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- PDB-5znj: Crystal structure of a bacterial ProRS with ligands -

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Basic information

Entry
Database: PDB / ID: 5znj
TitleCrystal structure of a bacterial ProRS with ligands
ComponentsProline--tRNA ligase
KeywordsLIGASE / Aminoacyl-tRNA synthetase / Protein biosynthesis / Inhibitor
Function / homology
Function and homology information


YbaK protein / YbaK/aminoacyl-tRNA synthetase-associated domain / Anticodon-binding domain / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Alpha-Beta Complex / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Chem-HFG / PHOSPHATE ION / :
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsCheng, B. / Yu, Y. / Zhou, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China81773636 China
CitationJournal: J.Med.Chem. / Year: 2022
Title: Structure-Guided Design of Halofuginone Derivatives as ATP-Aided Inhibitors Against Bacterial Prolyl-tRNA Synthetase.
Authors: Cheng, B. / Cai, Z. / Luo, Z. / Luo, S. / Luo, Z. / Cheng, Y. / Yu, Y. / Guo, J. / Ju, Y. / Gu, Q. / Xu, J. / Jiang, X. / Li, G. / Zhou, H.
History
DepositionApr 9, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2023Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proline--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0706
Polymers63,9381
Non-polymers1,1325
Water4,918273
1
A: Proline--tRNA ligase
hetero molecules

A: Proline--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,14012
Polymers127,8762
Non-polymers2,26410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area7970 Å2
ΔGint-61 kcal/mol
Surface area45780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.139, 77.535, 74.226
Angle α, β, γ (deg.)90.00, 99.36, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Proline--tRNA ligase / Prolyl-tRNA synthetase / ProRS


Mass: 63937.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: MRSA (R3708) / Gene: proS, CT123_02285 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A227M497, proline-tRNA ligase

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Non-polymers , 6 types, 278 molecules

#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-HFG / 7-bromo-6-chloro-3-{3-[(2R,3S)-3-hydroxypiperidin-2-yl]-2-oxopropyl}quinazolin-4(3H)-one / Halofuginone


Mass: 414.681 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H17BrClN3O3 / Comment: alkaloid, medication*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsThe authors did not cloned this gene from the standard strain of Staphylococcus aureus, but from a ...The authors did not cloned this gene from the standard strain of Staphylococcus aureus, but from a clinically drug-resistant strain (MRSA R3708). The author confirmed ProRS of MRSA R3708 shows THR 230, ALA 278.

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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: 2.89 Å3/Da / Density % sol: 57.43 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 32 - 40% (v/v) Pentaerythritol propoxylate (5/4 PO/OH), 0.1 - 0.2 M KCl and 50 mM HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.84→50 Å / Num. obs: 62796 / % possible obs: 98.5 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 34.6
Reflection shellResolution: 1.84→1.91 Å / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 6339 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2J3L

2j3l


Resolution: 1.84→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.455 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.119 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22249 3053 4.9 %RANDOM
Rwork0.19728 ---
obs0.19852 59229 98.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 43.912 Å2
Baniso -1Baniso -2Baniso -3
1--1.05 Å20 Å20.72 Å2
2--1.62 Å20 Å2
3----0.77 Å2
Refinement stepCycle: 1 / Resolution: 1.84→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4384 0 67 273 4724
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0194625
X-RAY DIFFRACTIONr_bond_other_d0.0020.024311
X-RAY DIFFRACTIONr_angle_refined_deg1.1751.9736288
X-RAY DIFFRACTIONr_angle_other_deg0.85439915
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8865584
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.59824.612219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.07715776
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4291528
X-RAY DIFFRACTIONr_chiral_restr0.0640.2700
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025318
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021058
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7953.272297
X-RAY DIFFRACTIONr_mcbond_other0.7953.272296
X-RAY DIFFRACTIONr_mcangle_it1.394.8982882
X-RAY DIFFRACTIONr_mcangle_other1.394.8982883
X-RAY DIFFRACTIONr_scbond_it0.743.2992328
X-RAY DIFFRACTIONr_scbond_other0.743.2992328
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.2974.9293403
X-RAY DIFFRACTIONr_long_range_B_refined4.40725.7345225
X-RAY DIFFRACTIONr_long_range_B_other4.40725.7345225
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.84→1.888 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 238 -
Rwork0.28 4437 -
obs--99.85 %
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)
10.66750.431-0.17820.6806-0.18960.8620.00490.12820.061-0.0709-0.03960.1083-0.0484-0.14180.03460.09130.0054-0.0590.1448-0.01130.0611-18.2258-2.26320.4504
20.2811-0.0322-0.26460.1028-0.02760.55120.0006-0.0117-0.0424-0.0341-0.0107-0.018-0.0980.1030.010.0917-0.0281-0.01930.08960.00180.09745.03860.966632.8917
30.7598-0.2180.02991.0849-0.94330.87190.0161-0.07420.1091-0.1999-0.1368-0.13520.17120.1170.12070.1125-0.00950.03370.121-0.01590.094811.371-2.325212.2061
40.0175-0.0415-0.07231.1869-0.05450.7180.0390.0014-0.0082-0.2718-0.2683-0.4025-0.1262-0.12760.22930.13210.03690.05050.14620.04780.20115.747819.5513-2.9908
50.31940.62390.75351.85050.56843.1038-0.1223-0.134-0.0519-0.1875-0.3363-0.4826-0.6406-0.11320.45860.15290.0181-0.0490.1020.08630.242416.09125.60891.7722
60.30040.1596-0.64032.6579-0.51631.38180.0273-0.1818-0.1738-0.6036-0.4738-0.31550.04670.42170.44640.14130.09540.04490.18280.17950.305120.149915.1467-2.4541
70.36040.0534-0.16630.189-0.05490.1985-0.05550.0087-0.0811-0.1176-0.0104-0.03890.0487-0.01450.06590.1142-0.04540.00480.1117-0.01530.0806-9.5933-12.803123.3773
83.23962.1046-0.80833.1771-0.10721.387-0.21610.5412-0.6937-0.22610.1691-0.30290.1656-0.06220.0470.137-0.05280.04060.1357-0.15530.1878-17.1034-29.368315.9626
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 43
2X-RAY DIFFRACTION2A44 - 188
3X-RAY DIFFRACTION3A189 - 237
4X-RAY DIFFRACTION4A238 - 309
5X-RAY DIFFRACTION5A310 - 363
6X-RAY DIFFRACTION6A364 - 399
7X-RAY DIFFRACTION7A400 - 535
8X-RAY DIFFRACTION8A536 - 567

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