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- PDB-8vu0: Co-crystal structure of Aquifex aeolicus Trbp111 in complex with ... -

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Basic information

Entry
Database: PDB / ID: 8vu0
TitleCo-crystal structure of Aquifex aeolicus Trbp111 in complex with E. coli tRNA-Ile
Components
  • Methionyl-tRNA synthetase beta subunit
  • RNA (76-MER)
KeywordsRNA BINDING PROTEIN/RNA / OB fold / EMAPII-like domain / tRNA-binding / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / tRNA binding / ATP binding
Similarity search - Function
: / Methionyl-tRNA synthetase, beta subunit, C-terminal / tRNA-binding domain / tRNA-binding domain profile. / Putative tRNA binding domain / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
RNA / RNA (> 10) / Methionyl-tRNA synthetase beta subunit
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 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
C: RNA (76-MER)
D: RNA (76-MER)
B: Methionyl-tRNA synthetase beta subunit
A: Methionyl-tRNA synthetase beta subunit


Theoretical massNumber of molelcules
Total (without water)73,7424
Polymers73,7424
Non-polymers00
Water3,621201
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)190.495, 55.028, 87.160
Angle α, β, γ (deg.)90.000, 94.420, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"
d_1ens_2(chain "C" and (resid 1 through 15 or resid 18 through 76))
d_2ens_2(chain "D" and (resid 1 through 15 or resid 18 through 76))

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_1ens_1ALAALASERSERAD5 - 1117 - 113
d_2ens_1ALAALASERSERBC5 - 1117 - 113
d_1ens_2GGAACA1 - 91 - 9
d_2ens_2GGAADB1 - 91 - 9

NCS ensembles :
ID
ens_1
ens_2

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Components

#1: RNA chain RNA (76-MER)


Mass: 24604.627 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 3.09 Å3/Da / Density % sol: 60.17 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / Details: 0.2 M ammonium phosphate dibasic, 23% 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: Dec 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.64→43.09 Å / Num. obs: 26578 / % possible obs: 98.79 % / Redundancy: 12.6 % / Biso Wilson estimate: 59.56 Å2 / CC1/2: 0.977 / Rpim(I) all: 0.0438 / Net I/σ(I): 9.76
Reflection shellResolution: 2.64→2.73 Å / Mean I/σ(I) obs: 0.87 / Num. unique obs: 2645 / CC1/2: 0.909 / Rpim(I) all: 0.197

