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- PDB-8vtz: Crystal structure of Aquifex aeolicus Trbp111 -

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Basic information

Entry
Database: PDB / ID: 8vtz
TitleCrystal structure of Aquifex aeolicus Trbp111
ComponentsMethionyl-tRNA synthetase beta subunit
KeywordsRNA BINDING PROTEIN / OB fold / EMAPII-like domain / tRNA-binding protein
Function / homology
Function and homology information


methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / tRNA binding / ATP binding
Similarity search - Function
: / Methionyl-tRNA synthetase, beta subunit, C-terminal / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Methionine--tRNA ligase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsUmuhire Juru, A. / Zhang, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)ZIADK075136 United States
CitationJournal: Nat Commun / Year: 2024
Title: Structural basis of tRNA recognition by the widespread OB fold.
Authors: Umuhire Juru, A. / Ghirlando, R. / Zhang, J.
History
DepositionJan 27, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methionyl-tRNA synthetase beta subunit
B: Methionyl-tRNA synthetase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6293
Polymers24,5332
Non-polymers961
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-36 kcal/mol
Surface area11090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.002, 82.221, 88.882
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11B-331-

HOH

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Components

#1: Protein Methionyl-tRNA synthetase beta subunit


Mass: 12266.301 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: metG', aq_422 / Production host: Escherichia coli (E. coli) / References: UniProt: O66738
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.17 Å3/Da / Density % sol: 43.32 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M lithium sulfate monohydrate, 0.1 M Tris-HCl pH 8.5 and 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→47.4 Å / Num. obs: 9724 / % possible obs: 99.7 % / Redundancy: 18.6 % / Biso Wilson estimate: 28.85 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.041 / Net I/σ(I): 9.53
Reflection shellResolution: 2.3→2.38 Å / Mean I/σ(I) obs: 1.79 / Num. unique obs: 930 / CC1/2: 0.954 / Rpim(I) all: 0.119

