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- PDB-6hhz: Klebsiella pneumoniae Seryl-tRNA Synthetase in Complex with 5'-O-... -

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Basic information

Entry
Database: PDB / ID: 6hhz
TitleKlebsiella pneumoniae 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


L-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
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsPang, L. / De Graef, S. / Weeks, S.D. / Strelkov, S.V.
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 29, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_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: Serine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,65910
Polymers48,6691
Non-polymers9909
Water3,261181
1
A: Serine--tRNA ligase
hetero molecules

A: Serine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,31720
Polymers97,3382
Non-polymers1,97918
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area8300 Å2
ΔGint-58 kcal/mol
Surface area35370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.351, 83.351, 229.329
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-772-

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: 48669.180 Da / Num. of mol.: 1 / Fragment: Seryl-tRNA synthetase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: serS, KPN78578_09000, KPN_00925 / Plasmid: pETRUK / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 pLysS / References: UniProt: A6T6Z0, serine-tRNA ligase

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Non-polymers , 6 types, 190 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 409.372 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N5O9S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 4.09 Å3/Da / Density % sol: 69.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Holo protein, concentrated to 10 mg/mL in 10 mM Tris pH 7, 100 mM NaCl, 5 mM DTT, was mixed with an equal volume of 7.5% w/v PEG 8000, 50 mM CaCl2, 20% v/v ethylene glycol, 100 mM Morpheus ...Details: Holo protein, concentrated to 10 mg/mL in 10 mM Tris pH 7, 100 mM NaCl, 5 mM DTT, was mixed with an equal volume of 7.5% w/v PEG 8000, 50 mM CaCl2, 20% v/v ethylene glycol, 100 mM Morpheus buffer system 1 (MES/Imidazole) pH 6.5. Suitable crystals were soaked with 2 mM compound in a similar crystallization solution containing a 10% w/v PEG 8000.

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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: 1.93→114.66 Å / Num. obs: 61829 / % possible obs: 99.9 % / Redundancy: 8.5 % / Biso Wilson estimate: 50.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.034 / Rrim(I) all: 0.1 / Net I/σ(I): 10.7 / Num. measured all: 523095 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1 / % possible all: 99.8

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
1.93-2.038.41.8588740.7260.6741.972
6.1-114.667.40.04122340.9990.0160.044

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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 from structure 2DQ3

2dq3


Resolution: 2.15→43 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.92 / SU R Cruickshank DPI: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.151 / SU Rfree Blow DPI: 0.139 / SU Rfree Cruickshank DPI: 0.137
RfactorNum. reflection% reflectionSelection details
Rfree0.226 2295 5.1 %RANDOM
Rwork0.2 ---
obs0.201 44959 100 %-
Displacement parametersBiso max: 158.34 Å2 / Biso mean: 55.1 Å2 / Biso min: 32.14 Å2
Baniso -1Baniso -2Baniso -3
1--7.2789 Å20 Å20 Å2
2---7.2789 Å20 Å2
3---14.5578 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: final / Resolution: 2.15→43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3337 0 53 181 3571
Biso mean--57.97 56.84 -
Num. residues----428
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1240SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes98HARMONIC2
X-RAY DIFFRACTIONt_gen_planes506HARMONIC5
X-RAY DIFFRACTIONt_it3449HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion445SEMIHARMONIC5
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_contact3933SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3449HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4664HARMONIC21.06
X-RAY DIFFRACTIONt_omega_torsion3.6
X-RAY DIFFRACTIONt_other_torsion16.48
LS refinement shellResolution: 2.15→2.21 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 175 5.38 %
Rwork0.2123 3079 -
all0.2168 3254 -
obs--99.97 %
Refinement TLS params.Method: refined / Origin x: -11.7862 Å / Origin y: -31.1086 Å / Origin z: -9.6704 Å
111213212223313233
T-0.0362 Å20.031 Å2-0.0234 Å2--0.0667 Å20.0292 Å2---0.0955 Å2
L0.3784 °20.1282 °20.0698 °2-0.205 °20.423 °2--1.0732 °2
S0.0364 Å °-0.0215 Å °-0.0404 Å °-0.0388 Å °-0.0199 Å °-0.0534 Å °0.0804 Å °0.2522 Å °-0.0165 Å °
Refinement TLS groupSelection details: {A|*}

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