[English] 日本語
Yorodumi
- PDB-4erl: Crystal structure of the lysine riboswitch bound to a lysine-glyc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4erl
TitleCrystal structure of the lysine riboswitch bound to a lysine-glycine dipeptide
ComponentsLysine riboswitch RNA
KeywordsTRANSCRIPTION / Riboswitch aptamer domain / regulatory mRNA
Function / homologyGLYCINE / LYSINE / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesThermotoga Maritima (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsGarst, A.D. / Porter, E. / Batey, R.T.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Insights into the regulatory landscape of the lysine riboswitch.
Authors: Garst, A.D. / Porter, E.B. / Batey, R.T.
History
DepositionApr 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Database references
Revision 1.2Sep 13, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: Lysine riboswitch RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6883
Polymers52,4651
Non-polymers2222
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)119.878, 119.878, 58.743
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

-
Components

#1: RNA chain Lysine riboswitch RNA


Mass: 52465.289 Da / Num. of mol.: 1 / Fragment: Lysine riboswitch aptamer domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga Maritima (bacteria) / Gene: asd
#2: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N2O2
#3: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.64 Å3/Da / Density % sol: 73.52 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10 mM Na-HEPES pH 7.0, 2 M Li2SO4, and 5 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 303K

-
Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→19.62 Å / Num. all: 18847 / % possible obs: 97.8 % / Observed criterion σ(F): 1.97 / Observed criterion σ(I): 2 / Redundancy: 1.92 % / Biso Wilson estimate: 47.24 Å2 / Rmerge(I) obs: 0.113 / Rsym value: 0.113 / Net I/σ(I): 5.1
Reflection shellResolution: 3→3.11 Å / Redundancy: 1.93 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 1.9 / Num. unique all: 1853 / Rsym value: 0.321 / % possible all: 96.5

-
Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIX(phenix.refine: 1.7.3_928)refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3D0U)

3d0u


Resolution: 3→19.62 Å / SU ML: 0.43 / σ(F): 1.97 / Phase error: 26.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2338 965 5.16 %RANDOM
Rwork0.1953 ---
obs0.1974 18687 99.16 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 11.901 Å2 / ksol: 0.254 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.5935 Å20 Å20 Å2
2--2.5935 Å2-0 Å2
3---10.4317 Å2
Refine analyzeLuzzati d res low obs: 0.43 Å
Refinement stepCycle: LAST / Resolution: 3→19.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3479 14 10 3503
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073910
X-RAY DIFFRACTIONf_angle_d0.9336101
X-RAY DIFFRACTIONf_dihedral_angle_d13.8481941
X-RAY DIFFRACTIONf_chiral_restr0.06805
X-RAY DIFFRACTIONf_plane_restr0.008162
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.15820.37251360.31912537X-RAY DIFFRACTION98
3.1582-3.35510.2911180.26342508X-RAY DIFFRACTION99
3.3551-3.61270.30931590.2332532X-RAY DIFFRACTION99
3.6127-3.97350.26021300.20792517X-RAY DIFFRACTION99
3.9735-4.54230.22281290.17422564X-RAY DIFFRACTION100
4.5423-5.69940.18991580.15762512X-RAY DIFFRACTION100
5.6994-19.62010.16431350.14052552X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -23.1393 Å / Origin y: 45.4269 Å / Origin z: 1264.8736 Å
111213212223313233
T0.0362 Å2-0.0029 Å2-0.1095 Å2-0.0814 Å20.0996 Å2--0.073 Å2
L0.545 °2-0.1584 °20.2187 °2-0.2064 °2-0.1208 °2--0.3659 °2
S0.0491 Å °-0.044 Å °-0.0035 Å °0.0085 Å °0.0701 Å °0.0342 Å °-0.0629 Å °0.1073 Å °0.0133 Å °
Refinement TLS groupSelection details: all

+
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