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- PDB-7l3o: Crystal Structure of the RNA binding domain of Threonyl-tRNA synt... -

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Basic information

Entry
Database: PDB / ID: 7l3o
TitleCrystal Structure of the RNA binding domain of Threonyl-tRNA synthetase from Cryptosporidium parvum Iowa II
ComponentsThreonyl-tRNA synthetase
KeywordsLIGASE / SSGCID / Threonyl-tRNA synthetase / class-II aminoacyl-tRNA synthetase family / Cryptosporidium parvum / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


threonine-tRNA ligase / threonyl-tRNA aminoacylation / threonine-tRNA ligase activity / mitochondrion / ATP binding / metal ion binding
Similarity search - Function
Threonine-tRNA ligase, class IIa / Threonine-tRNA ligase catalytic core domain / Threonyl and Alanyl tRNA synthetase second additional domain / : / Threonyl/alanyl tRNA synthetase, SAD / TGS domain / Threonyl and Alanyl tRNA synthetase second additional domain / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / TGS domain profile. / TGS ...Threonine-tRNA ligase, class IIa / Threonine-tRNA ligase catalytic core domain / Threonyl and Alanyl tRNA synthetase second additional domain / : / Threonyl/alanyl tRNA synthetase, SAD / TGS domain / Threonyl and Alanyl tRNA synthetase second additional domain / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / TGS domain profile. / TGS / 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. / Beta-grasp domain superfamily / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
Similarity search - Domain/homology
threonine--tRNA ligase
Similarity search - Component
Biological speciesCryptosporidium parvum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of the RNA binding domain of Threonyl-tRNA synthetase from Cryptosporidium parvum Iowa II
Authors: Abendroth, J. / Dranow, D.M. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionDec 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Threonyl-tRNA synthetase
B: Threonyl-tRNA synthetase
C: Threonyl-tRNA synthetase
D: Threonyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,95910
Polymers205,6174
Non-polymers3426
Water16,916939
1
A: Threonyl-tRNA synthetase
D: Threonyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,9805
Polymers102,8092
Non-polymers1713
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-117 kcal/mol
Surface area32620 Å2
MethodPISA
2
B: Threonyl-tRNA synthetase
C: Threonyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,9805
Polymers102,8092
Non-polymers1713
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-117 kcal/mol
Surface area33100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.730, 67.450, 143.180
Angle α, β, γ (deg.)91.585, 97.530, 120.777
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
Threonyl-tRNA synthetase


Mass: 51404.312 Da / Num. of mol.: 4 / Fragment: UNP Residues 330-763
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum (strain Iowa II) (eukaryote)
Strain: Iowa II / Gene: cgd7_1710 / Plasmid: CrpaA.18896.a.B3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5CYN0, threonine-tRNA ligase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 939 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.62 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Microlytic MCSG1 screen e9: 200mM CaCl2, 20% (w/V) PEG 3350: CrpaA.18896.a.B3.PW38874 at 18mg/ml: tray 317798 e9: cryo: 20% EG in 2 steps: puck dxt2-9.

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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: RAYONIX MX-300 / Detector: CCD / Date: Sep 24, 2020 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 116442 / % possible obs: 95.8 % / Redundancy: 3.242 % / Biso Wilson estimate: 41.307 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.075 / Χ2: 0.939 / Net I/σ(I): 12.35
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.1-2.153.0040.4222.9385510.8510.51495.2
2.15-2.213.2950.353.8185020.8930.42296.7
2.21-2.283.2980.314.4382690.9070.37496.6
2.28-2.353.2970.275.0380430.9270.32596.6
2.35-2.423.2830.2215.9577590.9510.26697.1
2.42-2.513.2810.1787.1275200.9670.21596.9
2.51-2.63.2720.1498.2872130.9750.1897
2.6-2.713.2680.1189.6769860.9840.14296.6
2.71-2.833.2520.09911.2566810.9870.11996.7
2.83-2.973.2370.07713.663950.9920.09396.5
2.97-3.133.2330.06815.3460510.9920.08295.8
3.13-3.323.2240.05418.2856260.9950.06595
3.32-3.553.2230.04621.1652250.9960.05694.2
3.55-3.833.2320.04223.2848680.9960.05194
3.83-4.23.2360.04125.2744720.9960.04993.5
4.2-4.73.2440.03926.6241260.9960.04794.9
4.7-5.423.2510.03826.7335780.9960.04694.3
5.42-6.643.260.03926.1630480.9960.04794.3
6.64-9.393.2440.03827.0923520.9950.04594.5
9.39-503.150.03728.0811770.9950.04587.8

