[English] 日本語
Yorodumi
- PDB-6vwt: Transitional unit cell 1 of adenine riboswitch aptamer crystal ph... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6vwt
TitleTransitional unit cell 1 of adenine riboswitch aptamer crystal phase transition upon ligand binding
Componentsadenine riboswitch aptamer variant
KeywordsRNA / riboswitch / phase transition / time-resolved
Function / homologyADENINE / : / RNA / RNA (> 10)
Function and homology information
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 3.03 Å
AuthorsStagno, J.R. / Wang, Y.-X.
CitationJournal: Nat Commun / Year: 2021
Title: Synchronous RNA conformational changes trigger ordered phase transitions in crystals.
Authors: Ramakrishnan, S. / Stagno, J.R. / Conrad, C.E. / Ding, J. / Yu, P. / Bhandari, Y.R. / Lee, Y.T. / Pauly, G. / Yefanov, O. / Wiedorn, M.O. / Knoska, J. / Oberthur, D. / White, T.A. / Barty, A. ...Authors: Ramakrishnan, S. / Stagno, J.R. / Conrad, C.E. / Ding, J. / Yu, P. / Bhandari, Y.R. / Lee, Y.T. / Pauly, G. / Yefanov, O. / Wiedorn, M.O. / Knoska, J. / Oberthur, D. / White, T.A. / Barty, A. / Mariani, V. / Li, C. / Brehm, W. / Heinz, W.F. / Magidson, V. / Lockett, S. / Hunter, M.S. / Boutet, S. / Zatsepin, N.A. / Zuo, X. / Grant, T.D. / Pandey, S. / Schmidt, M. / Spence, J.C.H. / Chapman, H.N. / Wang, Y.X.
History
DepositionFeb 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Oct 6, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: adenine riboswitch aptamer variant
B: adenine riboswitch aptamer variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,83912
Polymers45,3752
Non-polymers46510
Water00
1
A: adenine riboswitch aptamer variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9206
Polymers22,6871
Non-polymers2325
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: adenine riboswitch aptamer variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9206
Polymers22,6871
Non-polymers2325
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.340, 25.200, 78.740
Angle α, β, γ (deg.)99.290, 90.550, 90.210
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
12chain A
22chain B

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GGCCchain AAA13 - 831 - 71
21GGCCchain BBB13 - 831 - 71
12ADEADEADEADEchain XAC101
22ADEADEADEADEchain YBH101

NCS ensembles :
ID
1
2

-
Components

#1: RNA chain adenine riboswitch aptamer variant


Mass: 22687.383 Da / Num. of mol.: 2 / Mutation: variant / Source method: obtained synthetically / Source: (synth.) Vibrio vulnificus (bacteria) / References: GenBank: 675337566
#2: Chemical ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H5N5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.38 % / Description: plates
Crystal growTemperature: 295 K / Method: batch mode / pH: 6.5
Details: 40 mM sodium cacodylate, pH 6.5, 80 mM potassium chloride, 100 mM magnesium chloride, 12 mM spermine tetrahydrochloride, 65% v/v (+/-)-2-methyl-2,4-pentanediol

-
Data collection

DiffractionMean temperature: 295 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.34 Å
DetectorType: CS-PAD CXI-1 / Detector: PIXEL / Date: Jul 19, 2017 / Frequency: 120
RadiationMonochromator: Beryllium lens / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34 Å / Relative weight: 1
ReflectionResolution: 3→25.17 Å / Num. obs: 7656 / % possible obs: 100 % / Redundancy: 751 % / Biso Wilson estimate: 82.8 Å2 / CC1/2: 0.9976 / CC star: 0.9994 / R split: 0.0734 / Net I/σ(I): 13.49
Reflection shellResolution: 3→3.11 Å / Redundancy: 207.7 % / Mean I/σ(I) obs: 0.58 / Num. unique obs: 803 / CC1/2: 0.682 / CC star: 0.901 / R split: 1.9061 / % possible all: 100
Serial crystallography measurementFocal spot size: 2 µm2 / Pulse duration: 40 fsec. / Pulse energy: 3.2 µJ / Pulse photon energy: 9.49 keV / XFEL pulse repetition rate: 120 Hz
Serial crystallography sample deliveryDescription: liquid injection / Method: injection
Serial crystallography sample delivery injectionDescription: GDVN / Filter size: 20 µm / Flow rate: 10 µL/min / Injector diameter: 75 µm / Injector nozzle: double-flow focusing
Serial crystallography data reductionCrystal hits: 76905 / Frames indexed: 28850 / Frames total: 8208739