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Processing

Software
NameVersionClassification
DIALSdata scaling
DIALSdata reduction
PHASERphasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.64→43.09 Å / SU ML: 0.4524 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.9231
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2217 1319 4.97 %
Rwork0.1825 25211 -
obs0.1845 26530 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.49 Å2
Refinement stepCycle: LAST / Resolution: 2.64→43.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1628 3262 0 201 5091
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00315288
X-RAY DIFFRACTIONf_angle_d0.7397894
X-RAY DIFFRACTIONf_chiral_restr0.04261032
X-RAY DIFFRACTIONf_plane_restr0.0048430
X-RAY DIFFRACTIONf_dihedral_angle_d13.56842046
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2DAX-RAY DIFFRACTIONTorsion NCS0.668569009287
ens_2d_2ACX-RAY DIFFRACTIONTorsion NCS0.805739687209
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.64-2.750.39781510.37922780X-RAY DIFFRACTION99.29
2.75-2.870.38771550.3122781X-RAY DIFFRACTION99.16
2.87-3.020.34551370.25152771X-RAY DIFFRACTION98.88
3.02-3.210.28981450.23472755X-RAY DIFFRACTION97.84
3.21-3.460.26361330.21352821X-RAY DIFFRACTION99.56
3.46-3.810.23451480.16832823X-RAY DIFFRACTION99.5
3.81-4.360.18691410.1532801X-RAY DIFFRACTION99.16
4.36-5.490.17061480.13472818X-RAY DIFFRACTION97.98
5.49-43.090.15681610.14862861X-RAY DIFFRACTION98.12
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
17.465066304770.03567118644040.8612660379288.867372210590.5412699380992.82850416474-0.384476139741-0.00553727843196-0.0918952700299-0.106728389141-0.165132511581-0.4094228412770.5089728691180.441212918060.4812168434450.2539643260890.02338979945220.01060373133610.284146389839-0.0002313347259850.40416525065945.9967293816-40.2811479142-21.0922837625
28.878268714974.71499530761-4.360431152127.25740298119-6.079505861156.80407885163-0.4110575547810.3775916720470.383136307799-0.5163035184421.185338691731.02787484649-0.317613379116-0.663052238133-0.3424867212640.374786277236-0.01420756678930.02293526414320.427649368263-0.08629632728140.45623783444627.9526215471-42.3961413271-24.689039405
36.820602100134.469552274210.4674128885077.942362904814.080299857845.231324292480.07393115616970.2022803102510.2462205543890.3783451581330.2571196878550.0979082747823-0.435554584130.0199866818593-0.2820100625920.4356384430670.01923062836970.0154521797340.3078814106770.08093749307180.38528675364644.2256547453-24.4891106493-19.9824528351
42.01773187051-1.0280770357-1.520734000844.59587725823-3.732909242634.33780552536-0.306753211009-1.509210790290.7434471653361.63544104608-0.503064270371-0.614829694607-0.861457442607-0.7663001376890.7516944931170.495480829532-0.0552808401653-0.09834760693330.553469494934-0.05218285978660.39660972395640.6130864679-20.1816675999-3.73933068063
52.39330565893-1.56766239086-2.408582895273.101450910853.015942281063.42767538466-0.135992386679-0.288418828109-0.0416995730965-0.290390269656-0.3108753662190.160904687936-1.33618060614-0.5940862813830.6453351518810.459089592620.0349810360713-0.0995806045790.4441204704740.01734431800240.50031499272242.6389591296-21.3543156907-17.8988003203
64.6141061187-4.37893746515-4.951292796088.557928438515.510288420545.632280570560.4743941897430.5697635520520.534765203156-0.994602317619-0.5779477097770.649756953858-2.25094246712-0.6438402238030.08308064155170.5589476925160.0686704308472-0.08506712667140.6003171317120.02618829235210.60476755822238.806864041-22.4298613207-23.8094679748
70.924617899156-0.322711491542-1.599358773492.988193320711.101752824323.77327946627-0.1490584760580.03178131759550.46494709194-0.0384984961547-0.05070959342050.102882114245-0.1794693399710.3798583269540.1223069270260.2709903941710.0114559450621-0.07243570099540.30899957369-0.0351718116570.52241032106143.7607675272-27.8678325106-15.4350504366
84.510646395665.173610898624.064637988329.390805783045.194581616293.88987196844-0.05544387143170.2649741857110.666118933318-0.2949677954830.01713835760160.393419772775-0.724127427470.01045938591920.1681664546470.3612835748740.0895415576712-0.02135096065670.483306103357-0.09564395755480.50639711943232.2895020286-20.198393697-13.5253597225
96.927398802442.30030265599-2.286070911456.32999428377-4.922877311043.85961982932-0.384294835298-0.628720723869-0.5628921499660.631888449526-0.8946025228850.4041292529521.04424884657-0.01543326049151.300128364990.6252932411040.09581560410120.14916936220.295733315047-0.09886043502290.53837728515339.6841959346-34.1259914079-14.1257737057
108.10965733240.43140359336-1.59402139078.474283466480.4374993378999.07954163578-0.1006577140730.2600158294560.139269162743-0.05879254600920.1191401222960.0027864312460.02187961978720.571756821466-0.0517955752670.1739833763810.0268541361972-0.02834487552490.305795001959-0.02856610960340.39291382703346.1249692034-36.2666904667-21.3033325598
