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- PDB-6uyh: Crystal structure of prolyl-tRNA synthetase from Naegleria fowler... -

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Basic information

Entry
Database: PDB / ID: 6uyh
TitleCrystal structure of prolyl-tRNA synthetase from Naegleria fowleri in complex with halofuginone and AMPPNP
ComponentsProlyl-tRNA synthetase
KeywordsLIGASE / SSGCID / Structural Genomics / halofuginone / AMPPNP / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


proline-tRNA ligase / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / ATP binding / cytoplasm
Similarity search - Function
C-terminal domain of ProRS / Proline-tRNA ligase, class IIa / Proline-tRNA ligase, class II, C-terminal / Prolyl-tRNA synthetase, C-terminal / Prolyl-tRNA synthetase, C-terminal / Proline-tRNA ligase, class IIa, archaeal-type / Prolyl-tRNA synthetase, class II / Translation Initiation Factor IF3 / Anticodon-binding domain / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) ...C-terminal domain of ProRS / Proline-tRNA ligase, class IIa / Proline-tRNA ligase, class II, C-terminal / Prolyl-tRNA synthetase, C-terminal / Prolyl-tRNA synthetase, C-terminal / Proline-tRNA ligase, class IIa, archaeal-type / Prolyl-tRNA synthetase, class II / Translation Initiation Factor IF3 / Anticodon-binding domain / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / Anticodon-binding / Anticodon binding domain / Anticodon-binding domain superfamily / 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) / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Chem-HFG / Proline--tRNA ligase
Similarity search - Component
Biological speciesNaegleria fowleri (brain-eating amoeba)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of prolyl-tRNA synthetase from Naegleria fowleri in complex with halofuginone and AMPPNP
Authors: Dranow, D.M. / Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionNov 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: 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.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Prolyl-tRNA synthetase
B: Prolyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,46131
Polymers119,0752
Non-polymers3,38629
Water15,997888
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10160 Å2
ΔGint-13 kcal/mol
Surface area38670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.290, 66.540, 112.560
Angle α, β, γ (deg.)90.00, 101.74, 90.00
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Prolyl-tRNA synthetase


Mass: 59537.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Naegleria fowleri (brain-eating amoeba)
Plasmid: NafoA.18681.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A4V8H034*PLUS

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Non-polymers , 6 types, 917 molecules

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


Mass: 506.196 Da / Num. of mol.: 2 / 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 / Halofuginone


Mass: 414.681 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H17BrClN3O3 / Comment: alkaloid, medication*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 888 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.39 Å3/Da / Density % sol: 48.46 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: NafoA.18681.a.B2.PW37988 at 34 mg/ml, incubated with 2 mM MgCl2, AMPPNP, halofuginone, mixed 1:1 with MCSG1(a6): 25% (w/v) PEG-3350, 0.1 M Bis-Tris/HCl, pH = 5.5, 0.2 M ammonium sulfate, ...Details: NafoA.18681.a.B2.PW37988 at 34 mg/ml, incubated with 2 mM MgCl2, AMPPNP, halofuginone, mixed 1:1 with MCSG1(a6): 25% (w/v) PEG-3350, 0.1 M Bis-Tris/HCl, pH = 5.5, 0.2 M ammonium sulfate, cryoprotected with ethlyene glycol. Barcode: 310518a6, puck: xux0-7.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9785 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 23, 2019
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 114792 / % possible obs: 99.9 % / Redundancy: 4.173 % / Biso Wilson estimate: 22.34 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rrim(I) all: 0.06 / Χ2: 1.032 / Net I/σ(I): 15.69
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.75-1.84.2030.5172.5284310.8130.59299.9
1.8-1.844.2130.43.2882700.8890.45899.9
1.84-1.94.2120.3294.0680250.9180.37799.9
1.9-1.964.2110.2515.3877750.950.28899.9
1.96-2.024.2170.1966.8875350.9660.22499.9
2.02-2.094.20.1558.6973110.9790.17899.9
2.09-2.174.1990.12310.7870060.9860.14199.9
2.17-2.264.1760.10112.8767960.9910.11699.8
2.26-2.364.1810.08514.8165150.9930.09899.8
2.36-2.474.1790.07616.9862100.9940.08799.9
2.47-2.614.1660.06319.8459400.9960.07299.7
2.61-2.774.1640.05522.0256230.9970.06399.8
2.77-2.964.1430.04824.7452900.9970.05599.9
2.96-3.24.1430.04228.1949070.9980.04899.9
3.2-3.54.1210.03532.1845350.9980.041100
3.5-3.914.0710.03235.0741260.9980.03799.9
3.91-4.524.1010.02937.4936440.9990.034100
4.52-5.534.1190.02738.2330850.9990.0399.9
5.53-7.834.0970.0273724120.9990.03199.9
7.83-503.9020.02338.513560.9990.02798.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.17RC1_3602refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NAB

