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- PDB-4lck: Co-crystal structure of a T-box riboswitch stem I domain in compl... -

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Basic information

Entry
Database: PDB / ID: 4lck
TitleCo-crystal structure of a T-box riboswitch stem I domain in complex with its cognate tRNA
Components
  • Ribosomal protein YbxFRibosome
  • T-BOX RIBOSWITCH STEM I
  • tRNA-Gly
KeywordsRIBOSOMAL PROTEIN/RNA / riboswitch mRNA / tRNA-mRNA complex / gene expression regulation / bacteria / RIBOSOMAL PROTEIN-RNA complex
Function / homology
Function and homology information


ribosome / ribonucleoprotein complex / RNA binding / cytoplasm
Similarity search - Function
Ribosomal protein L7Ae, putative / Ribosomal protein L30/S12 / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
STRONTIUM ION / RNA / RNA (> 10) / RNA (> 100) / RNA-binding protein YbxF
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
Oceanobacillus iheyensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT, SAD / Resolution: 3.2 Å
AuthorsZhang, J. / Ferre-D'Amare, A.R.
CitationJournal: Nature / Year: 2013
Title: Co-crystal structure of a T-box riboswitch stem I domain in complex with its cognate tRNA.
Authors: Zhang, J. / Ferre-D'Amare, A.R.
History
DepositionJun 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2013Group: Database references
Revision 1.2Nov 23, 2016Group: Source and taxonomy
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 20, 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 / struct_site
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribosomal protein YbxF
B: tRNA-Gly
C: T-BOX RIBOSWITCH STEM I
D: Ribosomal protein YbxF
E: tRNA-Gly
F: T-BOX RIBOSWITCH STEM I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,69692
Polymers131,6046
Non-polymers7,09286
Water39622
1
A: Ribosomal protein YbxF
B: tRNA-Gly
C: T-BOX RIBOSWITCH STEM I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,81851
Polymers65,8023
Non-polymers4,01648
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Ribosomal protein YbxF
E: tRNA-Gly
F: T-BOX RIBOSWITCH STEM I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,87841
Polymers65,8023
Non-polymers3,07638
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.382, 108.474, 266.886
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 2 molecules AD

#1: Protein Ribosomal protein YbxF / Ribosome


Mass: 8435.608 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Strain: 168 / Gene: rplGB, ybaB, ybxF, BSU01090 / Production host: Escherichia coli (E. coli) / References: UniProt: P46350

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RNA chain , 2 types, 4 molecules BECF

#2: RNA chain tRNA-Gly


Mass: 24258.438 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: in vitro transcription using T7 RNA polymerase / Source: (synth.) Oceanobacillus iheyensis (bacteria)
#3: RNA chain T-BOX RIBOSWITCH STEM I


Mass: 33107.746 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: in vitro transcription using T7 RNA polymerase / Source: (synth.) Oceanobacillus iheyensis (bacteria)

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Non-polymers , 3 types, 108 molecules

#4: Chemical...
ChemComp-SR / STRONTIUM ION / Strontium


Mass: 87.620 Da / Num. of mol.: 79 / Source method: obtained synthetically / Formula: Sr
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.76 Å3/Da / Density % sol: 55.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50 mM Bis-Tris (HCl) pH 6.5, 300 mM Li2SO4, and 20% (w/v) PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
41
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 24-ID-E10.9793
SYNCHROTRONAPS 24-ID-C20.9793
SYNCHROTRONALS 5.0.130.9793
SYNCHROTRONALS 5.0.240.9793
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDAug 2, 2012
ADSC QUANTUM 3152CCD
ADSC QUANTUM 315r3CCD
ADSC QUANTUM 315r4CCD
RadiationMonochromator: Kohzu HLD8-24 monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.2→28.42 Å / % possible obs: 98.9 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 / Redundancy: 6.1 % / Biso Wilson estimate: 128.66 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 11.1
Reflection shell
Resolution (Å)Diffraction-ID% possible all
3.2-3.2653198
3.2653-3.3362199
3.3362-3.41361100
3.4136-3.4989199
3.4989-3.59331100
3.5933-3.6988199