-
Processing

Software
NameVersionClassification
PHENIX1.18rc5_3822refinement
SCALAdata scaling
PDB_EXTRACT3.25data extraction
CrystFEL0.9.0data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4tzx

4tzx


Resolution: 3.03→25.17 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 32.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2503 434 5.96 %
Rwork0.2259 6851 -
obs0.2274 7285 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 154.68 Å2 / Biso mean: 91.2944 Å2 / Biso min: 56.57 Å2
Refinement stepCycle: final / Resolution: 3.03→25.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3006 28 0 3034
Biso mean--76.39 --
Num. residues----142
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1503X-RAY DIFFRACTIONPOSITIONAL0.095
12B1503X-RAY DIFFRACTIONPOSITIONAL0.095
21A10X-RAY DIFFRACTIONPOSITIONAL0.006
22B10X-RAY DIFFRACTIONPOSITIONAL0.006
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.03-3.140.3265400.389570774796
3.14-3.270.2743300.311464367398
3.27-3.420.2999540.282167472898
3.42-3.60.293560.301970776398
3.6-3.820.2973340.262465068499
3.82-4.110.2346340.228871875299
4.11-4.530.344570.2574682739100
4.53-5.180.1852550.226767873398
5.18-6.50.2429360.181669172799
6.51-25.170.2013380.1725701739100
Refinement TLS params.Method: refined / Origin x: 24.983 Å / Origin y: -11.544 Å / Origin z: -0.177 Å
111213212223313233
T0.4551 Å20.001 Å20.0019 Å2-0.5763 Å20.0008 Å2--0.7094 Å2
L-0.5502 °2-0.0178 °20.302 °2-1.0658 °2-0.021 °2--5.0676 °2
S-0.0777 Å °0.0038 Å °-0.0986 Å °-0.0163 Å °-0.0059 Å °0.0032 Å °-0.052 Å °0.0032 Å °0.0642 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 13:83 OR RESID 101:101 OR RESID 102:105 ) ) OR ( CHAIN B AND ( RESID 102:105 OR RESID 13:83 OR RESID 101:101 ) )A13 - 83
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 13:83 OR RESID 101:101 OR RESID 102:105 ) ) OR ( CHAIN B AND ( RESID 102:105 OR RESID 13:83 OR RESID 101:101 ) )A101
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 13:83 OR RESID 101:101 OR RESID 102:105 ) ) OR ( CHAIN B AND ( RESID 102:105 OR RESID 13:83 OR RESID 101:101 ) )A102 - 105
4X-RAY DIFFRACTION1( CHAIN A AND ( RESID 13:83 OR RESID 101:101 OR RESID 102:105 ) ) OR ( CHAIN B AND ( RESID 102:105 OR RESID 13:83 OR RESID 101:101 ) )B102 - 105
5X-RAY DIFFRACTION1( CHAIN A AND ( RESID 13:83 OR RESID 101:101 OR RESID 102:105 ) ) OR ( CHAIN B AND ( RESID 102:105 OR RESID 13:83 OR RESID 101:101 ) )B13 - 83
6X-RAY DIFFRACTION1( CHAIN A AND ( RESID 13:83 OR RESID 101:101 OR RESID 102:105 ) ) OR ( CHAIN B AND ( RESID 102:105 OR RESID 13:83 OR RESID 101:101 ) )B101

+
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