[English] 日本語
Yorodumi
- PDB-4lx5: X-ray crystal structure of the M6" riboswitch aptamer bound to py... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4lx5
TitleX-ray crystal structure of the M6" riboswitch aptamer bound to pyrimido[4,5-d]pyrimidine-2,4-diamine (PPDA)
ComponentsMutated adenine riboswitch aptamer
KeywordsRNA / Riboswitch / Gene expression platform
Function / homologypyrimido[4,5-d]pyrimidine-2,4-diamine / : / RNA / RNA (> 10)
Function and homology information
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsDunstan, M.S. / Leys, D.
CitationJournal: J.Am.Chem.Soc. / Year: 2014
Title: Modular riboswitch toolsets for synthetic genetic control in diverse bacterial species.
Authors: Robinson, C.J. / Vincent, H.A. / Wu, M.C. / Lowe, P.T. / Dunstan, M.S. / Leys, D. / Micklefield, J.
History
DepositionJul 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2014Group: Database references
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 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_ref_seq_dif / 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_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.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.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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mutated adenine riboswitch aptamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9456
Polymers22,6851
Non-polymers2595
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.050, 149.710, 24.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: RNA chain Mutated adenine riboswitch aptamer


Mass: 22685.416 Da / Num. of mol.: 1 / Mutation: U28G, G42C, U47C, U51C / Source method: obtained synthetically / Details: in vitro transcription / Source: (synth.) Vibrio vulnificus (bacteria) / References: GenBank: AE016796
#2: Chemical ChemComp-29G / pyrimido[4,5-d]pyrimidine-2,4-diamine


Mass: 162.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6N6
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSynthetic construct from In vitro transcription

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 3M 1,6 hexanediol, 0.1M Tris (pH 9.0) , VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 14, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.13→46.6 Å / Num. all: 10788 / Num. obs: 10766 / % possible obs: 99.8 % / Observed criterion σ(F): 2.13 / Observed criterion σ(I): 2.13 / Biso Wilson estimate: 59.89 Å2

-
Processing

Software
NameVersionClassificationNB
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LA5

3la5


Resolution: 2.13→46.6 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.31 / σ(F): 1.34 / Phase error: 32.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2567 513 4.78 %
Rwork0.199 --
obs0.2017 10722 99.72 %
all-10788 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.9851 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: LAST / Resolution: 2.13→46.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1502 16 17 1535
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051690
X-RAY DIFFRACTIONf_angle_d0.9862626
X-RAY DIFFRACTIONf_dihedral_angle_d14.301849
X-RAY DIFFRACTIONf_chiral_restr0.042355
X-RAY DIFFRACTIONf_plane_restr0.00672
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.13-2.34440.40411290.30632487X-RAY DIFFRACTION100
2.3444-2.68360.38631280.29822501X-RAY DIFFRACTION100
2.6836-3.38090.29191290.22972529X-RAY DIFFRACTION100
3.3809-46.62310.2121270.16512692X-RAY DIFFRACTION99
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)
10.4992-1.01420.45512.1474-1.03490.43470.93230.3378-1.80820.2536-0.8803-1.3741-0.2482-0.3313-0.11850.22480.19090.00020.4613-0.10251.486610.59966.29964.2192
21.8647-1.43581.4035.2275-0.84671.59430.33370.2030.0509-0.4239-0.08790.5065-0.01130.0015-0.08330.36590.04260.00280.4249-0.0050.4539-10.143230.0316-4.9918
31.9677-0.40441.37322.43340.84551.5562-0.0558-0.38280.07321.61460.6221-1.79-0.44520.5864-0.65460.77390.0721-0.18780.7477-0.1510.632811.215721.42869.8235
42.9439-0.38181.45756.77220.29493.268-0.0580.52490.0241-0.65710.06191.7154-0.38750.1595-0.0810.52590.0056-0.17790.3766-0.07390.3999-9.345317.3554-6.8239
53.3889-1.4258-0.10981.6521.45582.080.33080.1962-1.2908-0.766-0.58382.965-0.2008-0.874-0.08870.40740.0709-0.28730.42030.04971.1362-20.449922.7089-3.6732
61.3208-1.17540.78317.45911.15383.4127-0.17130.1758-1.42730.1470.4641-1.01270.439-0.3498-0.19360.27050.01760.04380.5768-0.13140.931413.24796.10744.2547
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 23 )
2X-RAY DIFFRACTION2chain 'A' and (resid 24 through 46 )
3X-RAY DIFFRACTION3chain 'A' and (resid 47 through 51 )
4X-RAY DIFFRACTION4chain 'A' and (resid 52 through 61 )
5X-RAY DIFFRACTION5chain 'A' and (resid 62 through 72 )
6X-RAY DIFFRACTION6chain 'A' and (resid 73 through 83 )

+
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