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- PDB-6h9x: Klebsiella pneumoniae Seryl-tRNA Synthetase in Complex with the I... -

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Basic information

Entry
Database: PDB / ID: 6h9x
TitleKlebsiella pneumoniae Seryl-tRNA Synthetase in Complex with the Intermediate Analog 5'-O-(N-(L-Seryl)-Sulfamoyl)Adenosine
ComponentsSerine--tRNA ligase
KeywordsLIGASE / coil-coil / beta barrel / tRNA synthetase / 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)ADENOSINE / Serine--tRNA ligase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 - Flanders1109117N Belgium
CitationJournal: Eur.J.Med.Chem. / Year: 2019
Title: Acylated sulfonamide adenosines as potent inhibitors of the adenylate-forming enzyme superfamily.
Authors: De Ruysscher, D. / Pang, L. / De Graef, S. / Nautiyal, M. / De Borggraeve, W.M. / Rozenski, J. / Strelkov, S.V. / Weeks, S.D. / Van Aerschot, A.
History
DepositionAug 6, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 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.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)49,4098
Polymers48,6691
Non-polymers7407
Water3,351186
1
A: Serine--tRNA ligase
hetero molecules

A: Serine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,81816
Polymers97,3382
Non-polymers1,48014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area8740 Å2
ΔGint-33 kcal/mol
Surface area35240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.407, 84.407, 229.874
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#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, AGG09_05015, B1727_25560, B4U21_07300, B4U22_08075, BB785_18280, BL124_0015080, BN49_2024, C3483_17160, C3F39_05595, C9J88_18700, CPT10_05250, CSC88_02630, CWQ24_18365, PMK1_03261, SM57_00973
Plasmid: pETRUK / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 pLysS / References: UniProt: W9BNU9, serine-tRNA ligase
#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 / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 4.21 Å3/Da / Density % sol: 70.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Holo protein at 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 ...Details: Holo protein at 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 1 mM seryl-adenylate analogue in the same crystallization solution but containing a 10% w/v PEG 8000 concentration.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 25, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.87→68.03 Å / Num. obs: 69469 / % possible obs: 99.8 % / Redundancy: 10.9 % / Biso Wilson estimate: 46.63 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.035 / Rrim(I) all: 0.115 / Net I/σ(I): 9.1 / Num. measured all: 759889
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.87-1.9711.82.30799330.7950.72.41299.8
5.92-68.039.70.05624840.9970.0180.05999.6

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimless0.5.32data scaling
PDB_EXTRACT3.24data extraction
PHASER1.13-2998phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DQ3

2dq3


Resolution: 2.1→68.03 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.912 / SU R Cruickshank DPI: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.138 / SU Rfree Blow DPI: 0.127 / SU Rfree Cruickshank DPI: 0.126
RfactorNum. reflection% reflectionSelection details
Rfree0.222 2458 4.97 %RANDOM
Rwork0.2 ---
obs0.201 49454 99.9 %-
Displacement parametersBiso max: 161.24 Å2 / Biso mean: 57.7 Å2 / Biso min: 35.06 Å2
Baniso -1Baniso -2Baniso -3
1--10.1106 Å20 Å20 Å2
2---10.1106 Å20 Å2
3---20.2212 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: final / Resolution: 2.1→68.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3348 0 44 186 3578
Biso mean--52.61 58.62 -
Num. residues----428
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1255SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes101HARMONIC2
X-RAY DIFFRACTIONt_gen_planes523HARMONIC5
X-RAY DIFFRACTIONt_it3479HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion448SEMIHARMONIC5
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_contact4125SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3479HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4714HARMONIC21.06
X-RAY DIFFRACTIONt_omega_torsion3.72
X-RAY DIFFRACTIONt_other_torsion16.76
LS refinement shellResolution: 2.1→2.15 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2504 181 5.05 %
Rwork0.2096 3400 -
all0.2115 3581 -
obs--99.92 %
Refinement TLS params.Method: refined / Origin x: -12.6253 Å / Origin y: -32.428 Å / Origin z: -9.3621 Å
111213212223313233
T-0.0093 Å20.0467 Å2-0.0225 Å2--0.0725 Å20.0303 Å2---0.1101 Å2
L0.4503 °20.1702 °20.1421 °2-0.2499 °20.409 °2--1.1628 °2
S0.0468 Å °-0.0239 Å °-0.073 Å °-0.0403 Å °-0.0219 Å °-0.0854 Å °0.1385 Å °0.2367 Å °-0.0249 Å °
Refinement TLS groupSelection details: { A|* }

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