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.19rc4-4035refinement
PDB_EXTRACT3.27data extraction
MoRDaphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4hwt in two domains as per MoRDa

4hwt


Resolution: 2.1→47.26 Å / SU ML: 0.2533 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 23.6971
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2129 1978 1.7 %0
Rwork0.1782 114415 --
obs0.1788 116393 95.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.1 Å2
Refinement stepCycle: LAST / Resolution: 2.1→47.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12811 0 6 939 13756
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006713221
X-RAY DIFFRACTIONf_angle_d0.821417916
X-RAY DIFFRACTIONf_chiral_restr0.04781929
X-RAY DIFFRACTIONf_plane_restr0.00742317
X-RAY DIFFRACTIONf_dihedral_angle_d13.45414833
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.27121710.24348073X-RAY DIFFRACTION95.21
2.15-2.210.30921730.22628222X-RAY DIFFRACTION96.58
2.21-2.280.3021250.22218325X-RAY DIFFRACTION96.62
2.28-2.350.25321500.21258242X-RAY DIFFRACTION96.66
2.35-2.430.26741290.20898271X-RAY DIFFRACTION96.92
2.43-2.530.26321740.20138237X-RAY DIFFRACTION96.83
2.53-2.650.26531380.20178252X-RAY DIFFRACTION96.89
2.65-2.790.23891240.20438241X-RAY DIFFRACTION96.66
2.79-2.960.25691290.20438264X-RAY DIFFRACTION96.44
2.96-3.190.23481400.20228144X-RAY DIFFRACTION95.66
3.19-3.510.21931190.18648121X-RAY DIFFRACTION94.89
3.51-4.020.17911430.15597989X-RAY DIFFRACTION93.68
4.02-5.060.15641270.13098076X-RAY DIFFRACTION94.24
5.06-47.260.16431360.15727958X-RAY DIFFRACTION93.54
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)
14.42963812479-1.118112417130.2002232355664.61439739485-0.008419111293632.028832295480.132067838009-0.719860400958-0.2536626852220.5213672220470.0828412212555-0.3367919986020.2084233446990.0225909787002-0.1559530439720.406064144958-0.0987795813191-0.07697243345260.2786249519870.05918700495790.33942453827-27.8755108762-34.371568894-44.5371394327
20.08301003995860.574081077662-0.5231569346925.31788964315-3.523553857493.401181881460.324797207265-0.507180844116-0.5415499784080.1120324826760.272964827321.085358690580.680536798103-1.20510569585-0.5497087999790.424904342774-0.19607523118-0.06124712918460.5951898066990.2140001307390.585285175968-36.9763996388-36.0829292237-45.7416112023
30.902511380608-0.0473630736402-0.9272161782132.19476376734-0.2379458975910.9971354652690.17565759633-0.0715198932538-0.6594426096320.174058383222-0.0358872214584-0.1055347047440.927329582966-0.230787808092-0.2541764200130.784971861482-0.153690285071-0.3017871866530.2811673368620.1884858131630.7764635785-31.6908534322-45.1701973253-49.4183050956
41.14262028006-1.332043057312.011079540396.38053269608-6.32586809046.77349718704-0.00237768778985-0.0383660673241-0.198962514485-0.835138503718-0.0624673283071-0.785633228281.390886446950.1590843358150.08244567393790.6026034162460.0340101226475-0.03863419571090.221829356605-0.03812428712540.484842137533-23.1080182013-37.3592754861-58.2055835272
51.851289799560.7809777256460.1669118914711.861621503410.06887777695511.93030160380.0754958312151-0.1925892060720.3433373903460.0702881309447-0.05427611364180.480525148341-0.233627717594-0.18851341726-0.03273780329490.1895754519790.04908424149050.03326925804660.269239340269-0.01686522286240.3354102343152.532797211498.3975395176522.0299284122
