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- PDB-7qc1: Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline-tRNA ... -

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Basic information

Entry
Database: PDB / ID: 7qc1
TitleCrystal Structure of Prolyl-tRNA synthetase (ProRS, Proline-tRNA ligase) from Plasmodium falciparum in complex with MAT436
ComponentsProline--tRNA ligase
KeywordsLIGASE / Proline / Aminoacyl-tRNA synthetase / Protein biosynthesis
Function / homology
Function and homology information


Ala-tRNA(Pro) hydrolase activity / proline-tRNA ligase / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / tRNA aminoacylation for protein translation / aminoacyl-tRNA synthetase multienzyme complex / ATP binding / cytoplasm
Similarity search - Function
YbaK/aminoacyl-tRNA synthetase-associated domain / Aminoacyl-tRNA editing domain / YbaK/aminoacyl-tRNA synthetase-associated domain superfamily / 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 ...YbaK/aminoacyl-tRNA synthetase-associated domain / Aminoacyl-tRNA editing domain / YbaK/aminoacyl-tRNA synthetase-associated domain superfamily / 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 / 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 / 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-9XM / Proline--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.51 Å
AuthorsJohansson, C. / Tye, M. / Payne, N.C. / Mazitschek, R. / Oppermann, U.C.T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline-tRNA ligase) from Plasmodium falciparum in complex with MAT436
Authors: Johansson, C. / Tye, M. / Payne, N.C. / Mazitschek, R. / Oppermann, U.C.T.
History
DepositionNov 22, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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
D: Proline--tRNA ligase
I: Proline--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,86016
Polymers175,5813
Non-polymers3,27913
Water1,31573
1
A: Proline--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7237
Polymers58,5271
Non-polymers1,1976
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Proline--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5374
Polymers58,5271
Non-polymers1,0103
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: Proline--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5995
Polymers58,5271
Non-polymers1,0724
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)207.210, 207.210, 115.850
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 Proline--tRNA ligase / Prolyl-tRNA synthetase / ProRS


Mass: 58526.926 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / Gene: proRS, PFL0670c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8I5R7, proline-tRNA ligase
#2: Chemical ChemComp-9XM / [(2~{R},3~{S})-2-[3-(7-bromanyl-6-chloranyl-4-oxidanylidene-quinazolin-3-yl)-2-oxidanylidene-propyl]piperidin-3-yl] ~{N}-[4-[[3-(2,3-dihydro-1~{H}-inden-2-ylcarbamoyl)pyrazin-2-yl]carbamoyl]piperazin-1-yl]sulfonylcarbamate


Mass: 886.171 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C36H38BrClN10O8S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 3.54 Å3/Da / Density % sol: 65.27 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 1.5 M Malic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.51→65.53 Å / Num. obs: 86283 / % possible obs: 100 % / Redundancy: 26.7 % / Biso Wilson estimate: 69.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.256 / Net I/σ(I): 11.5
Reflection shellResolution: 2.51→2.51 Å / Rmerge(I) obs: 5.81 / Num. unique obs: 4261 / CC1/2: 0.359

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.61 Å65.53 Å
Translation5.61 Å65.53 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASER2.8.0phasing
PHENIX1.19.2-4158refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6T7K

