[English] 日本語
Yorodumi
- PDB-2bcz: Crystal Structure of a minimal, mutant all-RNA hairpin ribozyme (... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2bcz
TitleCrystal Structure of a minimal, mutant all-RNA hairpin ribozyme (U39C, G8I, 2'deoxy A-1)
Components
  • 5'-R(*CP*GP*GP*UP*GP*AP*IP*AP*AP*GP*GP*G)-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*CP*CP*(DA)P*GP*UP*CP*CP*AP*CP*CP*G)-3')
  • 5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3'
KeywordsRNA / ribozyme / G8 / inosine
Function / homologyCOBALT HEXAMMINE(III) / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.4 Å
AuthorsSalter, J.D. / Wedekind, J.E.
Citation
Journal: Biochemistry / Year: 2006
Title: Water in the Active Site of an All-RNA Hairpin Ribozyme and Effects of Gua8 Base Variants on the Geometry of Phosphoryl Transfer.
Authors: Salter, J.D. / Krucinska, J. / Alam, S. / Grum-Tokars, V. / Wedekind, J.E.
#1: 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.
History
DepositionOct 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 5'-R(*UP*CP*CP*CP*(DA)P*GP*UP*CP*CP*AP*CP*CP*G)-3')
B: 5'-R(*CP*GP*GP*UP*GP*AP*IP*AP*AP*GP*GP*G)-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'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9377
Polymers19,5194
Non-polymers4183
Water905
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.490, 94.490, 127.580
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

-
Components

-
RNA chain , 4 types, 4 molecules ABCD

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


Mass: 4036.471 Da / Num. of mol.: 1 / Mutation: A1(DA) / Source method: obtained synthetically
#2: RNA chain 5'-R(*CP*GP*GP*UP*GP*AP*IP*AP*AP*GP*GP*G)-3'


Mass: 3955.433 Da / Num. of mol.: 1 / Mutation: G8I / 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 / Mutation: U39C / Source method: obtained synthetically

-
Non-polymers , 3 types, 8 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CoH18N6
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 4.21 Å3/Da / Density % sol: 70.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: PEG550 MME, lithium sulfate, spermidine, cobalt hexamine, , pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG550 MME11
2lithium sulfate11
3spermidine11
4cobalt hexamine11
5H2O11
6PEG550 MME12
7lithium sulfate12
8cobalt hexamine12

-
Data collection

DiffractionMean temperature: 83 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9764 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 5, 2005
RadiationMonochromator: bent triangular asymmetric cut si(111) monochromator, RH-coated si for vertical focussing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9764 Å / Relative weight: 1
ReflectionResolution: 2.4→44.3 Å / Num. all: 13689 / Num. obs: 13689 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.25 % / Biso Wilson estimate: 104.9 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 19.1
Reflection shellResolution: 2.4→2.48 Å / Redundancy: 5.91 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 4.3 / % possible all: 98.7

-
Processing

Software
NameVersionClassification
CNS1.1refinement
CrystalClear(MSC/RIGAKU)data reduction
CrystalClear(MSC/RIGAKU)data scaling
CNS1.1phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 1ZFR

1zfr
PDB Unreleased entry


Resolution: 2.4→44.3 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1771956.51 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: CNS v1.1
RfactorNum. reflection% reflectionSelection details
Rfree0.27 829 6.1 %RANDOM
Rwork0.24 ---
all0.24 13643 --
obs0.24 13643 99.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 75.3413 Å2 / ksol: 0.319713 e/Å3
Displacement parametersBiso mean: 75.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å2-3.03 Å20 Å2
2---15.42 Å20 Å2
3---14.47 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.48 Å
Luzzati d res low-45 Å
Luzzati sigma a0.83 Å0.86 Å
Refinement stepCycle: LAST / Resolution: 2.4→44.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1309 19 5 1333
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d17.6
X-RAY DIFFRACTIONc_improper_angle_d1.73
LS refinement shellResolution: 2.4→2.64 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 4
RfactorNum. reflection% reflection
Rfree0.515 190 5.7 %
Rwork0.495 3141 -
obs--99.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1ion.paramdna-rna.top
X-RAY DIFFRACTION2dna-rna_rep.paramcobalt.top
X-RAY DIFFRACTION3cobalt.parion.top
X-RAY DIFFRACTION4water_rep.paramwater.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