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- PDB-4tzp: As Grown, Untreated Co-crystals of the Ternary Complex Containing... -

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Basic information

Entry
Database: PDB / ID: 4tzp
TitleAs Grown, Untreated Co-crystals of the Ternary Complex Containing a T-box Stem I RNA, its cognate tRNAGly, and B. subtilis YbxF protein
Components
  • Ribosome-associated protein L7Ae-like
  • engineered tRNA
  • glyQ T-box Stem I
KeywordsRibosomal Protein/RNA / RNA / Riboswitch / T-box / tRNA / 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 L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA-binding protein YbxF
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
Oceanobacillus iheyensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 8.503 Å
AuthorsZhang, J. / Ferre-D'Amare, A.R.
Citation
Journal: Structure / Year: 2014
Title: Dramatic Improvement of Crystals of Large RNAs by Cation Replacement and Dehydration.
Authors: Zhang, J. / Ferre-D'Amare, A.R.
#1: Journal: 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
DepositionJul 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_entity_src_syn / pdbx_initial_refinement_model / pdbx_struct_oper_list / refine_hist
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribosome-associated protein L7Ae-like
B: engineered tRNA
C: glyQ T-box Stem I
D: Ribosome-associated protein L7Ae-like
E: engineered tRNA
F: glyQ T-box Stem I


Theoretical massNumber of molelcules
Total (without water)131,7186
Polymers131,7186
Non-polymers00
Water00
1
A: Ribosome-associated protein L7Ae-like
B: engineered tRNA
C: glyQ T-box Stem I


Theoretical massNumber of molelcules
Total (without water)65,8593
Polymers65,8593
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Ribosome-associated protein L7Ae-like
E: engineered tRNA
F: glyQ T-box Stem I


Theoretical massNumber of molelcules
Total (without water)65,8593
Polymers65,8593
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.730, 108.749, 291.811
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Ribosome-associated protein L7Ae-like


Mass: 8492.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: rplGB, ybaB, ybxF, BSU01090 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P46350
#2: RNA chain engineered tRNA


Mass: 24258.438 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Bacillus subtilis (bacteria)
#3: RNA chain glyQ T-box Stem I


Mass: 33107.746 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Oceanobacillus iheyensis (bacteria)
Has protein modificationY

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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: 3.32 Å3/Da / Density % sol: 62.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 50 mM Bis-Tris (HCl) pH 6.5, 300 mM Li2SO4, and 20% (w/v) PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
PH range: 6.5-7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 13, 2013
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: 8.5→48.63 Å / Num. obs: 1651 / % possible obs: 99.9 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 10.6
Reflection shellHighest resolution: 8.5 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.08 / Mean I/σ(I) obs: 1.7 / % possible all: 100

