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- PDB-6he3: Pseudomonas aeruginosa Seryl-tRNA Synthetase in Complex with 5'-O... -

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Basic information

Entry
Database: PDB / ID: 6he3
TitlePseudomonas aeruginosa Seryl-tRNA Synthetase in Complex with 5'-O-(N-(L-seryl)-sulfamoyl)cytidine
ComponentsSerine--tRNA ligase
KeywordsLIGASE / Coil-coil / Beta barrel / tRNA Synthetase / Inhibitor / Complex
Function / homology
Function and homology information


selenocysteine biosynthetic process / serine-tRNA ligase / serine-tRNA ligase activity / seryl-tRNA aminoacylation / 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
5'-O-(N-(L-seryl)-sulfamoyl)cytidine / Serine--tRNA ligase / Serine--tRNA ligase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsPang, L. / De Graef, S. / Strelkov, S.V. / Weeks, S.D.
Funding support Belgium, 3items
OrganizationGrant numberCountry
Research Foundation - FlandersG077814N Belgium
Research Foundation - FlandersG0A4616N Belgium
Research Foundation - Flanders1S53516N Belgium
CitationJournal: Acs Chem.Biol. / Year: 2020
Title: Structural Insights into the Binding of Natural Pyrimidine-Based Inhibitors of Class II Aminoacyl-tRNA Synthetases.
Authors: Pang, L. / Nautiyal, M. / De Graef, S. / Gadakh, B. / Zorzini, V. / Economou, A. / Strelkov, S.V. / Van Aerschot, A. / Weeks, S.D.
History
DepositionAug 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 15, 2020Group: Database references / Category: citation / Item: _citation.title / _citation.year
Revision 1.3Mar 4, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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)95,84812
Polymers94,6112
Non-polymers1,23710
Water6,179343
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-6 kcal/mol
Surface area31410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.006, 122.183, 65.489
Angle α, β, γ (deg.)90.000, 114.670, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 47305.516 Da / Num. of mol.: 2 / Fragment: Seryl-tRNA Synthetase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: serS, ALP65_01227 / Plasmid: pETRUK / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 pLysS
References: UniProt: A0A3P3Q1W7, UniProt: Q9I0M6*PLUS, serine-tRNA ligase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-FZQ / 5'-O-(N-(L-seryl)-sulfamoyl)cytidine


Mass: 409.372 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N5O9S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / 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: 2.9 Å3/Da / Density % sol: 57.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Holo protein, concentrated to 10 mg/mL in 10 mM Tris pH 7, 100 mM NaCl, 5mM DTT, was mixed with an equal volume of 100 mM Tris pH 8, 200 mM NaCl, 23% w/v PEG 3350 and 5% v/v ethylene glycol. ...Details: Holo protein, concentrated to 10 mg/mL in 10 mM Tris pH 7, 100 mM NaCl, 5mM DTT, was mixed with an equal volume of 100 mM Tris pH 8, 200 mM NaCl, 23% w/v PEG 3350 and 5% v/v ethylene glycol. Suitable crystals were soaked with 2 mM 5'-O-(N-(L-seryl)-sulfamoyl)N3-cytidine in a solution similar to the crystallization condition but containing 22% v/v ethylene glycol.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972422 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972422 Å / Relative weight: 1
ReflectionResolution: 2.1→91.25 Å / Num. obs: 62738 / % possible obs: 99.3 % / Redundancy: 3.4 % / Biso Wilson estimate: 51 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.036 / Rrim(I) all: 0.067 / Net I/σ(I): 11.7 / Num. measured all: 214186 / Scaling rejects: 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.1-2.213.50.60591700.7520.3740.71399.5
6.63-91.253.30.0320350.9980.0190.03699.1

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.6.2data scaling
BUSTER2.10.3refinement
PDB_EXTRACT3.24data extraction
PHASER1.13-2998phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Model generated using 2DQ3 as a template

