[English] 日本語
Yorodumi
- PDB-1x9k: An all-RNA Hairpin Ribozyme with mutation U39C -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1x9k
TitleAn all-RNA Hairpin Ribozyme with mutation U39C
Components
  • 5'-R(*AP*AP*UP*AP*GP*AP*GP*AP*AP*GP*CP*GP*A)-3'
  • 5'-R(*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3'
  • 5'-R(*UP*CP*GP*CP*AP*GP*UP*CP*CP*UP*AP*UP*U)-3'
  • 5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3'
KeywordsRNA / Hairpin ribozyme / all-RNA / mutation / high salt / S-turn / E-loop / catalytic RNA
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.17 Å
AuthorsAlam, S. / Grum-Tokars, V. / Krucinska, J. / Kundracik, M.L. / Wedekind, J.E.
Citation
Journal: Biochemistry / Year: 2005
Title: Conformational Heterogeneity at Position U37 of an All-RNA Hairpin Ribozyme with Implications for Metal Binding and the Catalytic Structure of the S-Turn.
Authors: Alam, S. / Grum-Tokars, V. / Krucinska, J. / Kundracik, M.L. / Wedekind, J.E.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Crystallization and X-ray diffraction analysis of an all-RNA U39C mutant of the minimal hairpin ribozyme
Authors: Grum-Tokars, V. / Milovanovic, M. / Wedekind, J.E.
History
DepositionAug 21, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 5'-R(*UP*CP*GP*CP*AP*GP*UP*CP*CP*UP*AP*UP*U)-3'
B: 5'-R(*AP*AP*UP*AP*GP*AP*GP*AP*AP*GP*CP*GP*A)-3'
C: 5'-R(*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3'
D: 5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)19,8344
Polymers19,8344
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.46, 94.46, 129.12
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

-
Components

#1: RNA chain 5'-R(*UP*CP*GP*CP*AP*GP*UP*CP*CP*UP*AP*UP*U)-3'


Mass: 4055.421 Da / Num. of mol.: 1 / Mutation: U39C / Source method: obtained synthetically / Details: Solid Phase Chemical Synthesis
#2: RNA chain 5'-R(*AP*AP*UP*AP*GP*AP*GP*AP*AP*GP*CP*GP*A)-3'


Mass: 4251.654 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: RNA chain 5'-R(*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3'


Mass: 5535.445 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: RNA chain 5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3'


Mass: 5991.568 Da / Num. of mol.: 1 / Source method: obtained synthetically

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.2 Å3/Da / Density % sol: 70 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: ammonium sulfate, spermidine, cobalt hexaamine, cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1ammonium sulfate11
2spermidine11
3cobalt hexaamineHexamminecobalt(III) chloride11
4cacodylateCacodylic acid11
5H2O11
6ammonium sulfate12
7cacodylateCacodylic acid12
8H2O12

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 17, 2002
Details: insertion device, double crystal monochromator, vertical focusing mirror
RadiationMonochromator: Si-220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.17→25 Å / Num. obs: 6480 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 71.5 Å2 / Rsym value: 0.064 / Net I/σ(I): 13.4
Reflection shellResolution: 3.17→3.28 Å / Redundancy: 7 % / Mean I/σ(I) obs: 3.9 / Num. unique all: 594 / Rsym value: 0.412 / % possible all: 100

-
Processing

Software
NameVersionClassification
CNS1.1refinement
CrystalClear(MSC/RIGAKU)data reduction
CrystalClear(MSC/RIGAKU)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1M5K

1m5k


Resolution: 3.17→24.63 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 13729086.57 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3
Stereochemistry target values: Parkinson et al., (1996) Acta Cryst. D52, 57-64
RfactorNum. reflection% reflectionSelection details
Rfree0.252 648 10.5 %RANDOM
Rwork0.236 ---
all0.243 6192 --
obs0.236 6161 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.1897 Å2 / ksol: 0.1 e/Å3
Displacement parametersBiso mean: 160.9 Å2
Baniso -1Baniso -2Baniso -3
1--21.28 Å2-34.31 Å20 Å2
2--13.14 Å20 Å2
3---8.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.71 Å0.72 Å
Luzzati d res low-5 Å
Luzzati sigma a0.75 Å1.03 Å
Refinement stepCycle: LAST / Resolution: 3.17→24.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1313 0 0 1313
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.89
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: 3.17→3.49 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 4
RfactorNum. reflection% reflection
Rfree0.457 147 9.8 %
Rwork0.517 1346 -
obs--99.8 %
Xplor fileSerial no: 1 / Param file: DNA-RNA_REP.PARAM / Topol file: DNA-RNA.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