[English] 日本語
Yorodumi
- PDB-2eet: Guanine Riboswitch A21G, U75C mutant bound to hypoxanthine -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2eet
TitleGuanine Riboswitch A21G, U75C mutant bound to hypoxanthine
ComponentsGuanine Riboswitch
KeywordsRNA / mRNA / riboswitch / hypoxanthine / guanine / RNA-ligand complex / double helix / three-way junction / base triple
Function / homologyACETATE ION / HYPOXANTHINE / COBALT HEXAMMINE(III) / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsGilbert, S.D. / Edwards, A.L. / Batey, R.T.
CitationJournal: Biochemistry / Year: 2007
Title: Mutational analysis of the purine riboswitch aptamer domain
Authors: Gilbert, S.D. / Love, C.E. / Edwards, A.L. / Batey, R.T.
History
DepositionFeb 18, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE Residues G21 and C75 were engineered from A and U, respectively, based on the guanine ...SEQUENCE Residues G21 and C75 were engineered from A and U, respectively, based on the guanine riboswitch found in the 5'UTR of the xpt-pbuX gene in Bacillus subtilis.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Guanine Riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,65015
Polymers21,5221
Non-polymers2,12914
Water4,684260
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.790, 35.280, 41.660
Angle α, β, γ (deg.)90.00, 90.66, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: RNA chain Guanine Riboswitch


Mass: 21521.801 Da / Num. of mol.: 1 / Mutation: A21G, U75C / Source method: obtained synthetically
Details: This sequence was engineered based on the guanine riboswitch in the 5'UTR of the xpt-pbuX gene in Bacillus subtilis.
References: PDB-PDB
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: CoH18N6
#4: Chemical ChemComp-HPA / HYPOXANTHINE


Mass: 136.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N4O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.28 Å3/Da / Density % sol: 46.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% Polyethylene glycol 3000, 400mM ammonium acetate, 12mM cobalt hexammine chloride, 10 mM K(+)-Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1Polyethylene glycol 300011
2ammonium acetate11
3cobalt hexammine chloride11
4K(+)-Hepes11
5H2O11
6Polyethylene glycol 300012
7ammonium acetate12
8cobalt hexammine chloride12
9K(+)-Hepes12
10H2O12

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jun 27, 2006
RadiationMonochromator: Nickel Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→19.95 Å / Num. all: 13552 / Num. obs: 13407 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 4.26 % / Biso Wilson estimate: 18.9 Å2 / Rsym value: 0.048 / Net I/σ(I): 19.3
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 4.13 % / Mean I/σ(I) obs: 6 / Num. unique all: 1018 / Rsym value: 0.15 / % possible all: 71.8

-
Processing

Software
NameVersionClassification
CNS1.1refinement
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1U8D

1u8d
PDB Unreleased entry


Resolution: 1.95→19.95 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1332366.22 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1005 7.5 %RANDOM
Rwork0.213 ---
all-13404 --
obs-13404 92.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 25 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 26.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.95 Å20 Å2-3.46 Å2
2---1.84 Å20 Å2
3----1.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.95→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1423 98 260 1781
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.39
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.276 133 7 %
Rwork0.267 1763 -
obs-1763 79.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1water_rep.paramwater_rep.top
X-RAY DIFFRACTION2dna-rna_rep_revise.paramdna-rna_rep_revise.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4cohex_rep.paramcohex_rep.top
X-RAY DIFFRACTION5acetate.paramacetate.top

+
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