[English] 日本語
Yorodumi
- PDB-5dh6: Two divalent metal ions and conformational changes play roles in ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5dh6
TitleTwo divalent metal ions and conformational changes play roles in the hammerhead ribozyme cleavage reaction-G12A mutant in Mg2+
Components
  • 5'-R(*GP*GP*GP*CP*GP*U)-D(P*C)-R(P*UP*GP*GP*GP*CP*AP*GP*UP*AP*CP*CP*CP*A)-3'
  • hammerhead ribozyme
KeywordsRNA / ribozyme / hammerhead
Function / homologyDNA/RNA hybrid / DNA/RNA hybrid (> 10) / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.784 Å
AuthorsMir, A. / Chen, J. / Neau, D. / Golden, B.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM095923 United States
CitationJournal: Biochemistry / Year: 2015
Title: Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction.
Authors: Mir, A. / Chen, J. / Robinson, K. / Lendy, E. / Goodman, J. / Neau, D. / Golden, B.L.
History
DepositionAug 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2015Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)22,0447
Polymers21,9222
Non-polymers1225
Water1448
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-37 kcal/mol
Surface area12190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.405, 85.964, 102.969
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-202-

HOH

-
Components

#1: RNA chain hammerhead ribozyme


Mass: 15484.287 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This RNA was made by in vitro transcription / Source: (synth.) synthetic construct (others)
#2: DNA/RNA hybrid 5'-R(*GP*GP*GP*CP*GP*U)-D(P*C)-R(P*UP*GP*GP*GP*CP*AP*GP*UP*AP*CP*CP*CP*A)-3'


Mass: 6437.895 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthesized oligonucleotide / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 4.11 Å3/Da / Density % sol: 70.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 33% MPD, 0.4 M potassium chloride, 50 mM potassium acetate, 10 mM MgCl2, pH 5.0, and 0.5mM spermine

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.976 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.784→50 Å / Num. all: 9318 / Num. obs: 9318 / % possible obs: 99.5 % / Redundancy: 14.3 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 61.7
Reflection shellResolution: 2.784→2.85 Å / Redundancy: 15 % / Rmerge(I) obs: 0.655 / Mean I/σ(I) obs: 6.3 / % possible all: 96.7

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.784→28.407 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2416 920 9.97 %
Rwork0.2108 --
obs0.2139 9231 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.784→28.407 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1454 5 8 1467
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021626
X-RAY DIFFRACTIONf_angle_d0.472532
X-RAY DIFFRACTIONf_dihedral_angle_d10.131807
X-RAY DIFFRACTIONf_chiral_restr0.023338
X-RAY DIFFRACTIONf_plane_restr0.00368
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7843-2.9310.36021260.35271141X-RAY DIFFRACTION96
2.931-3.11440.33061340.26071160X-RAY DIFFRACTION98
3.1144-3.35450.23361210.22311158X-RAY DIFFRACTION98
3.3545-3.69150.25851310.20651193X-RAY DIFFRACTION99
3.6915-4.22410.21071370.18711190X-RAY DIFFRACTION100
4.2241-5.31620.20541330.18491196X-RAY DIFFRACTION100
5.3162-28.40860.23731380.20781273X-RAY DIFFRACTION100

+
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