[English] 日本語
Yorodumi
- PDB-315d: CRYSTAL STRUCTURE OF AN ALTERNATING OCTAMER R(GUAUGUA)D(C) WITH A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 315d
TitleCRYSTAL STRUCTURE OF AN ALTERNATING OCTAMER R(GUAUGUA)D(C) WITH ADJACENT G-U WOBBLE PAIRS
ComponentsDNA/RNA (5'-R(*GP*UP*AP*UP*GP*UP*AP*)-D(*C)-3')
KeywordsDNA-RNA HYBRID / A-DNA/RNA / DOUBLE HELIX
Function / homologyDNA/RNA hybrid
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsBiswas, R. / Wahl, M.C. / Ban, C. / Sundaralingam, M.
CitationJournal: J.Mol.Biol. / Year: 1997
Title: Crystal structure of an alternating octamer r(GUAUGUA)dC with adjacent G x U wobble pairs
Authors: Biswas, R. / Wahl, M.C. / Ban, C. / Sundaralingam, M.
History
DepositionFeb 26, 1997Deposition site: NDB / Processing site: NDB
Revision 1.0Sep 23, 1997Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA/RNA (5'-R(*GP*UP*AP*UP*GP*UP*AP*)-D(*C)-3')
B: DNA/RNA (5'-R(*GP*UP*AP*UP*GP*UP*AP*)-D(*C)-3')


Theoretical massNumber of molelcules
Total (without water)5,0232
Polymers5,0232
Non-polymers00
Water1,24369
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.710, 39.710, 68.150
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-79-

HOH

21A-81-

HOH

31A-82-

HOH

41B-80-

HOH

51B-83-

HOH

61B-84-

HOH

71B-85-

HOH

-
Components

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


Mass: 2511.545 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 291.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA CACODYLATE11
4[CO(NH3)6]3+11
5WATER12
6MPD12
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11 mMRNA1drop
20.5 mMcobaltic hexammine chloride1drop
340 mMsodium cacodylate1drop
410 %(v/v)MPD1drop
560 %(v/v)MPD1reservoir
61

-
Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE
DetectorType: SIEMENS / Detector: AREA DETECTOR
RadiationMonochromator: GRAPHITE / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 1.38 Å / Num. obs: 5744 / Observed criterion σ(F): 1.5 / Rsym value: 0.0347
Reflection
*PLUS
Observed criterion σ(F): 1.5 / Rmerge(I) obs: 0.0349

-
Processing

Software
NameVersionClassification
X-PLOR3refinement
XENGENV. 2.0data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AHH071

Resolution: 1.38→10 Å / σ(F): 1.5
RfactorNum. reflection
Rfree0.231 -
Rwork0.176 -
obs0.176 4035
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.38→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 332 0 69 401
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.38→1.58 Å
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / σ(F): 1.5
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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