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- PDB-6r1m: Crystal structure of E. coli seryl-tRNA synthetase complexed to s... -

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Basic information

Entry
Database: PDB / ID: 6r1m
TitleCrystal structure of E. coli seryl-tRNA synthetase complexed to seryl sulfamoyl adenosine
ComponentsSerine--tRNA ligase
KeywordsLIGASE / aminoacyl-tRNA synthetase / class II / protein synthesis / inhibitor
Function / homology
Function and homology information


selenocysteine biosynthetic process / serine-tRNA ligase / serine-tRNA ligase activity / seryl-tRNA aminoacylation / 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
PHOSPHATE ION / 5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE / Serine--tRNA ligase / Serine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 1.1Jan 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
B: Serine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,81825
Polymers98,5162
Non-polymers2,30223
Water16,105894
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11370 Å2
ΔGint37 kcal/mol
Surface area34300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.070, 63.520, 75.890
Angle α, β, γ (deg.)75.44, 70.25, 89.20
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 49257.895 Da / Num. of mol.: 2
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
#2: Chemical ChemComp-SSA / 5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE


Mass: 433.397 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H19N7O8S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 894 / 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: 2.8 Å3/Da / Density % sol: 56.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium phosphate monobasic monohydrate, pH 4.7 20 % w/v PEG 3350 25 % ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.5→61.29 Å / Num. obs: 163583 / % possible obs: 95.5 % / Redundancy: 2.4 % / Biso Wilson estimate: 20.15 Å2 / CC1/2: 0.997 / Net I/σ(I): 9.3
Reflection shellResolution: 1.5→1.53 Å / Num. unique obs: 7950

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Processing

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

2dq3


Resolution: 1.5→59.18 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.958 / SU R Cruickshank DPI: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.062 / SU Rfree Blow DPI: 0.062 / SU Rfree Cruickshank DPI: 0.06
RfactorNum. reflection% reflectionSelection details
Rfree0.18 7960 4.87 %RANDOM
Rwork0.162 ---
obs0.163 163577 95.5 %-
Displacement parametersBiso mean: 25.95 Å2
Baniso -1Baniso -2Baniso -3
1--2.7811 Å21.5088 Å23.2725 Å2
2--2.1749 Å2-1.1801 Å2
3---0.6062 Å2
Refine analyzeLuzzati coordinate error obs: 0.17 Å
Refinement stepCycle: LAST / Resolution: 1.5→59.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6649 0 146 895 7690
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017094HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.039600HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2561SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1258HARMONIC5
X-RAY DIFFRACTIONt_it7094HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.18
X-RAY DIFFRACTIONt_other_torsion14.4
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion908SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies40HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9249SEMIHARMONIC4
LS refinement shellResolution: 1.5→1.51 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2038 163 4.98 %
Rwork0.1916 3109 -
all0.1922 3272 -
obs--93.83 %
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)
13.4178-0.41062.29744.1671-2.78394.49510.13190.2255-0.20530.0120.02270.1356-0.01860.239-0.15460.0491-0.0015-0.0482-0.0623-0.0042-0.0809-11.934914.1191-35.0581
21.5273-0.36260.23423.7046-0.551-0.28630.0178-0.18850.07870.071-0.0187-0.0487-0.02250.05760.0010.0930.0658-0.0165-0.0009-0.0052-0.1479-22.570241.7618-29.5711
30.7063-0.7221-0.75592.06660.53080.16980.1152-0.12190.11660.31820.11330.0592-0.2113-0.1964-0.22860.17640.14630.0147-0.0794-0.0011-0.1123-24.624238.2665-22.8162
40.2283-0.04960.04070.3520.00890.988-0.05760.0374-0.0058-0.08870.02280.0255-0.0447-0.01180.0348-0.032-0.0228-0.0169-0.03840.0019-0.0362-2.5659-0.9488-11.0724
50.30350.07510.15110.43080.05171.0124-0.03470.0639-0.005-0.15930.00030.0259-0.06040.04980.03440-0.0279-0.0044-0.01820.0059-0.03140.3245-3.1683-19.0309
60.8784-0.55630.65441.6617-0.93281.965-0.16450.14250.1638-0.1236-0.0238-0.1477-0.46350.19260.18830.1052-0.0865-0.059-0.06970.0381-0.07871.627816.5022-21.736
70.9728-0.27280.3721.43340.16731.9985-0.01060.0467-0.07950.03690.0137-0.13920.23080.1671-0.00310.00180.00830.0148-0.01110.0030.00458.5887-18.308-5.7622
85.630.5546-1.13732.19731.66352.047-0.1859-0.57680.14660.41840.07780.48320.20210.04480.1081-0.01280.02030.1119-0.03230.0232-0.0248-21.7328-2.523133.1736
92.17532.71950.58194.60951.3940.18420.1102-0.03280.01470.0789-0.0141-0.08150.12190.0523-0.09610.01-0.0317-0.0304-0.0261-0.0105-0.031-43.5897-18.761125.1477
10-0.01410.723-0.09771.68920.3626-0.055-0.0256-0.03380.077-0.26570.00140.19580.04830.08350.02430.0044-0.0222-0.0586-0.01870.00450.0467-45.5494-16.574818.8806
110.411-0.01520.04720.51670.07540.7745-0.045-0.0350.00930.04470.0230.0065-0.0465-0.00120.022-0.02220.0042-0.0089-0.01750.0019-0.00710.02042.072814.4691
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 - 257}
5X-RAY DIFFRACTION5{A|258 - 363}
6X-RAY DIFFRACTION6{A|364 - 394}
7X-RAY DIFFRACTION7{A|395 - 430}
8X-RAY DIFFRACTION8{B|1 - 26}
9X-RAY DIFFRACTION9{B|27 - 63}
10X-RAY DIFFRACTION10{B|64 - 102}
11X-RAY DIFFRACTION11{B|103 - 430}

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