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LCK

4lck


Resolution: 8.503→48.63 Å / SU ML: 1.11 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 47.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3733 160 9.71 %Random
Rwork0.2673 ---
obs0.2779 1648 99.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 8.503→48.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1048 7460 0 0 8508
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049404
X-RAY DIFFRACTIONf_angle_d0.81814456
X-RAY DIFFRACTIONf_dihedral_angle_d15.8784507
X-RAY DIFFRACTIONf_chiral_restr0.0391938
X-RAY DIFFRACTIONf_plane_restr0.005525
LS refinement shellResolution: 8.503→48.63 Å
RfactorNum. reflection% reflection
Rfree0.3733 160 -
Rwork0.2673 1488 -
obs--100 %
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)
10.07690.08420.05770.1090.00780.16490.3181-0.83140.87970.4665-0.03390.7429-0.1589-0.5372-010.56774.40221.6396.93820.808211.746-9.6546-11.2382-54.89
20.0535-0.0245-0.01560.01730.03340.0079-0.29290.09790.02250.3390.2644-0.1309-0.0268-0.15340.00015.43821.7171-2.09749.66010.3238.9883-4.7177-2.1248-52.6509
30.02670.0252-0.0290.0621-0.06870.0487-0.43550.28370.39870.48820.7112-0.01460.0049-0.3454-012.9814-0.5666-2.009210.4103-0.74576.15512.7149-7.0116-55.3678
41.9104-1.3865-5.76820.12790.62391.98620.02740.79840.1882-1.607-0.4386-0.5476-1.49960.6323-0.4331.80710.77310.335.4759-0.59664.32-5.6785-1.2438-54.4841
51.3731.5088-0.32082.4685-1.95313.73630.51770.3631-1.4219-0.3048-0.1354-0.65530.20930.0924-0.145310.09610.1016-3.24634.96560.55651.9138-12.4798-6.3163-49.8375
60.15430.12950.08190.00180.00990.02840.96960.15241.01170.4291-2.16610.51930.44680.099806.72043.8241-2.078811.6404-0.95198.2183-14.878-7.979.5885
7-0.4761-0.1806-0.0743-0.19080.2388-0.036-0.94467.2899-2.06995.21710.976-0.9837-0.60461.9864-04.03585.6609-3.71142.7712-1.46528.2014-3.9191-15.1164.3602
80.60180.45480.07920.18930.2278-0.04774.44751.086-0.0381-1.3973.48982.03481.17650.721107.7223-3.0148-0.608911.0794-5.96679.6208-1.6496-12.3735-2.8004
9-0.03090.23950.24420.4292-0.04640.21130.1224-0.9465-1.1858-0.1487-0.11170.94015.4348-0.843018.0854-2.247-4.91517.36852.37336.4898-16.8598-0.880924.6212
100.0245-0.06230.0586-0.1024-0.2419-0.090.95131.62861.0773-1.99082.4712-1.9264-0.98472.3551-06.38722.0152.67474.44582.74918.5891-25.675-11.0922-33.3092
110.0358-0.0114-0.21130.0988-0.10430.069-0.2606-0.22370.2256-0.34070.6403-0.5108-0.77030.625807.4789-0.9765.18593.5243-1.270610.6365-6.4903-27.6639-34.2528
120.0348-0.08140.0640.013-0.23250.0345-0.6699-1.17150.26962.3704-0.0719-2.5711-0.1795-0.1529010.41048.4883-4.394311.20668.66273.40129.7403-38.6115-9.2274
130.3820.44420.14790.05270.12680.0943-1.4985-0.1821-0.9522.87851.66380.69730.32090.680907.3453-2.986.714416.31910.63865.97585.4663-30.316319.4964
140.0942-0.06360.23030.2477-0.23240.1394-1.4037-0.72120.4471.5611-2.61440.79490.6104-2.7531-03.85240.47181.53411.3379-0.742813.710410.9201-23.37322.1007
150.13140.04860.031-0.0734-0.0245-0.12281.86260.39731.76921.6215-1.0556-3.401-0.32220.1731-04.8563-1.7624-0.00158.77830.48833.333411.6491-15.736127.6825
16-0.0013-0.05970.0050.02260.10620.13820.13030.26310.73470.8812-1.26711.0741-3.3564-0.0639-04.89938.066-0.47282.9417-2.68374.60815.5725-28.25319.6164
17-1.1649-0.31561.01630.19760.8361-0.15020.02121.1212-0.36221.711-0.76130.63040.8593-1.03010.3514-1.27293.88423.31540.540111.05280.0908-30.3023-25.5071
180.20630.04790.2022-0.1483-0.01970.096-0.77770.35030.3063-0.2798-0.49061.7038-0.5570.4136-011.6893-4.3952-2.469414.8741.39658.0766-27.6948-18.0076-31.079
19-0.0012-0.0054-0.05130.54870.67510.72270.4476-0.16980.61380.0106-0.3001-0.0126-0.5257-0.0048-0.20415.4043-2.3239-0.1788.29130.43614.268-39.309714.0597131.6411
200.0915-0.39060.05032.7752-0.14540.05260.51331.1122-0.84840.3054-1.22720.66620.43780.2670.00384.6619-5.81031.19547.6961-1.477413.1801-40.75215.8088124.0975
21-0.01410.0025-0.0070.01490.00010.00130.33190.38050.0639-0.0022-0.0768-0.1905-0.3794-0.4706-06.17262.32013.81925.98630.12978.5644-42.9142-0.7392125.8095
220.0276-0.0517-0.00870.1057-0.04480.0841-0.3183-0.04730.3207-0.0958-0.17070.4016-0.0509-0.1127-0.000411.71162.64661.3487.9671.34036.6191-51.0938.3533132.1425