6t7k


Resolution: 2.51→65.53 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2333 4283 4.97 %
Rwork0.1914 81878 -
obs0.1935 86161 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 161.72 Å2 / Biso mean: 75.5099 Å2 / Biso min: 40.81 Å2
Refinement stepCycle: final / Resolution: 2.51→65.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11624 0 211 73 11908
Biso mean--68.14 66.76 -
Num. residues----1455
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.51-2.540.42091520.4362663281599
2.54-2.570.44681360.416227062842100
2.57-2.60.39061590.412826652824100
2.6-2.630.42721450.403227252870100
2.63-2.670.42381320.397526812813100
2.67-2.70.42941330.357126792812100
2.7-2.740.39181400.314726892829100
2.74-2.780.29811420.297526912833100
2.78-2.830.35661370.285127382875100
2.83-2.870.33661440.273626762820100
2.87-2.920.27951280.251727082836100
2.92-2.980.31311380.2627272865100
2.98-3.030.29331370.25627002837100
3.03-3.10.28791390.267327062845100
3.1-3.160.32021330.267327172850100
3.16-3.240.29691530.2427052858100
3.24-3.320.27471260.229227412867100
3.32-3.410.24431370.201927382875100
3.41-3.510.24271620.185826772839100
3.51-3.620.22651600.181327352895100
3.62-3.750.19551440.1826982842100
3.75-3.90.22451400.174427282868100
3.9-4.080.22371490.170727232872100
4.08-4.290.20681370.152627722909100
4.29-4.560.18651260.133227612887100
4.56-4.910.1521630.132727522915100
4.91-5.410.20781390.145527782917100
5.41-6.190.22281670.170927612928100
6.19-7.790.18931470.167328422989100
7.8-65.530.19411380.15629963134100
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)
11.66380.1455-0.07970.87950.00420.915-0.0397-0.08990.00340.0382-0.0231-0.17970.14110.04670.0830.6431-0.01660.01190.5283-0.02420.624567.7983185.301126.0569
22.3798-0.2982-0.25371.20430.19451.71950.0695-0.0042-0.1144-0.006-0.06840.0980.279-0.21150.0040.5263-0.05890.00280.4554-0.0370.433750.6834183.515523.3551
33.5247-0.20990.33182.25460.04823.5004-0.09490.4161.088-0.1144-0.0951-0.6848-0.29130.26590.16060.55130.01520.18810.52580.14821.065586.0446201.537311.1079
42.94261.65620.42694.19550.18520.77920.06330.5116-0.2371-0.2409-0.0165-0.17980.39480.0156-0.03210.80930.11690.04880.7213-0.05890.480361.4976173.72864.6321
50.9672-0.18840.63321.23280.27082.25790.0660.06240.04010.01460.0648-0.18710.21460.37-0.1240.6165-0.09050.01010.7188-0.01380.556543.5301174.316-22.6409
61.21270.27510.09471.3742-0.06032.3616-0.04570.2960.0802-0.14620.0858-0.1394-0.21270.5812-0.03970.4971-0.12110.00070.6603-0.02190.425846.1643183.0791-37.918
73.6627-0.42051.03744.0425-0.53822.3833-0.1398-0.3526-0.06690.13480.28080.2482-0.3201-0.6398-0.15730.68040.01570.00670.80850.0030.544325.9434192.2265-2.9666
81.78120.2845-0.99780.68340.47852.63680.0202-0.0290.12460.09460.2445-0.3444-0.49680.6741-0.24670.7439-0.2245-0.06620.7826-0.04450.6356.8585197.4042-24.1874
92.1494-0.8911-0.69352.12150.39230.74310.0597-0.27940.24680.1334-0.01590.0810.06190.0318-0.03160.5674-0.09810.0060.5431-0.0860.544255.2725198.537140.2904
101.8776-0.3962-0.29111.79470.18081.41250.0589-0.28990.1760.15540.0602-0.16420.12510.1603-0.1140.5598-0.0433-0.03370.4467-0.07320.546369.5666198.518542.442
114.0469-1.90380.59962.47170.50221.65040.0832-0.28820.71090.1896-0.0225-0.26570.18130.0514-0.060.5401-0.06110.03090.4274-0.0390.5967.5121205.151843.4306
122.00470.20841.00164.8388-1.05395.521-0.18710.24640.0973-1.0446-0.01841.2742-0.5877-0.70880.18590.85080.1478-0.25810.80690.02940.92635.2982214.565718.6989
131.42570.54640.27021.50330.41892.29190.0951-0.07310.5159-0.1409-0.11070.4481-0.5672-0.36360.02890.58810.08330.06280.5651-0.08920.86647.5327220.788239.6851
143.47490.1835-0.9992.0197-0.69914.89550.4689-0.1878-0.10230.5017-0.2960.31260.553-0.369-0.1750.7446-0.1839-0.03970.6308-0.1260.679963.0581209.90364.4928
156.35311.73790.7042.56320.11812.4710.3351-1.24780.3943-0.1165-0.3645-0.2452-0.34220.35020.06040.7203-0.16480.06660.7909-0.2630.704869.6237218.667363.7202
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 244 through 343 )A244 - 343
2X-RAY DIFFRACTION2chain 'A' and (resid 344 through 523 )A344 - 523
3X-RAY DIFFRACTION3chain 'A' and (resid 524 through 620 )A524 - 620
4X-RAY DIFFRACTION4chain 'A' and (resid 621 through 746 )A621 - 746
5X-RAY DIFFRACTION5chain 'D' and (resid 244 through 360 )D244 - 360
6X-RAY DIFFRACTION6chain 'D' and (resid 361 through 523 )D361 - 523
7X-RAY DIFFRACTION7chain 'D' and (resid 524 through 620 )D524 - 620
8X-RAY DIFFRACTION8chain 'D' and (resid 621 through 746 )D621 - 746
9X-RAY DIFFRACTION9chain 'I' and (resid 252 through 343 )I252 - 343
10X-RAY DIFFRACTION10chain 'I' and (resid 344 through 458 )I344 - 458
11X-RAY DIFFRACTION11chain 'I' and (resid 459 through 539 )I459 - 539
12X-RAY DIFFRACTION12chain 'I' and (resid 540 through 582 )I540 - 582
13X-RAY DIFFRACTION13chain 'I' and (resid 583 through 682 )I583 - 682
14X-RAY DIFFRACTION14chain 'I' and (resid 683 through 720 )I683 - 720
15X-RAY DIFFRACTION15chain 'I' and (resid 721 through 746 )I721 - 746

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