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- PDB-6r1n: Crystal structure of S. aureus seryl-tRNA synthetase complexed to... -

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Basic information

Entry
Database: PDB / ID: 6r1n
TitleCrystal structure of S. aureus 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 / transferase activity / ATP binding / 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
DI(HYDROXYETHYL)ETHER / 5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE / Serine--tRNA ligase / Serine--tRNA ligase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 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: Derived calculations / Refinement description / Category: pdbx_struct_conn_angle / software / struct_conn
Item: _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id ..._pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _software.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
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)51,9798
Polymers51,1671
Non-polymers8127
Water6,918384
1
A: Serine--tRNA ligase
hetero molecules

A: Serine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,95716
Polymers102,3332
Non-polymers1,62414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area7840 Å2
ΔGint-1 kcal/mol
Surface area35040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.438, 116.413, 91.611
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-737-

HOH

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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: 51166.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: serS, serS_3, CSC83_09220, CSC87_00755, CV021_04380, EP54_05580, EQ90_05790, HMPREF3211_02116, NCTC10654_00091, NCTC10702_00150, NCTC13196_01224, NCTC5664_00935, RK64_00725, SAMEA1466939_02107, SAMEA1708674_02321
Production host: Escherichia coli (E. coli)
References: UniProt: X5DWM7, UniProt: P95689*PLUS, serine-tRNA ligase

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Non-polymers , 5 types, 391 molecules

#2: Chemical ChemComp-SSA / 5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE


Mass: 433.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H19N7O8S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / 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: 2.46 Å3/Da / Density % sol: 50.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.2 M sodium malonate pH 5 13 % w/v PEG 3350

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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: 2.026→91.611 Å / Num. obs: 33080 / % possible obs: 99.8 % / Redundancy: 11.8 % / Biso Wilson estimate: 31.32 Å2 / CC1/2: 0.999 / Net I/σ(I): 16.1
Reflection shellResolution: 2.026→2.061 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: 2.03→57.25 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.923 / SU R Cruickshank DPI: 0.161 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.177 / SU Rfree Blow DPI: 0.157 / SU Rfree Cruickshank DPI: 0.151
RfactorNum. reflection% reflectionSelection details
Rfree0.221 1602 4.85 %RANDOM
Rwork0.173 ---
obs0.175 33037 99.7 %-
Displacement parametersBiso mean: 36.55 Å2
Baniso -1Baniso -2Baniso -3
1-6.2017 Å20 Å20 Å2
2---6.6576 Å20 Å2
3---0.456 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: 1 / Resolution: 2.03→57.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3307 0 53 384 3744
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013441HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.054647HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1242SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes606HARMONIC5
X-RAY DIFFRACTIONt_it3441HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.73
X-RAY DIFFRACTIONt_other_torsion16.45
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion453SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies11HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4442SEMIHARMONIC4
LS refinement shellResolution: 2.03→2.04 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3389 -4.08 %
Rwork0.2191 634 -
all0.2233 661 -
obs--97.43 %
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)
12.4213-0.30650.60013.4442-0.79421.8785-0.127-0.5442-0.45860.38070.23930.4367-0.1429-0.3836-0.1123-0.1010.00210.10310.10070.1041-0.0356-3.8794-41.243312.5543
20-2.91041.51383.0811-1.26562.75770.0299-0.0199-0.41640.10040.23380.120.11240.2882-0.2637-0.0663-0.07460.029-0.1087-0.02650.009617.1921-58.35915.8169
31.07-2.9104-0.69634.9456-2.3812.26240.0573-0.1112-0.137-0.3050.05880.06650.54420.1636-0.11610.06150.0193-0.0822-0.0882-0.12760.039217.2015-61.18238.3356
42.4692-1.39631.16161.3034-1.03471.7483-0.1787-0.3973-0.18950.11440.19510.1858-0.1246-0.3496-0.0164-0.1250.01050.04780.02180.0056-0.0337-19.7412-22.3327-1.6513
50.92220.09260.29790.55480.1590.84960.0058-0.0421-0.01140.0211-0.04310.00630.0499-0.01880.0374-0.0503-0.00160.0260.03330.00030.0071-2.53-27.2394-16.3603
61.4462-0.96690.80420-0.4331.9857-0.0463-0.1052-0.1855-0.051-0.01820.11760.0625-0.2510.0645-0.05040.00790.02750.0462-0.01810.0363-7.605-28.2381-15.5937
71.1013-0.13270.25230.447-0.19650.8422-0.0533-0.2769-0.01250.08350.05980.0003-0.0752-0.0317-0.0065-0.09650.01120.00420.0279-0.0083-0.0625-5.678-23.1599-2.8055
83.50481.8415-1.17083.9203-0.46763.4891-0.05640.30310.4753-0.24530.00050.1624-0.1134-0.27520.0558-0.03260.0576-0.0257-0.00170.00660.0082-16.8292-7.6877-24.312
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|1 - 24}
2X-RAY DIFFRACTION2{A|25 - 64}
3X-RAY DIFFRACTION3{A|65 - 103}
4X-RAY DIFFRACTION4{A|104 - 139}
5X-RAY DIFFRACTION5{A|140 - 251}
6X-RAY DIFFRACTION6{A|252 - 279}
7X-RAY DIFFRACTION7{A|280 - 399}
8X-RAY DIFFRACTION8{A|400 - 427}

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