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.257 3745 10 %
Rwork0.225 --
all-38006 -
obs-38006 83.3 %
Refinement stepCycle: LAST / Resolution: 1.72→13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2590 0 97 315 3002
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0228030.8
X-RAY DIFFRACTIONt_angle_deg1.49237791.3
X-RAY DIFFRACTIONt_dihedral_angle_d15.54816350
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_trig_c_planes0.012882
X-RAY DIFFRACTIONt_gen_planes0.0184325
X-RAY DIFFRACTIONt_it1.63273420
X-RAY DIFFRACTIONt_nbd0.0274810
Software
*PLUS
Name: BUSTER/TNT / Classification: refinement
Refinement
*PLUS
Lowest resolution: 13 Å / Num. reflection obs: 29968 / σ(I): 3 / % reflection Rfree: 10 % / Rfactor all: 0.225 / Rfactor obs: 0.209
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_planar_d0.0122
X-RAY DIFFRACTIONt_plane_restr0.0185

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