[English] 日本語
Yorodumi
- PDB-1fix: THE STRUCTURE OF AN RNA/DNA HYBRID: A SUBSTRATE OF THE RIBONUCLEA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1fix
TitleTHE STRUCTURE OF AN RNA/DNA HYBRID: A SUBSTRATE OF THE RIBONUCLEASE ACTIVITY OF HIV-1 REVERSE TRANSCRIPTASE
Components
  • DNA (5'-D(*GP*GP*CP*GP*CP*CP*CP*GP*AP*A)-3')
  • RNA (5'-R(*UP*UP*CP*GP*GP*GP*CP*GP*CP*C)-3')
KeywordsDNA-RNA HYBRID / RIGHT HANDED DNA/RNA HYBRID / DOUBLE HELIX / HIV-1 PRIMER BINDING SITE
Function / homologyDNA / RNA
Function and homology information
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.3 Å
AuthorsHorton, N.C. / Finzel, B.C.
CitationJournal: J.Mol.Biol. / Year: 1996
Title: The structure of an RNA/DNA hybrid: a substrate of the ribonuclease activity of HIV-1 reverse transcriptase.
Authors: Horton, N.C. / Finzel, B.C.
History
DepositionOct 24, 1996Deposition site: NDB / Processing site: NDB
Revision 1.0Dec 11, 1996Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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: RNA (5'-R(*UP*UP*CP*GP*GP*GP*CP*GP*CP*C)-3')
B: DNA (5'-D(*GP*GP*CP*GP*CP*CP*CP*GP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)6,2242
Polymers6,2242
Non-polymers00
Water1,29772
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.300, 31.300, 137.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

-
Components

#1: RNA chain RNA (5'-R(*UP*UP*CP*GP*GP*GP*CP*GP*CP*C)-3')


Mass: 3168.925 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*GP*GP*CP*GP*CP*CP*CP*GP*AP*A)-3')


Mass: 3055.006 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.64 Å3/Da / Density % sol: 46.5 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 4.5 / Details: pH 4.50, VAPOR DIFFUSION, HANGING DROP / Temp details: ROOM TEMPERATURE
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3CACL211
4NA ACETATE11
Crystal
*PLUS
Crystal grow
*PLUS
pH: 4.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
125.5 %(w/v)methylpentanediol1drop
20.2 M1dropCaCl2
30.1 Msodium acetate1drop
40.56 mMduplex1drop

-
Data collection

DiffractionAmbient temp details: ROOM TEMPERATURE
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Oct 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.3→5 Å / Num. all: 20393 / Num. obs: 3315 / % possible obs: 94.4 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.081 / Rsym value: 0.081
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 5 Å / % possible obs: 94.4 % / Observed criterion σ(I): 2 / Num. measured all: 20393 / Rmerge(I) obs: 0.076

-
Processing

Software
NameClassification
XTALmodel building
X-PLORrefinement
XENGENdata reduction
XENGENdata scaling
XTALphasing
RefinementMethod to determine structure: MIR
Starting model: A-FORM DUPLEX

Resolution: 2.3→5 Å / σ(F): 2
Details: NUCLEIC ACID RNA-DNA PARAMETER FILE: G. PARKINSON,ET AL. (1996) ACTA CRYST. D52, 57-64
RfactorNum. reflection% reflection
Rwork0.145 --
obs0.145 2457 80 %
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.3→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 412 0 72 484
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
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_deg2.2
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: 2.3→2.39 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rwork0.272 117 -
obs--30 %
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 5 Å / σ(F): 2 / Rfactor obs: 0.139
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 2.2

+
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