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- PDB-1i6k: 1.7 HIGH RESOLUTION EXPERIMENTAL PHASES FOR TRYPTOPHANYL-TRNA SYN... -

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Basic information

Entry
Database: PDB / ID: 1i6k
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 / tryptophanyl-tRNA aminoacylation / tryptophan-tRNA ligase activity / 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 ...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 / MULTIPLE ANOMALOUS Dispersion / 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 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: TRYPTOPHANYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,28714
Polymers37,6951
Non-polymers1,59213
Water6,612367
1
A: TRYPTOPHANYL-TRNA SYNTHETASE
hetero molecules

A: TRYPTOPHANYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,57428
Polymers75,3892
Non-polymers3,18526
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area11000 Å2
ΔGint-188 kcal/mol
Surface area25130 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: 37694.621 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, 380 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


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


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


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


Mass: 18.015 Da / Num. of mol.: 367 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.42 Å3/Da / Density % sol: 48.87 %
Crystal growTemperature: 310 K / Method: microdialysis / pH: 7.6
Details: POTASSIUM PHOSPHATE, AMMONIUM SULFATE, MAGNESIUM CHLORIDE, PEG 400, pH 7.60, MICRODIALYSIS, temperature 310K
Crystal grow
*PLUS
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: 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
10.9781
20.9791
30.9851
ReflectionResolution: 1.72→25 Å / Num. obs: 546675 / % possible obs: 94.5 % / Redundancy: 4.8 % / Rsym value: 0.083 / Net I/σ(I): 6.1
Reflection
*PLUS
Num. obs: 46732 / Redundancy: 2.43 % / Num. measured all: 546675 / Rmerge(I) obs: 0.083
Reflection shell
*PLUS
% possible obs: 80.9 % / Rmerge(I) obs: 0.354

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Processing

Software
NameClassification
SHARPphasing
BUSTER-TNTrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MULTIPLE ANOMALOUS Dispersion
Resolution: 1.72→19.94 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.268 4451 10 %
Rwork0.233 --
all-45151 -
obs-45151 97 %
Refinement stepCycle: LAST / Resolution: 1.72→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2590 0 97 367 3054
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01927720.8
X-RAY DIFFRACTIONt_angle_deg1.36437331.3
X-RAY DIFFRACTIONt_dihedral_angle_d15.76316040
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_trig_c_planes0.011862
X-RAY DIFFRACTIONt_gen_planes0.0154275
X-RAY DIFFRACTIONt_it1.504266320
X-RAY DIFFRACTIONt_nbd0.0627910
Software
*PLUS
Name: BUSTER/TNT / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 32467 / σ(I): 3 / % reflection Rfree: 10 % / Rfactor all: 0.233 / Rfactor obs: 0.211
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_bond_d0.021
X-RAY DIFFRACTIONt_angle_deg1.418
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg15.850
X-RAY DIFFRACTIONt_planar_d0.0112
X-RAY DIFFRACTIONt_plane_restr0.0155

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