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- PDB-5ekd: Human mitochondrial tryptophanyl-tRNA synthetase bound by indolmy... -

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Basic information

Entry
Database: PDB / ID: 5ekd
TitleHuman mitochondrial tryptophanyl-tRNA synthetase bound by indolmycin and Mn*ATP.
ComponentsTryptophan--tRNA ligase, mitochondrial
KeywordsLIGASE/ANTIBIOTIC / TrpRS / indolmycin / mitochondrial / complex / LIGASE-ANTIBIOTIC complex
Function / homology
Function and homology information


mitochondrial tryptophanyl-tRNA aminoacylation / Mitochondrial tRNA aminoacylation / tryptophan-tRNA ligase / tryptophan-tRNA ligase activity / tryptophanyl-tRNA aminoacylation / tRNA aminoacylation for protein translation / vasculogenesis / mitochondrial matrix / mitochondrion / nucleoplasm ...mitochondrial tryptophanyl-tRNA aminoacylation / Mitochondrial tRNA aminoacylation / tryptophan-tRNA ligase / tryptophan-tRNA ligase activity / tryptophanyl-tRNA aminoacylation / tRNA aminoacylation for protein translation / vasculogenesis / mitochondrial matrix / mitochondrion / nucleoplasm / ATP binding / plasma membrane
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
Chem-5BX / ADENOSINE-5'-TRIPHOSPHATE / : / Tryptophan--tRNA ligase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsWilliams, T.L. / Carter Jr., C.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM40906 United States
CitationJournal: To Be Published
Title: Binding of Mg2+ATP Enhances Inhibition of Human Mitochondrial Tryptophanyl-tRNA Synthetase by Indolmycin
Authors: Williams, T.L. / Carter Jr., C.W.
History
DepositionNov 3, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2016Group: Structure summary
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_special_symmetry / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tryptophan--tRNA ligase, mitochondrial
B: Tryptophan--tRNA ligase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,02112
Polymers76,0882
Non-polymers1,93310
Water9,746541
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6470 Å2
ΔGint-41 kcal/mol
Surface area26330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.289, 78.087, 153.996
Angle α, β, γ (deg.)90.00, 96.55, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-404-

MN

21B-404-

MN

31A-755-

HOH

41A-778-

HOH

51B-703-

HOH

61B-739-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Tryptophan--tRNA ligase, mitochondrial / (Mt)TrpRS / Tryptophanyl-tRNA synthetase / TrpRS


Mass: 38043.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WARS2 / Plasmid: pet28 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UGM6, tryptophan-tRNA ligase

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Non-polymers , 5 types, 551 molecules

#2: Chemical ChemComp-5BX / (5S)-5-[(1R)-1-(1H-indol-3-yl)ethyl]-2-(methylamino)-1,3-oxazol-4(5H)-one / Indolemycin / Indolmycin


Mass: 257.288 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H15N3O2
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 541 / 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: 2.29 Å3/Da / Density % sol: 46.26 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: sodium acetate, glycerol, peg 5000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.82→29.06 Å / Num. all: 139667 / Num. obs: 60563 / % possible obs: 98.5 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 8.1
Reflection shellResolution: 1.82→1.885 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.594 / Mean I/σ(I) obs: 1.5 / % possible all: 94.08

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
SCALAdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DK4

5dk4


Resolution: 1.82→29.06 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2071 3070 5.07 %
Rwork0.1701 --
obs0.172 60550 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.82→29.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5125 0 116 541 5782
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045380
X-RAY DIFFRACTIONf_angle_d0.9127314
X-RAY DIFFRACTIONf_dihedral_angle_d17.3822050
X-RAY DIFFRACTIONf_chiral_restr0.047849
X-RAY DIFFRACTIONf_plane_restr0.004905
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8198-1.84820.32311140.28342282X-RAY DIFFRACTION88
1.8482-1.87850.29261310.26512720X-RAY DIFFRACTION99
1.8785-1.91090.30481390.26152553X-RAY DIFFRACTION99
1.9109-1.94560.30251420.24572676X-RAY DIFFRACTION99
1.9456-1.9830.27821410.22212560X-RAY DIFFRACTION99
1.983-2.02350.25871380.21172645X-RAY DIFFRACTION99
2.0235-2.06750.23561330.19842590X-RAY DIFFRACTION99
2.0675-2.11560.21871410.19252672X-RAY DIFFRACTION99
2.1156-2.16840.21131320.18532613X-RAY DIFFRACTION99
2.1684-2.22710.23811440.1792672X-RAY DIFFRACTION99
2.2271-2.29260.22791430.17282580X-RAY DIFFRACTION99
2.2926-2.36650.20521310.16722640X-RAY DIFFRACTION99
2.3665-2.45110.22091480.16562644X-RAY DIFFRACTION99
2.4511-2.54910.21181410.16332605X-RAY DIFFRACTION99
2.5491-2.66510.23121410.16622621X-RAY DIFFRACTION99
2.6651-2.80550.20591420.16512634X-RAY DIFFRACTION99
2.8055-2.98110.21911610.16822593X-RAY DIFFRACTION99
2.9811-3.2110.19351420.15822654X-RAY DIFFRACTION99
3.211-3.53360.18621570.15612614X-RAY DIFFRACTION99
3.5336-4.04380.16711540.13912623X-RAY DIFFRACTION98
4.0438-5.09030.14931250.13442636X-RAY DIFFRACTION98
5.0903-29.06510.19721300.1662653X-RAY DIFFRACTION96

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