[English] 日本語
Yorodumi
- PDB-1idw: STRUCTURE OF THE HYBRID RNA/DNA R-GCUUCGGC-D[CL]U IN PRESENCE OF ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1idw
TitleSTRUCTURE OF THE HYBRID RNA/DNA R-GCUUCGGC-D[CL]U IN PRESENCE OF RH(NH3)6+++
Components5'-R(*GP*CP*UP*UP*CP*GP*GP*C)-D(P*(UCL))-3'
KeywordsDNA/RNA / RNA/DNA HYBRID / RHODIUM HEXAMMINE / C-U MISMATCH / G-U MISMATCH / DNA-RNA COMPLEX
Function / homologyRHODIUM HEXAMINE ION / DNA/RNA hybrid
Function and homology information
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsCruse, W. / Saludjian, P. / Neuman, A. / Prange, T.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Destabilizing effect of a fluorouracil extra base in a hybrid RNA duplex compared with bromo and chloro analogues
Authors: Cruse, W. / Saludjian, P. / Neuman, A. / Prange, T.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: Structure of a Mispaired RNA Double Helix at 1.6 A Resolution and Implications for the Prediction of RNA Secondary Structure
Authors: Cruse, W. / Saludjian, P. / Biala, E. / Strazewski, P. / Prange, T. / Kennard, O.
History
DepositionApr 5, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.5Aug 9, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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(*GP*CP*UP*UP*CP*GP*GP*C)-D(P*(UCL))-3'
B: 5'-R(*GP*CP*UP*UP*CP*GP*GP*C)-D(P*(UCL))-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,1676
Polymers5,6862
Non-polymers4814
Water82946
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.820, 19.380, 50.300
Angle α, β, γ (deg.)90.00, 109.90, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe second strand of the dimer is not symmetric

-
Components

#1: DNA/RNA hybrid 5'-R(*GP*CP*UP*UP*CP*GP*GP*C)-D(P*(UCL))-3'


Mass: 2843.149 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: phosphoramidite method
#2: Chemical ChemComp-RHD / RHODIUM HEXAMINE ION


Mass: 205.089 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H18N6Rh
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.18 Å3/Da / Density % sol: 43.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: cacodylate buffer, MPD, Rhodium-hexammine, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1cacodylate buffer11
2MPD11
3rhodium-hexammine11
4MPD12
Crystal grow
*PLUS
pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.05 Mlithium cacodylate1drop
45 %1drop
535-40 %MPD1reservoir
2RNA/DNA hybrid1drop0.1mg
3rhodium/iridium hexammine1drop0.1mg

-
Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 Å
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Mar 20, 1997 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.81→6 Å / Num. all: 3738 / Num. obs: 3641 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 3.5 % / Biso Wilson estimate: 16.4 Å2 / Rmerge(I) obs: 0.039 / Rsym value: 0.041 / Net I/σ(I): 18
Reflection shellResolution: 1.8→2 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 3 / Num. unique all: 517 / Rsym value: 0.206 / % possible all: 43.2
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 6 Å / % possible obs: 85 % / Num. measured all: 13027

-
Processing

Software
NameVersionClassification
MADNESSdata collection
ROTAVATAdata reduction
AMoREphasing
SHELXL-97refinement
MADNESSdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 165D

165d


Resolution: 1.8→6 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 4
Stereochemistry target values: personal dictionary from small molecules
Details: Chloro-uracil 9 B disordered at the C2 position. Refined as two-component 1:1 static orientations paired to their symmetry-related mates. The two rhodium atoms are refined anisotropically. ...Details: Chloro-uracil 9 B disordered at the C2 position. Refined as two-component 1:1 static orientations paired to their symmetry-related mates. The two rhodium atoms are refined anisotropically. One chlorine atom is disordered.
RfactorNum. reflection% reflectionSelection details
Rfree0.202 311 -RANDOM
Rwork0.172 ---
all0.176 3738 --
obs0.172 3641 95 %-
Displacement parametersBiso mean: 18.4 Å2
Refinement stepCycle: LAST / Resolution: 1.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 389 20 46 455
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.032
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.097
X-RAY DIFFRACTIONs_from_restr_planes0.071
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDRfactor Rfree error% reflection obs (%)
1.8-20.21400.169X-RAY DIFFRACTION0.0243.2
2-2.30.191930.164X-RAY DIFFRACTION0.0298.5
2.3-2.70.211800.176X-RAY DIFFRACTION0.0298.7
2.7-3.50.187690.168X-RAY DIFFRACTION0.0296.8
3.5-60.19300.195X-RAY DIFFRACTION0.0276.5
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 6 Å / σ(F): 2 / % reflection Rfree: 8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.071
X-RAY DIFFRACTIONs_chiral_restr0.097

+
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