[English] 日本語
Yorodumi
- PDB-6zw3: Racemic compound of RNA duplexes. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zw3
TitleRacemic compound of RNA duplexes.
Components
  • RNA (5'-R(*(0C)P*(0C)P*(0G)P*(0C)P*(0C)P*(0U)P*(0G)P*(0G))-3')
  • RNA (5'-R(*(0C)P*(0U)P*(0G)P*(0G)P*(0G)P*(0C)P*(0G)P*(0G))-3')
  • RNA (5'-R(*CP*CP*GP*CP*CP*UP*GP*G)-3')
  • RNA (5'-R(*CP*UP*GP*GP*GP*CP*GP*G)-3')
KeywordsRNA / racemic compound
Function / homologyRNA
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.522 Å
AuthorsRypniewski, W.
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Broken symmetry between RNA enantiomers in a crystal lattice.
Authors: Kiliszek, A. / Blaszczyk, L. / Bejger, M. / Rypniewski, W.
History
DepositionJul 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 15, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Jul 26, 2023Group: Derived calculations / Polymer sequence / Category: atom_type / entity_poly
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _entity_poly.type
Revision 2.1Jan 31, 2024Group: 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
K: RNA (5'-R(*(0C)P*(0U)P*(0G)P*(0G)P*(0G)P*(0C)P*(0G)P*(0G))-3')
L: RNA (5'-R(*(0C)P*(0C)P*(0G)P*(0C)P*(0C)P*(0U)P*(0G)P*(0G))-3')
M: RNA (5'-R(*CP*UP*GP*GP*GP*CP*GP*G)-3')
N: RNA (5'-R(*CP*CP*GP*CP*CP*UP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,68811
Polymers10,2304
Non-polymers4587
Water3,369187
1
K: RNA (5'-R(*(0C)P*(0U)P*(0G)P*(0G)P*(0G)P*(0C)P*(0G)P*(0G))-3')
L: RNA (5'-R(*(0C)P*(0C)P*(0G)P*(0C)P*(0C)P*(0U)P*(0G)P*(0G))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,3776
Polymers5,1152
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
M: RNA (5'-R(*CP*UP*GP*GP*GP*CP*GP*G)-3')
N: RNA (5'-R(*CP*CP*GP*CP*CP*UP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,3115
Polymers5,1152
Non-polymers1963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)20.950, 26.490, 38.660
Angle α, β, γ (deg.)106.033, 96.057, 92.598
Int Tables number1
Space group name H-MP1

-
Components

-
RNA chain , 4 types, 4 molecules KLMN

#1: RNA chain RNA (5'-R(*(0C)P*(0U)P*(0G)P*(0G)P*(0G)P*(0C)P*(0G)P*(0G))-3')


Mass: 2597.601 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chain K is L-enantiomer. It pairs with chain L. / Source: (synth.) Thermus thermophilus (bacteria)
#2: RNA chain RNA (5'-R(*(0C)P*(0C)P*(0G)P*(0C)P*(0C)P*(0U)P*(0G)P*(0G))-3')


Mass: 2517.553 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chain L is L-enantiomer. It pairs with chain K. / Source: (synth.) Thermus thermophilus (bacteria)
#3: RNA chain RNA (5'-R(*CP*UP*GP*GP*GP*CP*GP*G)-3')


Mass: 2597.601 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chain M is D-enantiomer. It pairs with chain N. / Source: (synth.) Thermus thermophilus (bacteria)
#4: RNA chain RNA (5'-R(*CP*CP*GP*CP*CP*UP*GP*G)-3')


Mass: 2517.553 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chain N is D-enantiomer. It pairs with chain M. / Source: (synth.) Thermus thermophilus (bacteria)

-
Non-polymers , 2 types, 194 molecules

#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.45 % / Description: needle
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M zinc acetate, 0.1 M cacodylate buffer, 18% w/v polyethylene glycol 8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.283 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.283 Å / Relative weight: 1
ReflectionResolution: 1.52→37 Å / Num. obs: 10572 / % possible obs: 86.7 % / Redundancy: 3.5 % / CC1/2: 0.975 / Rrim(I) all: 0.198 / Rsym value: 0.168 / Net I/σ(I): 4.19
Reflection shellResolution: 1.52→1.61 Å / Num. unique obs: 1353 / CC1/2: 0.652 / Rrim(I) all: 1.252 / Rsym value: 1.061

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZQ9

6zq9


Resolution: 1.522→36.874 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.64 / SU ML: 0.116 / Cross valid method: FREE R-VALUE / ESU R: 0.126 / ESU R Free: 0.13
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2721 563 5.335 %
Rwork0.2128 9990 -
all0.216 --
obs-10553 86.756 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 20.915 Å2
Baniso -1Baniso -2Baniso -3
1--0.731 Å20.709 Å20.242 Å2
2--1.541 Å20.039 Å2
3----0.802 Å2
Refinement stepCycle: LAST / Resolution: 1.522→36.874 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 676 7 187 870
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.011752
X-RAY DIFFRACTIONr_bond_other_d0.0030.019292
X-RAY DIFFRACTIONr_angle_refined_deg1.4361.4521168
X-RAY DIFFRACTIONr_angle_other_deg1.1822.383726
X-RAY DIFFRACTIONr_chiral_restr0.0620.2128
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.02412
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02124
X-RAY DIFFRACTIONr_nbd_refined0.2150.298
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2720.2372
X-RAY DIFFRACTIONr_nbtor_refined0.2530.2254
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0620.2151
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2680.2172
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.3180.22
X-RAY DIFFRACTIONr_metal_ion_refined0.0810.27
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1310.216
X-RAY DIFFRACTIONr_nbd_other0.1690.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2420.230
X-RAY DIFFRACTIONr_scbond_it1.3041.992752
X-RAY DIFFRACTIONr_scbond_other1.3031.992751
X-RAY DIFFRACTIONr_scangle_it1.8732.9931168
X-RAY DIFFRACTIONr_scangle_other1.8722.9931169
X-RAY DIFFRACTIONr_lrange_it6.74222.0631124
X-RAY DIFFRACTIONr_lrange_other5.43219.9671038
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.522-1.5610.872240.4763850.59200.450.39544.45650.476
1.561-1.6040.375420.3737210.3738570.5090.51989.03150.37
1.604-1.650.377330.3347320.3368720.590.64387.72940.336
1.65-1.7010.305380.3046720.3047970.7260.70789.08410.306
1.701-1.7560.337360.3096950.318480.7890.75186.20280.308
1.756-1.8180.342320.2926430.2947430.7660.79490.84790.292
1.818-1.8860.281380.2736210.2737410.7830.82788.93390.275
1.886-1.9630.257440.2485940.2497020.8720.84990.88320.245
1.963-2.050.285400.256100.2527280.8730.86789.28570.25
2.05-2.150.294360.2135560.2186460.8980.90491.64090.218
2.15-2.2660.287260.1935560.1966300.8330.92392.3810.202
2.266-2.4030.193260.1775300.1786030.9480.93792.20560.188
2.403-2.5680.281280.1994600.2045470.9040.92589.21390.21
2.568-2.7720.265220.1864620.1895180.8850.93893.43630.216
2.772-3.0350.249240.2044280.2064820.8910.92993.77590.243
3.035-3.3910.299210.173670.1754350.9120.9689.19540.232
3.391-3.910.352120.1593330.1643770.8740.96191.51190.215
3.91-4.7750.147190.1522860.1523250.9770.96593.84620.207
4.775-6.6970.253130.1512170.1562560.9490.96889.84380.213
6.697-36.8740.24290.191210.1931360.9380.95595.58820.252

+
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