230.04380.1178-0.03970.1423-0.00980.019-0.37770.5622-0.2605-0.12190.086-0.9066-0.26010.7412-0.0018.2918-0.2724-1.71394.91872.956811.2225-44.372814.146128.452
24-0.03150.06520.1532-0.0267-0.00080.0198-0.0396-0.3712-1.07890.6395-0.56850.4008-0.1430.477607.673-2.9467-2.15168.97134.738911.8548-46.5128.648365.9883
250.0912-0.3104-0.11390.11120.08270.0371-0.8369-2.7736-1.21824.8489-0.8871.08961.75241.268809.98922.71392.60159.7824-1.356411.8461-39.3905-2.756770.3986
260.39650.20980.2061.41490.2644-0.0918-3.1126-5.0253-0.29610.15233.64250.88242.99173.9914-013.9588-1.50180.54529.64795.320218.8162-42.2031-5.584477.3354
27-0.02180.01940.0809-0.00990.0405-0.0556-0.58910.02030.52430.3896-0.854-1.4042-0.20220.7028-05.2470.7696-0.24952.3448-2.50486.0997-47.45410.716346.4867
280.039-0.0699-0.04830.0518-0.14260.0048-0.759-0.17891.0899-1.7828-1.646-1.26490.85780.2725-07.34784.49941.8148.728912.658812.5193-58.859313.718654.5724
290.18680.1063-0.18090.0220.16220.0690.82320.2184-0.7629-0.53240.01620.6645-0.2983-0.0744-05.908-1.45474.47139.7274-5.128513.0679-60.209928.213351.7574
30-0.1138-0.1594-0.2878-0.1118-0.3477-0.11322.9525-1.3649-1.2233-0.59920.40050.82881.0655-1.667305.9823-9.65390.94162.289221.87294.603-36.790415.2106108.6894
310.10430.1061-0.04830.1126-0.14090.08451.62221.5611.63241.1160.491.3846-0.48180.1871-07.5044-6.9376-1.15726.00472.71746.0142-19.7698-8.3792100.8152
32-0.0743-0.06790.33190.0340.2169-0.104-2.30770.3358-4.8505-1.9705-2.97690.56260.14581.369509.02234.997-0.46467.63720.64146.292-16.1569-17.829372.4868
330.0320.2998-0.2787-0.0377-0.23410.3101-4.83264.10011.64681.814-3.4542-3.084-1.89280.7274-05.33142.71791.775413.75644.58952.8034-32.2989-14.782245.4442
340.5655-0.0984-0.34110.3409-0.01580.13670.6582-0.5252.70971.6825.58333.69750.29410.16904.6187-0.6168-0.635511.9573.123.041-29.1091-18.599253.657
350.58880.5310.54010.33780.2563-0.07274.0085-1.1152-1.5663-0.2627-1.1537-3.57873.27862.8215-013.9983-2.3779-6.61665.52812.285110.9011-19.7052-10.921493.8685
360.56260.3850.36730.30720.53960.311.21932.51860.54122.11040.1557-0.91862.5221-0.9503-011.9753-1.858-9.238817.05237.259417.5492-30.583113.8352109.4776
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 29 )
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 38 )
3X-RAY DIFFRACTION3chain 'A' and (resid 39 through 52 )
4X-RAY DIFFRACTION4chain 'A' and (resid 53 through 63 )
5X-RAY DIFFRACTION5chain 'A' and (resid 64 through 82 )
6X-RAY DIFFRACTION6chain 'B' and (resid 5 through 15 )
7X-RAY DIFFRACTION7chain 'B' and (resid 16 through 30 )
8X-RAY DIFFRACTION8chain 'B' and (resid 31 through 51 )
9X-RAY DIFFRACTION9chain 'B' and (resid 52 through 79 )
10X-RAY DIFFRACTION10chain 'C' and (resid 1 through 10 )
11X-RAY DIFFRACTION11chain 'C' and (resid 11 through 20 )
12X-RAY DIFFRACTION12chain 'C' and (resid 21 through 33 )
13X-RAY DIFFRACTION13chain 'C' and (resid 34 through 43 )
14X-RAY DIFFRACTION14chain 'C' and (resid 44 through 50 )
15X-RAY DIFFRACTION15chain 'C' and (resid 51 through 65 )
16X-RAY DIFFRACTION16chain 'C' and (resid 66 through 74 )
17X-RAY DIFFRACTION17chain 'C' and (resid 75 through 95 )
18X-RAY DIFFRACTION18chain 'C' and (resid 96 through 102 )
19X-RAY DIFFRACTION19chain 'D' and (resid 2 through 15 )
20X-RAY DIFFRACTION20chain 'D' and (resid 16 through 38 )
21X-RAY DIFFRACTION21chain 'D' and (resid 39 through 57 )
22X-RAY DIFFRACTION22chain 'D' and (resid 58 through 63 )
23X-RAY DIFFRACTION23chain 'D' and (resid 64 through 82 )
24X-RAY DIFFRACTION24chain 'E' and (resid 5 through 15 )
25X-RAY DIFFRACTION25chain 'E' and (resid 16 through 30 )
26X-RAY DIFFRACTION26chain 'E' and (resid 31 through 51 )
27X-RAY DIFFRACTION27chain 'E' and (resid 52 through 60 )
28X-RAY DIFFRACTION28chain 'E' and (resid 61 through 68 )
29X-RAY DIFFRACTION29chain 'E' and (resid 69 through 79 )
30X-RAY DIFFRACTION30chain 'F' and (resid 1 through 13 )
31X-RAY DIFFRACTION31chain 'F' and (resid 14 through 23 )
32X-RAY DIFFRACTION32chain 'F' and (resid 24 through 38 )
33X-RAY DIFFRACTION33chain 'F' and (resid 39 through 57 )
34X-RAY DIFFRACTION34chain 'F' and (resid 58 through 74 )
35X-RAY DIFFRACTION35chain 'F' and (resid 75 through 92 )
36X-RAY DIFFRACTION36chain 'F' and (resid 93 through 102 )

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