61.458984244070.9534104175850.06413401937761.93439906776-1.418563548543.819199128110.000845732082435-0.1924497425510.4431597536610.330857329007-0.02012891121670.303499496867-0.702268856312-0.0931401229482-0.02871018625750.3118681413620.05721513400120.06763712919430.282407578023-0.06452792441940.4061153968265.4261355485415.236153282323.5114909582
72.279113285480.608230288012-0.1013833483891.910333712370.1508081309171.936417395030.250819011162-0.6000558283830.2394895613110.413433417845-0.1962079852060.293039480778-0.278041876438-0.120328229043-0.07199545169760.286556986518-0.0217315709270.07784141060240.421257064879-0.06631369413540.26727206706610.78452768179.1136593604236.3177980116
86.895358880630.662620106138-1.966552506896.30390626109-1.748994283228.74087985382-0.08144865245210.826598551207-0.407275578833-1.455532383780.161321485770.1413126488730.728731182284-0.0288699455066-0.025626381740.4678601926760.02627593002610.02947918422930.48618208419-0.1603782010750.36664621411729.5567529992-8.17586475122.015096817
94.5190146424-1.36322111785-1.074969670694.046146210990.7412165347944.293964469540.0600866537639-0.14280647731-0.0210503395857-0.3585510536480.504504841301-1.16121436774-0.01531857111831.08995201157-0.3321317181510.28183608938-0.0318104233130.105706354450.589285423681-0.1855683625090.54842315479637.5876959254-2.222292311349.06733963893
104.38691700932-2.62712706111-5.751619375723.212248805394.567705050298.25216094513-0.198023818831-0.50192320304-0.4642417030350.1530078630010.260615754736-0.115842905960.6640272053160.77133968583-0.05890524229090.3157056942350.131225311947-0.03897204712040.478894843025-0.01530851263270.46726660969329.4226886573-10.563225446819.4140117839
110.921846386080.1738096833110.211217259620.8810226555460.3977170039381.7207279587-0.07398106139870.1678761187910.14386729061-0.3192800168860.09256071760650.267380868678-0.112750949528-0.094604455689-0.02133391104990.275253941111-0.00965507877959-0.04964801609790.3172082754490.05904757552510.2920833943-0.7757020644480.4428145968181.79919947427
121.152101242190.2588848623520.2811985482622.98084045814-2.22128581473.44444661253-0.0319400094301-0.060365965361-0.136665927937-0.169243977630.0724506043131-0.145698353960.263659636678-0.188628002751-0.0461460000020.250943952505-0.01269371980930.01869060261670.277954881725-0.01334875044250.2132232472363.37893440256-15.810910441417.1591822908
132.325938776320.312416316943-0.1094754777541.12358563969-0.2646387269991.99518962987-0.0524435736767-0.2711566217380.2711257510510.05770889107860.03032951753430.0588065451645-0.193455700042-0.1469400279130.01183926360540.2514536280030.01788520410850.003620545447760.190290423597-0.03093294127410.202862746119-21.9320129563-4.73710841376-47.421892022
141.907996033590.7714172131160.1917500610280.924117708145-0.8861733468812.58194233249-0.143982426679-0.1619734782110.3536839992070.1734831683710.0799765208977-0.0454508619083-0.2003951705270.09023075290940.02571793329580.3158417851970.03977909503280.02376338673740.233554822463-0.03761372187060.300929809082-16.63871960460.0634335754327-44.9961602343
151.64021184920.2259777594880.3655179190381.420267559550.7133704533143.630454411760.0509944705044-0.3813014396220.005336594469380.260944946799-0.0514481536108-0.03083942224330.0160014127993-0.02085463114260.004048402587590.3037336049660.0289562779312-0.03205302970210.3179830915550.009343072150040.184482603943-11.6392849841-10.4647831452-27.1109520075