112.3249750327-0.4545576759121.67322517723.47297622964-0.007185346252611.51323288775-0.104566415756-0.112987067706-0.3195802593690.1049113937170.1959532708050.1367232520030.14590506576-0.214185417238-0.02025301015580.3591883967990.04186025576990.07122402797130.418343137706-0.05264071176180.47900435654817.786334820916.59110669834.70100838789
120.6522618621670.1293060046620.703673540115-0.1195746203350.326318010727-0.498242778965-0.431145893227-1.209170625720.9524982681840.1184249682140.289727981002-0.1309365527620.027674253393-0.3565202336030.1964362049120.419168135720.1186096724210.008723785113840.904979070804-0.1355262968580.8807145797031.7181038629826.4765972710.8801281829
130.1873663732150.268915662734-0.5631243951948.273021942710.6385783617430.3423587852980.1206145264370.0134062046998-0.2116762321920.228277633579-0.3052660381530.02166728257090.0871411846025-0.05006921799810.1721544135560.383382842347-0.0218051679174-0.03367772567820.487806509088-0.07018310668080.56403884831431.71354110364.753524784875.12382509957
142.73901788912-0.0223973709351-1.726165668822.03901778256-0.4589867930292.0379284246-0.2376751954380.03115100179170.0299145730086-0.2184697211510.3814940883840.237411153623-0.235245374377-0.4924197098170.003775697895560.41753581269-0.053377228557-0.084647407060.442658511673-0.03607451588770.54154058938521.9309375539-93.8196152329-47.9258055426
151.5531912283-0.180562894526-1.01547926107-0.08867169763140.506357331047-0.402273594477-0.4170608645581.29920213822-1.15092922165-0.156576496530.224971190626-0.0822902509808-0.120404518347-0.3190836395260.1899663476260.455457974921-0.1554728066190.05841923681470.898012997385-0.1310810955090.8465481665745.35082767431-103.642139707-54.3972303122
160.303643805460.6697217020410.8117264698327.508091816030.01637508759540.207980744076-0.004314849410840.09063630919650.219086620345-0.201790348396-0.228339102908-0.269577256909-0.1615948675820.02102349378630.1987414759410.483577618766-0.01058944161450.1272426273980.465362027149-0.04788397640430.55652149174635.9768349045-83.1161219909-48.535207242
173.469786998480.935202170603-0.2628041946384.32902296534-6.242205542919.4018557473-0.402306645213-0.458747266633-0.00698743677659-0.5544326827930.6546479132210.5583034387450.479487169089-1.31661410846-0.05849584564590.3735883465543.93077241387E-50.02842729080330.483894185356-0.07822597234830.55540994830227.412621749-36.1911101787-18.6183339846
182.741061131090.3665899621871.979548625954.426192415811.772490889767.206621271760.08438410004620.395974789722-0.5972374118460.1094826578160.309847613688-0.4545127026411.263862706990.770691476297-0.4583460339920.3483463409630.0590725484595-0.03738127136490.307144905822-0.06920037439620.51223265386845.208827198-54.0440824757-27.8045475482
191.401809308010.538772885737-0.1992882119671.805199901061.628564981056.65818498942-0.0574215153756-0.0965321228517-0.1315523717680.216253889161-0.0284547896598-0.2765836050140.5144479856040.2172386395140.09100960186650.4273107123240.06341750305570.03185167075740.404517530737-0.06488449981830.68284399829245.8377037503-51.5148209191-24.0580598077
204.70328550257-4.87040272524-4.506476522595.241948219044.81467197284.799239582240.06042494081240.182305418533-0.9262193318680.1025790059-0.5075464856411.069721558790.448228165638-0.9033575111280.6695822447190.547217204765-0.01557178028750.06759424830430.417496927004-0.05455964052380.58624666603834.5000901541-53.8495532528-26.5928881898
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 88 through 111 )BC88 - 11184 - 107
22chain 'A' and (resid 5 through 16 )AD5 - 161 - 12
33chain 'A' and (resid 17 through 27 )AD17 - 2713 - 23
44chain 'A' and (resid 28 through 34 )AD28 - 3424 - 30
55chain 'A' and (resid 35 through 40 )AD35 - 4031 - 36
66chain 'A' and (resid 41 through 50 )AD41 - 5037 - 46
77chain 'A' and (resid 51 through 74 )AD51 - 7447 - 70
88chain 'A' and (resid 75 through 84 )AD75 - 8471 - 80
99chain 'A' and (resid 85 through 90 )AD85 - 9081 - 86
1010chain 'A' and (resid 91 through 111 )AD91 - 11187 - 107
1111chain 'C' and (resid 1 through 30 )CA1 - 30
1212chain 'C' and (resid 31 through 50 )CA31 - 50
1313chain 'C' and (resid 51 through 76 )CA51 - 76
1414chain 'D' and (resid 1 through 30 )DB1 - 30
1515chain 'D' and (resid 31 through 50 )DB31 - 50
1616chain 'D' and (resid 51 through 76 )DB51 - 76
1717chain 'B' and (resid 5 through 16 )BC5 - 161 - 12
1818chain 'B' and (resid 17 through 34 )BC17 - 3413 - 30
1919chain 'B' and (resid 35 through 69 )BC35 - 6931 - 65
2020chain 'B' and (resid 70 through 87 )BC70 - 8766 - 83

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