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- PDB-6r1o: Crystal structure of E. coli seryl-tRNA synthetase complexed to a... -

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Basic information

Entry
Database: PDB / ID: 6r1o
TitleCrystal structure of E. coli seryl-tRNA synthetase complexed to a seryl sulfamoyl adenosine derivative
ComponentsSerine--tRNA ligase
KeywordsLIGASE / aminoacyl-tRNA synthetase / class II / protein synthesis / inhibitor
Function / homology
Function and homology information


: / selenocysteine biosynthetic process / seryl-tRNA aminoacylation / serine-tRNA ligase / serine-tRNA ligase activity / magnesium ion binding / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Serine-tRNA synthetase, tRNA binding domain / Serine-tRNA synthetase, type1, N-terminal / Seryl-tRNA synthetase N-terminal domain / Serine-tRNA ligase, type1 / Serine-tRNA ligase catalytic core domain / Serine-tRNA synthetase, type1, N-terminal domain superfamily / Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / Bira Bifunctional Protein; Domain 2 ...Serine-tRNA synthetase, tRNA binding domain / Serine-tRNA synthetase, type1, N-terminal / Seryl-tRNA synthetase N-terminal domain / Serine-tRNA ligase, type1 / Serine-tRNA ligase catalytic core domain / Serine-tRNA synthetase, type1, N-terminal domain superfamily / Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Helix Hairpins / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-JPE / Serine--tRNA ligase / Serine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSalimraj, R. / Cain, R. / Roper, D.I.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/M017893/1 United Kingdom
CitationJournal: J.Med.Chem. / Year: 2019
Title: Structure-Guided Enhancement of Selectivity of Chemical Probe Inhibitors Targeting Bacterial Seryl-tRNA Synthetase.
Authors: Cain, R. / Salimraj, R. / Punekar, A.S. / Bellini, D. / Fishwick, C.W.G. / Czaplewski, L. / Scott, D.J. / Harris, G. / Dowson, C.G. / Lloyd, A.J. / Roper, D.I.
History
DepositionMar 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,89319
Polymers49,2581
Non-polymers2,63618
Water2,360131
1
A: Serine--tRNA ligase
hetero molecules

A: Serine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,78738
Polymers98,5162
Non-polymers5,27136
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area11570 Å2
ΔGint-42 kcal/mol
Surface area34190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.410, 85.410, 317.716
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Serine--tRNA ligase / Seryl-tRNA synthetase / SerRS / Seryl-tRNA(Ser/Sec) synthetase


Mass: 49257.895 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: serS, ECVG_02257 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A1X3JK72, UniProt: P0A8L1*PLUS, serine-tRNA ligase

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Non-polymers , 7 types, 149 molecules

#2: Chemical ChemComp-JPE / [(2~{R},3~{S},4~{R},5~{R})-5-(6-azanyl-2-pyridin-3-yl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-3-oxidanyl-propanoyl]sulfamate


Mass: 510.481 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H22N8O8S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O

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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: 3.4 Å3/Da / Density % sol: 63.78 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium citrate pH 5.5 0.8 M lithium sulfate 0.05 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.596→158.858 Å / Num. obs: 22345 / % possible obs: 100 % / Redundancy: 28.5 % / Biso Wilson estimate: 69.36 Å2 / CC1/2: 0.999 / Net I/σ(I): 17.4
Reflection shellResolution: 2.596→2.641 Å

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DQ3

2dq3


Resolution: 2.6→27.96 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.913 / SU R Cruickshank DPI: 0.318 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.36 / SU Rfree Blow DPI: 0.23 / SU Rfree Cruickshank DPI: 0.224
RfactorNum. reflection% reflectionSelection details
Rfree0.215 1075 4.84 %RANDOM
Rwork0.182 ---
obs0.184 22215 100 %-
Displacement parametersBiso mean: 63.41 Å2
Baniso -1Baniso -2Baniso -3
1--11.7789 Å20 Å20 Å2
2---11.7789 Å20 Å2
3---23.5579 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: 1 / Resolution: 2.6→27.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3251 0 143 131 3525
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013507HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.094750HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1232SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes662HARMONIC5
X-RAY DIFFRACTIONt_it3507HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.38
X-RAY DIFFRACTIONt_other_torsion17.69
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion447SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies6HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4165SEMIHARMONIC4
LS refinement shellResolution: 2.6→2.62 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2527 -4.94 %
Rwork0.2182 423 -
all0.22 445 -
obs--97.97 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.2346-1.91360.59255.77640.86261.2535-0.11330.42570.4850.0991-0.06880.2034-0.4357-0.33380.18210.11740.2451-0.051-0.14320.0853-0.1005-9.449834.6929-6.8173
23.8922-2.56822.25993.24771.90660.58580.2305-0.2217-0.11990.4897-0.3596-0.133-0.0012-0.00010.12920.08530.0175-0.0346-0.28580.1555-0.0636-28.958238.354214.765
32.4688-0.74541.54282.2581.887400.2665-0.2102-0.40790.4176-0.38350.03790.6777-0.14230.1170.1378-0.01870.0538-0.19160.1851-0.0496-29.844630.930815.107
40.3832-0.2193-0.22461.39310.1371.7491-0.07320.210.029-0.27170.0360.1379-0.22370.09370.0371-0.086-0.0397-0.04850.02560.028-0.03498.27018.2868-11.1671
51.13130.3787-0.07582.60490.13042.1873-0.0409-0.09970.04440.00380.00340.3831-0.2833-0.16730.0375-0.16470.0237-0.0125-0.02150.03120.0196-0.181410.37511.4583
60.9628-0.4333-0.48461.97470.45282.03550.05380.13610.1448-0.1613-0.03580.0437-0.5580.0534-0.018-0.0078-0.0518-0.0383-0.05540.0272-0.09199.104319.6357-7.5734
70.8276-0.7731-0.1684.9091.76531.9132-0.07740.1884-0.2499-0.35380.0759-0.59850.39210.40930.0015-0.1429-0.00930.06180.2188-0.0286-0.079625.6537-2.0136-15.6106
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|1 - 26}
2X-RAY DIFFRACTION2{A|27 - 64}
3X-RAY DIFFRACTION3{A|65 - 102}
4X-RAY DIFFRACTION4{A|103 - 216}
5X-RAY DIFFRACTION5{A|217 - 285}
6X-RAY DIFFRACTION6{A|286 - 405}
7X-RAY DIFFRACTION7{A|406 - 431}

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