162.00484962017-0.0535717863555-1.27286301881.273983697120.8904786939433.66704764778-0.06388745386540.0523403280163-0.0951341143608-0.1315206838740.122105414178-0.126322775501-0.1059636499090.234244458558-0.05208881779940.2041050503050.0260736501339-0.004319158342830.1921591441870.0493021890450.192744719646-6.50618257276-15.0353566311-55.1339535085
175.06947094834-2.80552383618-4.078301323753.163359227625.098002092439.48520644205-0.489935204723-0.314837166475-0.7353927251090.3599769895990.1460310418620.4614189786160.8130775838190.3311205496250.3752660804040.4441160040570.115082525560.1257822164960.2471628132010.07175739580570.469319902026-2.53439576512-29.2269301402-59.2290222539
181.664189213150.4493210056980.1116435171851.427712894340.1603783366751.68020389849-0.1071290353160.1426249557730.33610873317-0.1188041385460.05931868449530.162023724286-0.300874501506-0.188102278989-0.001648606310790.2468434260810.0251828166522-0.02865006329070.1931665836910.05029653697810.255027544409-28.4547088737-4.50799146986-59.151722065
191.480752339170.5798692238510.5498133445881.496471209880.1974950161461.79078517129-0.2146043245340.4346291377890.236976981738-0.3476441897940.1607340768260.140361173454-0.400909782713-0.0997251370188-0.01442780554770.345802238881-0.0457243674959-0.03490962083680.3162918923710.1027069769760.244381820103-29.0581449977-8.37173828609-72.6229188071
201.86309525609-0.000309590326397-0.1964021508232.70020058566-0.7332453225371.95043729055-0.3524647699520.8296991545830.290677649978-0.5451257488130.2594273894110.173649453854-0.305002596348-0.1057563294810.04592716429010.594296254661-0.116165224923-0.1222944815030.6543886559330.1067169438910.297605480633-33.3519044832-7.7308128264-86.9340933263
211.322073713381.40420084756-0.3797882755423.59552400002-1.297400363482.61911752849-0.1979763987150.3824259098280.306958181427-0.2603590933290.1883281222270.0771826457229-0.36881139598-0.0469465153972-0.04871185912250.334756144687-0.0261214604486-0.028630212050.3079298667040.09359625020740.264888316369-30.0226408095-7.02683236272-73.8830857425
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'C' and (resid 648 through 695 )CG648 - 695292 - 339
22chain 'C' and (resid 696 through 714 )CG696 - 714340 - 358
33chain 'C' and (resid 715 through 735 )CG715 - 735359 - 379
44chain 'C' and (resid 736 through 757 )CG736 - 757380 - 401
55chain 'D' and (resid 332 through 454 )DI332 - 4541 - 123
66chain 'D' and (resid 455 through 481 )DI455 - 481124 - 150
77chain 'D' and (resid 482 through 666 )DI482 - 666151 - 309
88chain 'D' and (resid 667 through 695 )DI667 - 695310 - 338
99chain 'D' and (resid 696 through 735 )DI696 - 735339 - 378
1010chain 'D' and (resid 736 through 757 )DI736 - 757379 - 400
1111chain 'A' and (resid 333 through 555 )AA333 - 5551 - 223
1212chain 'A' and (resid 556 through 757 )AA556 - 757224 - 400
1313chain 'B' and (resid 332 through 454 )BD332 - 4541 - 123
1414chain 'B' and (resid 455 through 481 )BD455 - 481124 - 150
1515chain 'B' and (resid 482 through 555 )BD482 - 555151 - 224
1616chain 'B' and (resid 556 through 735 )BD556 - 735225 - 379
1717chain 'B' and (resid 736 through 757 )BD736 - 757380 - 401
1818chain 'C' and (resid 332 through 436 )CG332 - 4361 - 105
1919chain 'C' and (resid 437 through 521 )CG437 - 521106 - 190
2020chain 'C' and (resid 522 through 555 )CG522 - 555191 - 224
2121chain 'C' and (resid 556 through 647 )CG556 - 647225 - 291

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