[English] 日本語
Yorodumi
- PDB-3fo4: Crystal structure of guanine riboswitch C74U mutant bound to 6-ch... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3fo4
TitleCrystal structure of guanine riboswitch C74U mutant bound to 6-chloroguanine
ComponentsGuanine riboswitch C74U mutant
KeywordsRNA / mRNA / riboswitch / 6-chloroguanine / adenine / RNA-ligand complex / double helix / three-way junction
Function / homology6-chloroguanine / ACETATE ION / COBALT HEXAMMINE(III) / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGilbert, S.D. / Batey, R.T.
CitationJournal: Structure / Year: 2009
Title: Adaptive ligand binding by the purine riboswitch in the recognition of Guanine and adenine analogs.
Authors: Gilbert, S.D. / Reyes, F.E. / Edwards, A.L. / Batey, R.T.
History
DepositionDec 27, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Guanine riboswitch C74U mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,99915
Polymers21,8371
Non-polymers2,16214
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)132.600, 35.170, 41.790
Angle α, β, γ (deg.)90.00, 90.38, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe asymmetric unit contains one biological unit

-
Components

#1: RNA chain Guanine riboswitch C74U mutant


Mass: 21836.975 Da / Num. of mol.: 1 / Mutation: C74U / Source method: obtained synthetically
Details: This sequence was engineered based on the guanine riboswitch found in the 5'UTR of the xpt-pbuX gene in Bacillus subtilis
#2: Chemical ChemComp-6GU / 6-chloroguanine / 6-chloro-9H-purin-2-amine


Mass: 169.572 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4ClN5
#3: Chemical ChemComp-ACT / ACETATE ION


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


Mass: 161.116 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: CoH18N6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2.23 Å3/Da / Density % sol: 44.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 2000, 480 mM Ammonium acetate, 12 mM Cobalt hexammine, 10 mM K+HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 200011
2Ammonium acetate11
3Cobalt hexammine11
4Potassium HEPES11
5PEG 200012
6Ammonium acetate12
7Cobalt hexammine12
8Potassium HEPES12

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 13, 2005
RadiationMonochromator: Nickel filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 16673 / Num. obs: 15304 / % possible obs: 91.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 3.56 % / Biso Wilson estimate: 19.9 Å2 / Rsym value: 0.048 / Net I/σ(I): 15.8
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.31 % / Rsym value: 0.201 / % possible all: 69.5

-
Processing

Software
NameClassification
CrystalCleardata collection
CNSrefinement
d*TREKdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1U8D

1u8d
PDB Unreleased entry


Resolution: 1.9→19.97 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1233811.58 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1065 7.3 %RANDOM
Rwork0.226 ---
obs0.226 14584 94.3 %-
all-14584 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.9172 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 27.3 Å2
Baniso -1Baniso -2Baniso -3
1-2.95 Å20 Å22.44 Å2
2---2.06 Å20 Å2
3----0.89 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1336 99 203 1638
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_d21.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.44
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: 1.9→2.02 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.356 163 7 %
Rwork0.315 2156 -
obs--91.1 %
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