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→47.4 Å / SU ML: 0.3188 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.3801
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.264 484 4.98 %
Rwork0.2141 9232 -
obs0.2165 9716 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.4 Å2
Refinement stepCycle: LAST / Resolution: 2.3→47.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1678 0 5 91 1774
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021702
X-RAY DIFFRACTIONf_angle_d0.49122296
X-RAY DIFFRACTIONf_chiral_restr0.0469284
X-RAY DIFFRACTIONf_plane_restr0.0043289
X-RAY DIFFRACTIONf_dihedral_angle_d4.663240
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.630.32321520.25793018X-RAY DIFFRACTION99.37
2.63-3.320.31621620.24573052X-RAY DIFFRACTION99.97
3.32-47.40.2231700.18523162X-RAY DIFFRACTION99.76
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)
15.97730755464-0.716168307714-3.282569182110.7697687143250.4432216147381.99347689430.05207164151140.2803681478080.01400092566120.0579215812483-0.0236463809563-0.03770118583850.168601758764-0.157852932289-0.03186216606070.2485004860760.00500343589809-0.03399468001020.3716017304070.04766937653770.26481165637120.08666306895.220046008914.2964423225
24.42647512834.371624872553.158855031775.470005919861.034106074416.392099257850.541784712055-0.190898705395-0.07916051983570.306110751071-0.532875386787-0.0868346396670.5635911271690.124732232795-0.04913703699940.2373495681370.02804728385140.04339349123780.531338355857-0.02555640718920.39356552172414.28984664558.8230111628636.0933849233
32.93103369399-1.151680785870.4232883549771.060238986911.490908240525.055568953260.105524097052-0.07790344208470.05029768862440.06475975537180.00623338895952-0.1404605239060.1247462337010.0611989866571-0.09690258069340.220291242149-0.02246440620450.02160850499380.2455482525730.03662963248860.2509458327813.04426829197.2077321549822.6507897363
42.346264012831.581228802060.6309921634244.981868376452.499989395464.15352672153-0.01514562768280.1426833530880.0954977368321-0.0821659059655-0.1294902428650.3953137454730.431898792055-0.9124048830140.04647351956310.269233086498-0.0380746102107-0.03820726116250.4955191742520.02275968984290.3214433327999.197189256648.902173731397.89485625589
52.15864667262-0.1288296947460.4101617433577.99121136523-4.064967582113.175327646360.1052826448690.110496783005-0.07802554905040.423330506013-0.266785281825-0.387115905019-0.2806678027240.3210269631720.1823702574980.1874783389560.02917753177220.03928655721950.330778649958-0.03920738647280.21197843524823.31334840838.201450028878.1765790515
64.525390203420.7601093194273.303254994626.309148170882.735964974888.63681804528-0.1128883956580.554731299039-0.29302265739-0.524352077072-0.0852114348254-0.284947680996-0.69527109490.2887021673310.1414541067350.3296244450970.03722825817590.03628048898950.2412247519240.03244380040260.25971751203721.513175227818.1329524259-7.66981571941
73.868529704390.08157167994763.252764952294.670178008240.84728617953.887776646540.114861770867-0.1274507165130.194284795898-0.384926909566-0.0698565021549-0.451285135184-0.1402226422170.590801691312-0.04514663204140.217711471049-0.07433342228860.03607488725980.4506394039850.03042632594240.36139301402521.758194834418.0602602116-0.0314996496985
85.26079818096-2.33123300069-4.714783197018.646747240534.191972177565.136204334570.03526910868360.113659653349-0.04835778787640.394116748110.291304633575-0.4715880670970.619906016161-0.496946099131-0.6856833461670.3036128418780.05879858224430.004492319974450.3959602204980.06974416718650.49460001121713.480520385223.90270588080.043369048664
93.36081654563-1.865922031511.187346655088.920683442870.5696376659533.865558069880.04570406037891.05295803049-0.294888226428-0.268114279796-0.5548732291510.6155928473660.068535332759-0.1093809388250.3135081632060.194612000744-0.00669833682147-0.05814937084570.2792062618750.0191013270090.21290095489326.318041481413.03316059145.55398206981
104.31530178634-1.344627375253.507154965847.62452141034-3.327634974133.654008918750.3567982208421.047221094050.2527534013670.288726662334-0.679206880076-0.3381706062720.7524012310041.846603732930.5086148240490.4233649200270.01934585773970.06965001100060.648116831999-0.09907619662690.32538079440229.436470220813.3974007358-8.90919177782
115.344109943613.44145720397-1.994283219925.52124697202-0.6785864391597.64358266243-0.295575226164-0.1290483025090.503887689208-0.1881072053540.02425405953390.2464362418130.228721379745-0.591596495870.2855198387530.2550501703120.01275323507890.02835927359320.3449455174550.0368880099020.25172484082414.35262169779.905194046842.12806768118
125.8895668165-0.1434373498791.329719554541.33231370379-3.052715404477.92348088427-0.54933509779-0.0363205476050.08459289193230.3569989924440.081308829996-0.358025217151-0.6835634186930.2453772806310.4144717456390.327697404733-0.03020161976110.004145517792720.225342082857-0.02118853539720.35563506699919.668153206119.190295967414.9464630995
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 27 )AA1 - 273 - 29
22chain 'A' and (resid 28 through 34 )AA28 - 3430 - 36
33chain 'A' and (resid 35 through 97 )AA35 - 9737 - 99
44chain 'A' and (resid 98 through 111 )AA98 - 111100 - 113
55chain 'B' and (resid 1 through 27 )BB1 - 273 - 29
66chain 'B' and (resid 28 through 40 )BB28 - 4030 - 42
77chain 'B' and (resid 41 through 57 )BB41 - 5743 - 59
88chain 'B' and (resid 58 through 64 )BB58 - 6460 - 66
99chain 'B' and (resid 65 through 74 )BB65 - 7467 - 76
1010chain 'B' and (resid 75 through 82 )BB75 - 8277 - 84
1111chain 'B' and (resid 83 through 97 )BB83 - 9785 - 99
1212chain 'B' and (resid 98 through 111 )BB98 - 111100 - 113

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