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- PDB-6mn8: Crystal Structure of Prolyl-tRNA Synthetase from Onchocerca volvu... -

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Basic information

Entry
Database: PDB / ID: 6mn8
TitleCrystal Structure of Prolyl-tRNA Synthetase from Onchocerca volvulus with bound Halofuginone and nucleotide
ComponentsUncharacterized protein
KeywordsLIGASE / SSGCID / ProRS / ATP-binding / aminoacylation / halofuginone / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


proline-tRNA ligase / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Proline-tRNA ligase, class IIa / Prolyl-tRNA synthetase, catalytic domain / 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 / Anticodon-binding domain / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) ...Proline-tRNA ligase, class IIa / Prolyl-tRNA synthetase, catalytic domain / 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 / 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
IMIDODIPHOSPHORIC ACID / ADENOSINE MONOPHOSPHATE / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / GLYCINE / Chem-HFG / SERINE / proline--tRNA ligase
Similarity search - Component
Biological speciesOnchocerca volvulus (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal Structure of Prolyl-tRNA Synthetase from Onchocerca volvulus with bound Halofuginone and nucleotide
Authors: Dranow, D.M. / Conrady, D.G. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionOct 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2018Provider: 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,14812
Polymers58,2191
Non-polymers1,92911
Water2,972165
1
A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,29724
Polymers116,4392
Non-polymers3,85822
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_445x-y-1/3,-y-2/3,-z+1/31
Buried area9200 Å2
ΔGint-57 kcal/mol
Surface area30920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.720, 159.720, 143.720
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Uncharacterized protein


Mass: 58219.285 Da / Num. of mol.: 1 / Fragment: residues 54-550
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Onchocerca volvulus (invertebrata) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2K6VKP7

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Non-polymers , 8 types, 176 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#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 / Feature type: SUBJECT OF INVESTIGATION / Comment: alkaloid, medication*YM
#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#6: Chemical ChemComp-2PN / IMIDODIPHOSPHORIC ACID


Mass: 176.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H5NO6P2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H5NO2
#8: Chemical ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 3.03 Å3/Da / Density % sol: 59.46 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: OnvoA.17194.a.B5.PW38185 at 17 mg/ml was incubated with 2 mM halofuginone, AMPPNP, and MgCl2, then was mixed 1:1 Morpheus(h12): 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (v/v) MPD, 0. ...Details: OnvoA.17194.a.B5.PW38185 at 17 mg/ml was incubated with 2 mM halofuginone, AMPPNP, and MgCl2, then was mixed 1:1 Morpheus(h12): 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (v/v) MPD, 0.02 M each sodium L-glutamate, DL-alanine, glycine, DL-lysine HCl, DL-serine, 0.1 M bicine/Trizma base, pH=8.5. Tray: 389737h12, puck: lte2-7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 5, 2018 / Details: Beryllium Lenses
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.35→42.276 Å / Num. obs: 29419 / % possible obs: 100 % / Redundancy: 9.479 % / Biso Wilson estimate: 43.814 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.085 / Rrim(I) all: 0.09 / Χ2: 1.003 / Net I/σ(I): 19.16 / Num. measured all: 278849 / Scaling rejects: 5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.35-2.419.5480.5983.9721660.9070.632100
2.41-2.489.5180.4924.7821020.9390.52100
2.48-2.559.5580.4285.5220320.9520.453100
2.55-2.639.5390.3367.0319790.9670.355100
2.63-2.719.5270.2957.9919430.9740.312100
2.71-2.819.5820.2349.8118690.9850.248100
2.81-2.929.5230.18912.0917910.9890.199100
2.92-3.039.5350.1613.8717390.9930.169100
3.03-3.179.50.12717.2216750.9950.134100
3.17-3.329.5380.09920.8315900.9970.105100
3.32-3.59.510.08125.3315110.9970.086100
3.5-3.729.5030.06630.1514460.9980.07100
3.72-3.979.520.05533.5513530.9980.059100
3.97-4.299.4440.05136.7112670.9980.054100
4.29-4.79.4640.04540.7411670.9990.048100
4.7-5.269.4030.04441.5810540.9980.04799.9
5.26-6.079.3120.04839.439450.9980.05100
6.07-7.439.2380.04739.558040.9980.0599.9
7.43-10.519.0390.0444.316220.9990.043100
10.51-42.2768.1480.0445.033640.9990.04397.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260)refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HVC