6nab


Resolution: 1.75→42.66 Å / SU ML: 0.174 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.49
Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
RfactorNum. reflection% reflection
Rfree0.18 1918 1.67 %
Rwork0.154 --
obs0.155 114783 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.61 Å2
Refinement stepCycle: LAST / Resolution: 1.75→42.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7889 0 206 888 8983
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068419
X-RAY DIFFRACTIONf_angle_d0.82611428
X-RAY DIFFRACTIONf_dihedral_angle_d13.0975061
X-RAY DIFFRACTIONf_chiral_restr0.0541226
X-RAY DIFFRACTIONf_plane_restr0.0061499
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.790.24871540.22277973X-RAY DIFFRACTION100
1.79-1.840.23511280.20128028X-RAY DIFFRACTION100
1.84-1.90.26041050.20448110X-RAY DIFFRACTION100
1.9-1.960.23811480.18667976X-RAY DIFFRACTION100
1.96-2.030.20471250.17378030X-RAY DIFFRACTION100
2.03-2.110.20631180.16298024X-RAY DIFFRACTION100
2.11-2.20.20041420.16178054X-RAY DIFFRACTION100
2.2-2.320.1721470.15988001X-RAY DIFFRACTION100
2.32-2.470.191350.15628057X-RAY DIFFRACTION100
2.47-2.660.16751470.15488053X-RAY DIFFRACTION100
2.66-2.920.18371370.15698057X-RAY DIFFRACTION100
2.92-3.350.18551320.15488123X-RAY DIFFRACTION100
3.35-4.220.15151530.12768111X-RAY DIFFRACTION100
4.22-42.660.15911470.14048268X-RAY DIFFRACTION100
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)
11.78040.2613-0.34080.98490.07860.87730.07110.04430.09430.0145-0.09970.0991-0.0606-0.14120.01420.1183-0.0264-0.01060.1616-0.02050.143241.87673.956621.6434
22.20940.4048-0.06931.13960.15460.84260.0576-0.1613-0.28890.1774-0.0997-0.04940.1114-0.0763-0.00530.1659-0.0517-0.01420.17080.00240.185640.5879-9.718427.6907
30.73520.44890.60980.66190.46632.04430.0766-0.18220.00240.0024-0.19140.1473-0.0011-0.31620.10210.1796-0.04640.02990.2802-0.06580.264921.4035-13.229315.0608
41.90070.0113-0.56980.54360.04821.32010.06420.02810.1401-0.0091-0.0686-0.0618-0.0235-0.02270.00760.157-0.032-0.00770.0970.00660.171761.46218.410321.6837
50.7845-0.0725-0.00860.6950.08711.0160.0498-0.1160.10880.0482-0.0430.0027-0.0104-0.1366-0.01450.1357-0.03240.00160.1123-0.010.139258.875612.116233.5783
60.41440.10130.15471.7457-0.22441.07610.0588-0.0131-0.0144-0.1879-0.0639-0.24270.12620.0903-0.0020.13080.01080.01290.13420.00320.216479.3126.436627.1098
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 4 THROUGH 123 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 124 THROUGH 382 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 383 THROUGH 505 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 4 THROUGH 90 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 91 THROUGH 304 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 305 THROUGH 505 )

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