2dq3


Resolution: 2.16→43.2 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.944 / SU R Cruickshank DPI: 0.185 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.183 / SU Rfree Blow DPI: 0.155 / SU Rfree Cruickshank DPI: 0.157
RfactorNum. reflection% reflectionSelection details
Rfree0.215 2239 3.91 %RANDOM
Rwork0.187 ---
obs0.188 57272 99.1 %-
Displacement parametersBiso max: 240.51 Å2 / Biso mean: 52.69 Å2 / Biso min: 30.86 Å2
Baniso -1Baniso -2Baniso -3
1--8.9641 Å20 Å22.1753 Å2
2--4.0054 Å20 Å2
3---4.9586 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: final / Resolution: 2.16→43.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6089 0 80 343 6512
Biso mean--42.88 56.91 -
Num. residues----799
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2179SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes157HARMONIC2
X-RAY DIFFRACTIONt_gen_planes943HARMONIC5
X-RAY DIFFRACTIONt_it6295HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion823SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7457SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6295HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg8540HARMONIC21.07
X-RAY DIFFRACTIONt_omega_torsion3.55
X-RAY DIFFRACTIONt_other_torsion16.19
LS refinement shellResolution: 2.16→2.22 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2246 145 3.44 %
Rwork0.1986 4067 -
all0.1995 4212 -
obs--99.46 %
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)
1-0.06480.167-0.10170.3936-0.60080.74990.0063-0.0901-0.002-0.1052-0.01590.07410.1512-0.07070.00960.37340.0181-0.00660.48180.01650.364-34.1527-25.09851.5844
20.41840.26860.16272.1722-0.25820.8771-0.1360.1305-0.0777-0.27940.141-0.37930.17050.0731-0.0050.2768-0.01060.04190.3286-0.05120.3409-22.3361-12.18430.8152
31.08490.1886-0.29812.1991-0.37541.3238-0.0776-0.0686-0.08110.18030.0616-0.0007-0.0545-0.08890.01590.27360.0087-0.02830.2811-0.00230.2933-31.8804-5.000715.0247
40.51030.07630.12582.06780.06381.2076-0.08690.038-0.0642-0.11110.09980.10480.1445-0.1346-0.01290.2795-0.0542-0.01990.3334-0.01140.3062-34.5379-13.80436.0017
53.7233-0.8003-2.905300.51963.2380.3161-1.32540.57140.29670.1518-0.8783-0.82480.9973-0.46790.6059-0.1552-0.17990.7394-0.22260.9632-2.787933.923319.5821
65.4760.619-1.13950.58940.82551.9498-0.1116-1.0178-0.13340.310.2943-0.6835-0.37130.5065-0.18270.4177-0.1333-0.14220.4765-0.12250.6034-5.634328.526218.7769
70.4094-0.0649-0.04991.8157-0.44460.8214-0.0258-0.03680.04430.2490.12840.164-0.1756-0.1374-0.10260.290.049-0.01090.32230.01010.2805-36.712314.710913.2071
82.08590.8077-0.78392.2004-0.53371.83940.0449-0.1085-0.01420.2212-0.0007-0.3266-0.14530.1174-0.04420.27180.013-0.09450.2804-0.00980.3532-21.453912.735813.8423
90.8909-0.22090.11761.7533-0.13341.01890.03950.03240.09190.07380.06830.008-0.2475-0.071-0.10780.28220.0441-0.01990.26570.03590.2682-31.505122.69697.6942
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|102 }A1 - 102
2X-RAY DIFFRACTION2{ A|103 - A|166 }A103 - 166
3X-RAY DIFFRACTION3{ A|167 - A|281 }A167 - 281
4X-RAY DIFFRACTION4{ A|282 - A|426 }A282 - 426
5X-RAY DIFFRACTION5{ B|1 - B|42 }B1 - 42
6X-RAY DIFFRACTION6{ B|43 - B|116 }B43 - 116
7X-RAY DIFFRACTION7{ B|117 - B|213 }B117 - 213
8X-RAY DIFFRACTION8{ B|214 - B|281 }B214 - 281
9X-RAY DIFFRACTION9{ B|282 - B|426 }B282 - 426

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