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- PDB-7ap1: Klebsiella pneumoniae Seryl-tRNA synthetase in Complex with Compo... -

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Basic information

Entry
Database: PDB / ID: 7ap1
TitleKlebsiella pneumoniae Seryl-tRNA synthetase in Complex with Compound SerS7HMDDA
ComponentsSerine-tRNA ligaseSerine—tRNA ligase
KeywordsLIGASE / protein-inhibitor complex / coiled-coil / tRNA synthetase
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, 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) / 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)
Similarity search - Domain/homology
Chem-RUZ / Serine--tRNA ligase / Serine--tRNA ligase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsPang, L. / De Graef, S. / Strelkov, S.V. / Weeks, S.D.
Funding support Belgium, 3items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)G077814N Belgium
Research Foundation - Flanders (FWO)G0A4616A Belgium
Research Foundation - Flanders (FWO)1109117N Belgium
CitationJournal: Molecules / Year: 2020
Title: Synthesis and Biological Evaluation of 1,3-Dideazapurine-Like 7-Amino-5-Hydroxymethyl-Benzimidazole Ribonucleoside Analogues as Aminoacyl-tRNA Synthetase Inhibitors.
Authors: Zhang, B. / Pang, L. / Nautiyal, M. / De Graef, S. / Gadakh, B. / Lescrinier, E. / Rozenski, J. / Strelkov, S.V. / Weeks, S.D. / Van Aerschot, A.
History
DepositionOct 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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

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Assembly

Deposited unit
A: Serine-tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4378
Polymers48,6691
Non-polymers7687
Water2,126118
1
A: Serine-tRNA ligase
hetero molecules

A: Serine-tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,87416
Polymers97,3382
Non-polymers1,53614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7050 Å2
ΔGint-40 kcal/mol
Surface area34770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.670, 84.670, 229.865
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 / 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) / Strain (production host): Rosetta 2 (DE3) pLysS
References: UniProt: W9BNU9, UniProt: A6T6Z0*PLUS, serine-tRNA ligase
#2: Chemical ChemComp-RUZ / [(2~{R},3~{S},4~{R},5~{R})-5-[7-azanyl-5-(hydroxymethyl)benzimidazol-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-3-oxidanyl-propanoyl]sulfamate / SerS7HMDDA


Mass: 461.447 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H23N5O9S / 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.: 118 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.23 Å3/Da / Density % sol: 70.94 % / Mosaicity: 0.09 °
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 5 mM synthesized compound in the same crystallization solution but containing a 10% w/v PEG 8000 concentration.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.99187 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 1, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99187 Å / Relative weight: 1
ReflectionResolution: 1.91→19.96 Å / Num. obs: 65882 / % possible obs: 99.8 % / Redundancy: 12.2 % / Biso Wilson estimate: 53.83 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.032 / Rrim(I) all: 0.11 / Net I/σ(I): 10.7 / Num. measured all: 805160 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.91-2.0112.64.00711955494630.7561.174.1760.699.6
6.04-19.9610.80.0442458222780.9990.0140.04638.997.3

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (18-SEP-2020)refinement
XDSdata reduction
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6H9X

6h9x


Resolution: 2.18→19.96 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.928 / SU R Cruickshank DPI: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.149 / SU Rfree Blow DPI: 0.138 / SU Rfree Cruickshank DPI: 0.138
RfactorNum. reflection% reflectionSelection details
Rfree0.2259 2050 4.61 %RANDOM
Rwork0.2 ---
obs0.2012 44514 100 %-
Displacement parametersBiso max: 128.26 Å2 / Biso mean: 61.19 Å2 / Biso min: 40.09 Å2
Baniso -1Baniso -2Baniso -3
1--9.5607 Å20 Å20 Å2
2---9.5607 Å20 Å2
3---19.1215 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: final / Resolution: 2.18→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3310 0 46 118 3474
Biso mean--61.05 60.56 -
Num. residues----421
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1254SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes620HARMONIC5
X-RAY DIFFRACTIONt_it3450HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion443SEMIHARMONIC5
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_contact2777SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3450HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg4674HARMONIC20.95
X-RAY DIFFRACTIONt_omega_torsion3.69
X-RAY DIFFRACTIONt_other_torsion16.12
LS refinement shellResolution: 2.18→2.19 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2682 44 4.94 %
Rwork0.2316 847 -
all0.2333 891 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -12.5785 Å / Origin y: -32.1722 Å / Origin z: -9.7281 Å
111213212223313233
T0.0175 Å20.0556 Å2-0.0257 Å2--0.0107 Å20.0227 Å2---0.0987 Å2
L0.2937 °20.2132 °20.1365 °2-0.2199 °20.534 °2--1.1708 °2
S0.0253 Å °-0.0523 Å °-0.0442 Å °-0.0331 Å °-0.0371 Å °-0.0079 Å °0.1035 Å °0.2031 Å °0.0118 Å °
Refinement TLS groupSelection details: { A|* }

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