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
XDSdata reduction
XDSdata scaling
SHELXDphasing
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT, SAD
Starting model: PDB ENTRIES 3L0U and 3V7E

3l0u

3v7e


Resolution: 3.2→28.416 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.801 / SU ML: 0.47 / σ(F): 1.34 / Phase error: 27.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2514 2318 5.06 %Random
Rwork0.1957 ---
obs0.1984 45770 98.74 %-
all-46354 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 382.53 Å2 / Biso mean: 128.0007 Å2 / Biso min: 37.84 Å2
Refinement stepCycle: LAST / Resolution: 3.2→28.416 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1048 7586 86 22 8742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0019547
X-RAY DIFFRACTIONf_angle_d0.36614681
X-RAY DIFFRACTIONf_chiral_restr0.021966
X-RAY DIFFRACTIONf_plane_restr0.001531
X-RAY DIFFRACTIONf_dihedral_angle_d15.4224573
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2-3.26530.381270.34722486261398
3.2653-3.33620.34751430.32142622276599
3.3362-3.41360.3771260.317625372663100
3.4136-3.49890.32291350.30752613274899
3.4989-3.59330.32921250.286725612686100
3.5933-3.69880.33331350.26762626276199
3.6988-3.81790.29031230.245825372660100
3.8179-3.9540.2991230.24126062729100
3.954-4.11190.30091370.213526192756100
4.1119-4.29840.22861620.203625352697100
4.2984-4.52420.27291610.193325592720100
4.5242-4.80640.22461680.189925232691100
4.8064-5.17540.24521320.184926092741100
5.1754-5.69250.24871750.15632555273099
5.6925-6.50760.2561320.17212517264998
6.5076-8.16650.24421250.17572533265897
8.1665-28.41680.181890.16132414250392
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)
14.4287-1.9362-0.33254.5778-1.46730.7277-1.0017-2.77880.18571.86790.83080.5915-0.8108-1.03080.11231.07560.06310.04261.8267-0.50170.817535.76490.0457258.1728
25.5553-0.22171.48930.4270.50211.143-0.7564-3.20211.30450.92260.71850.28291.2452-0.8301-0.0091.73130.1705-0.3241.7705-0.88361.538342.506196.4913259.0647
32.10171.17320.92477.61031.93566.2282-0.4556-1.1421.50850.29390.480.3441-0.6539-0.17830.18610.88720.3184-0.08881.7403-0.35230.650837.93184.9851253.3905
40.37750.4246-0.57263.89412.02593.1246-0.6798-1.5906-0.05360.58340.7409-0.5478-1.36080.07420.2620.80460.4791-0.07550.97450.03720.697144.855991.9867194.8057
50.9440.3459-0.82293.002-4.34879.842-0.1290.2764-0.49011.10080.17520.8878-0.7624-0.61190.19240.92380.3599-0.06990.9097-0.03110.818237.780297.7608187.2194
60.64150.55640.98741.26870.02932.1297-0.383-0.070.36110.30050.39650.7238-1.2812-0.912-0.00371.26430.30930.35631.36220.0660.908533.8987104.9769207.1823
71.61571.227-1.51920.9667-0.44935.22740.71410.60111.1368-0.2263-0.426-0.2789-1.3462-2.25470.16361.39950.57940.1311.4481-0.10471.067132.4493107.966213.0909
82.4108-1.4299-1.3890.87060.71451.6979-0.1543-0.18110.2527-0.07540.2753-0.321-0.2762-0.0398-0.08280.48650.1061-0.00420.5287-0.01380.549553.38788.0783181.0082
91.0914-0.7645-0.21241.11411.49451.6948-0.3850.43720.7987-0.0660.5774-0.0361-0.6893-0.9340.10740.56160.1046-0.03590.9573-0.35710.549425.562693.5301233.5518
101.977-1.2036-3.17711.79152.70535.66270.4069-0.6480.1248-0.5845-0.483-0.2386-2.4110.67810.24781.67450.7037-0.39862.2070.20280.781714.4871119.6724203.8813
111.955-1.8234-0.36952.36840.32932.28740.01720.090.6035-0.7876-0.0595-0.73990.18420.44190.07080.66910.12690.00560.3812-0.04380.668732.2619117.2761176.6655
