[English] 日本語
Yorodumi
- PDB-4tzp: As Grown, Untreated Co-crystals of the Ternary Complex Containing... -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water0
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

-
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)

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more