4hvc


Resolution: 2.35→42.276 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 16.71
RfactorNum. reflection% reflection
Rfree0.1795 1710 6 %
Rwork0.1416 --
obs0.1438 28483 96.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 147.16 Å2 / Biso mean: 44.2288 Å2 / Biso min: 16.82 Å2
Refinement stepCycle: final / Resolution: 2.35→42.276 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3185 0 118 165 3468
Biso mean--56.67 45.67 -
Num. residues----399
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073401
X-RAY DIFFRACTIONf_angle_d0.8774635
X-RAY DIFFRACTIONf_chiral_restr0.055494
X-RAY DIFFRACTIONf_plane_restr0.006625
X-RAY DIFFRACTIONf_dihedral_angle_d13.3312004
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3502-2.41940.23151280.18342121224992
2.4194-2.49740.20751170.17062116223393
2.4974-2.58670.20561410.15862133227494
2.5867-2.69020.2211390.15352181232096
2.6902-2.81260.19451330.15422215234896
2.8126-2.96090.17391540.15172225237997
2.9609-3.14640.20951530.14682230238398
3.1464-3.38920.19821640.14362250241499
3.3892-3.73010.15811590.12962266242599
3.7301-4.26940.14581380.12182303244199
4.2694-5.37720.15911310.116323452476100
5.3772-42.28280.18561530.16292388254199
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)
15.49821.6631-1.50335.6815-0.24348.95410.1332-0.55010.19930.8720.0285-0.1503-0.4122-0.167-0.15990.42510.0721-0.05190.3214-0.03830.3927-42.179-21.841.64
20.65010.09370.26791.39650.77313.913-0.061-0.25410.11030.0989-0.07610.1111-0.0579-0.46870.14590.23070.04090.01210.22780.02770.2658-46.036-37.14927.989
32.4315-2.33491.55252.5248-0.55434.4945-0.2070.01220.0945-0.13420.0327-0.377-0.17020.46910.1710.28830.00110.02010.2470.00670.2678-32.507-44.03813.114
41.7126-0.0427-0.39281.0680.58942.83970.0073-0.08530.088-0.00170.0105-0.0796-0.09930.0702-0.03560.1594-0.01030.00520.16280.03970.2097-35.11-42.78813.902
51.0425-1.8202-2.20525.86314.70877.50490.2440.22060.1178-0.5682-0.166-0.2426-0.6652-0.4078-0.19440.30870.0843-0.03110.32070.0920.3593-48.647-27.93610.173
61.0076-0.8374-1.10271.54511.84473.92810.038-0.04050.0985-0.15970.0861-0.0853-0.298-0.0215-0.17050.21430.0187-0.01130.25720.04750.3113-46.256-32.72416.748
73.3327-0.0226-0.84423.14920.92952.0269-0.0298-0.5689-0.05860.41740.07340.4548-0.0652-0.6973-0.01430.34050.12990.05880.62040.03030.3922-65.545-29.83644.576
89.31715.5486-5.42187.2317-4.48557.26750.25520.24881.020.17950.23020.4993-0.684-0.3878-0.48180.33910.1837-0.01250.420.03140.3789-58.973-18.58125.196
92222-5.205624.9588-6.8972-9.754211.86377.973-15.48569.390415.173-12.91390.92690.2487-0.1231.1106-0.17230.8487-57.029-38.14545.05
1022-9.2444223.7117-0.308313.0111-6.917-10.4387-5.2956-3.241811.1624-6.03765.62751.09440.43680.09141.0813-0.18920.7169-45.681-39.51642.447
11222222-4.37870.8381-17.5861-8.4896-1.2184-19.73014.689124.09635.6320.92510.07710.10521.84-0.16161.065-54.386-15.58538.987
122-3.741722221.1028-1.1932-2.5089-0.2772-0.61116.6210.06222.2866-0.56690.74070.1994-0.17881.29190.31661.0414-17.158-50.51830.772
135.99284.4854-3.35284.9822-0.66973.9587-4.21120.93446.7034-2.46850.84160.8266-19.0204-24.80873.41181.38580.2847-0.25081.3927-0.08841.1184-61.571-32.65420.098
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 47:72 )A47 - 72
2X-RAY DIFFRACTION2( CHAIN A AND RESID 73:109 )A73 - 109
3X-RAY DIFFRACTION3( CHAIN A AND RESID 110:138 )A110 - 138
4X-RAY DIFFRACTION4( CHAIN A AND RESID 139:216 )A139 - 216
5X-RAY DIFFRACTION5( CHAIN A AND RESID 217:267 )A217 - 267
6X-RAY DIFFRACTION6( CHAIN A AND RESID 268:353 )A268 - 353
7X-RAY DIFFRACTION7( CHAIN A AND RESID 354:438 )A354 - 438
8X-RAY DIFFRACTION8( CHAIN A AND RESID 439:461 )A439 - 461
9X-RAY DIFFRACTION9( CHAIN A AND RESID 607:607 )A607
10X-RAY DIFFRACTION10( CHAIN A AND RESID 608:608 )A608
11X-RAY DIFFRACTION11( CHAIN A AND RESID 609:609 )A609
12X-RAY DIFFRACTION12( CHAIN A AND RESID 610:610 )A610
13X-RAY DIFFRACTION13( CHAIN A AND RESID 611:611 )A611

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