12-0.19920.238-0.10760.8962-1.01960.6281-0.04290.14160.113-0.44930.2170.10260.0042-1.1004-0.06350.86360.2553-0.10061.1074-0.22440.794520.6648105.0087220.7804
130.08070.19030.12521.4179-0.16670.3783-0.12840.1997-0.128-2.77540.5135-0.2917-0.26180.1621-0.47372.84611.0806-0.74613.6533-2.22342.55958.916667.517877.3398
144.47440.7198-4.17064.21961.55455.06951.6403-0.02790.4784-0.0771-0.36891.0936-0.60160.03551.28363.3315-0.1311-1.11041.5886-0.70784.115856.365460.917278.617
151.2941-2.92750.54947.5389-2.28651.48891.76990.4723-1.9396-0.69140.06981.95250.52080.09522.93033.15010.0014-0.45621.5478-0.96142.009755.498259.145380.4889
161.96930.14492.98170.05610.30934.6957-1.01711.55640.5013-1.57180.6240.02970.8729-1.2496-0.15712.3245-0.15390.32842.4473-0.31873.047162.230965.254980.4787
171.7013-0.1946-0.8212.5518-0.12060.7574-0.71181.28230.6827-0.5221-0.7187-0.9043-0.32040.30710.73510.85760.2192-0.10330.92020.10160.885661.469561.7629139.4039
180.9005-1.7518-1.25343.67521.03058.76840.46760.2022-0.40490.54450.31541.1319-1.1254-0.2364-0.28631.09660.32910.22691.05290.24791.142153.319967.1724152.6283
190.8865-0.27440.4650.3283-0.61780.86850.37081.0311-0.78480.2102-0.15240.3262-0.47610.14270.19170.95230.168-0.20231.23820.01951.062746.509573.4768121.3803
201.4256-1.60920.14522.9594-1.71862.0516-0.3638-0.0269-0.7237-0.14840.75940.25080.3647-0.4343-0.31660.99850.01830.04750.76360.04111.126963.654952.1949151.4729
212.9372-0.683-0.26850.39032.15993.7930.88281.4594-0.3695-0.6435-1.20910.3903-1.0063-1.84210.06341.46350.1048-0.08161.0267-0.16170.857151.082183.3757109.6198
227.8551-3.50680.16244.70340.8863.9945-0.5149-0.317-0.70550.22920.16340.94660.3932-0.0680.36320.55580.0249-0.08430.6895-0.06780.82337.353778.6749151.6174
232.39070.2335-2.22691.47910.39552.19930.59170.69580.0441-0.6951-0.366-0.0314-1.2405-0.3718-0.19791.38540.2078-0.34460.9883-0.08170.878855.72283.0676101.5276
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 38 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 61 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 62 through 82 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 5 through 11 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 12 through 20 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 21 through 30 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 31 through 46 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 47 through 79 )B0
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 24 )C0
10X-RAY DIFFRACTION10chain 'C' and (resid 25 through 36 )C0
11X-RAY DIFFRACTION11chain 'C' and (resid 37 through 67 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 68 through 102 )C0
13X-RAY DIFFRACTION13chain 'D' and (resid 2 through 25 )D0
14X-RAY DIFFRACTION14chain 'D' and (resid 26 through 38 )D0
15X-RAY DIFFRACTION15chain 'D' and (resid 39 through 69 )D0
16X-RAY DIFFRACTION16chain 'D' and (resid 70 through 82 )D0
17X-RAY DIFFRACTION17chain 'E' and (resid 5 through 15 )E0
18X-RAY DIFFRACTION18chain 'E' and (resid 16 through 20 )E0
19X-RAY DIFFRACTION19chain 'E' and (resid 21 through 42 )E0
20X-RAY DIFFRACTION20chain 'E' and (resid 43 through 79 )E0
21X-RAY DIFFRACTION21chain 'F' and (resid 1 through 35 )F0
22X-RAY DIFFRACTION22chain 'F' and (resid 36 through 79 )F0
23X-RAY DIFFRACTION23chain 'F' and (resid 80 through 102 )F0

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