[English] 日本語
Yorodumi
- PDB-6jq6: Hatchet Ribozyme Structure soaking with Ir(NH3)6+ -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6jq6
TitleHatchet Ribozyme Structure soaking with Ir(NH3)6+
ComponentsRNA (81-MER)
KeywordsRNA / ribozyme / hatchet / cleavage / catalysis / non-coding RNA
Function / homologyIRIDIUM HEXAMMINE ION / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.626 Å
AuthorsRen, A. / Zheng, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China)91640104 China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Hatchet ribozyme structure and implications for cleavage mechanism.
Authors: Zheng, L. / Falschlunger, C. / Huang, K. / Mairhofer, E. / Yuan, S. / Wang, J. / Patel, D.J. / Micura, R. / Ren, A.
History
DepositionMar 29, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 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
U: RNA (81-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3002
Polymers26,0051
Non-polymers2941
Water1629
1
U: RNA (81-MER)
hetero molecules

U: RNA (81-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6004
Polymers52,0112
Non-polymers5892
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Buried area5310 Å2
ΔGint2 kcal/mol
Surface area24610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.830, 91.830, 140.627
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

-
Components

#1: RNA chain RNA (81-MER)


Mass: 26005.381 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-IRI / IRIDIUM HEXAMMINE ION


Mass: 294.400 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H18IrN6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 3.29 Å3/Da / Density % sol: 62.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.20M K-formate, 2.2M (NH4)2SO4

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.103 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.103 Å / Relative weight: 1
ReflectionResolution: 2.61→50 Å / Num. obs: 19049 / % possible obs: 99 % / Redundancy: 20 % / Rpim(I) all: 0.041 / Net I/σ(I): 20.2
Reflection shellResolution: 2.61→2.72 Å / Num. unique obs: 683 / Rpim(I) all: 2.29

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.626→50 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.28
RfactorNum. reflection% reflection
Rfree0.2293 1913 10.04 %
Rwork0.1961 --
obs0.1996 19049 96.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.626→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1720 7 9 1736
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061956
X-RAY DIFFRACTIONf_angle_d1.2363053
X-RAY DIFFRACTIONf_dihedral_angle_d17.113983
X-RAY DIFFRACTIONf_chiral_restr0.056409
X-RAY DIFFRACTIONf_plane_restr0.00982
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6257-2.69140.4762780.5324683X-RAY DIFFRACTION54
2.6914-2.76420.61991370.46341239X-RAY DIFFRACTION97
2.7642-2.84550.5641400.45041250X-RAY DIFFRACTION99
2.8455-2.93730.44041380.36071273X-RAY DIFFRACTION99
2.9373-3.04230.33841400.30331269X-RAY DIFFRACTION100
3.0423-3.16410.32331440.25881274X-RAY DIFFRACTION100
3.1641-3.30820.23271370.21521261X-RAY DIFFRACTION99
3.3082-3.48260.21821370.17941243X-RAY DIFFRACTION98
3.4826-3.70080.21721410.17961270X-RAY DIFFRACTION100
3.7008-3.98650.23481410.17121286X-RAY DIFFRACTION100
3.9865-4.38760.21861370.15341269X-RAY DIFFRACTION100
4.3876-5.02250.15041460.1481269X-RAY DIFFRACTION100
5.0225-6.32740.16781530.1481264X-RAY DIFFRACTION100
6.3274-79.56360.18311440.17121286X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -0.7861 Å / Origin y: 33.19 Å / Origin z: 55.7008 Å
111213212223313233
T0.3843 Å20.0453 Å20.0816 Å2-0.4884 Å20.0319 Å2--0.3857 Å2
L0.3856 °20.3491 °20.8492 °2-0.1095 °2-0.0798 °2--0.3828 °2
S0.0516 Å °-0.0261 Å °0.0009 Å °-0.0272 Å °-0.0846 Å °-0.0316 Å °-0.2338 Å °-0.3384 Å °-0.0001 Å °
Refinement TLS groupSelection details: all

+
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