[English] 日本語
Yorodumi
- PDB-353d: CRYSTAL STRUCTURE OF DOMAIN A OF THERMUS FLAVUS 5S RRNA AND THE C... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 353d
TitleCRYSTAL STRUCTURE OF DOMAIN A OF THERMUS FLAVUS 5S RRNA AND THE CONTRIBUTION OF WATER MOLECULES TO ITS STRUCTURE
Components
  • RNA (5'-R(*AP*UP*CP*CP*CP*CP*CP*GP*UP*GP*CP*C)-3')
  • RNA (5'-R(*GP*GP*UP*GP*CP*GP*GP*GP*GP*GP*AP*U)-3')
KeywordsRNA / A-RNA / DOUBLE STRAND
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsBetzel, C. / Lorenz, S. / Furste, J.P. / Bald, R. / Zhang, M. / Schneider, T.R. / Wilson, K.S. / Erdmann, V.A.
Citation
Journal: FEBS Lett. / Year: 1994
Title: Crystal structure of domain A of Thermus flavus 5S rRNA and the contribution of water molecules to its structure.
Authors: Betzel, C. / Lorenz, S. / Furste, J.P. / Bald, R. / Zhang, M. / Schneider, T.R. / Wilson, K.S. / Erdmann, V.A.
#1: Journal: To be Published
Title: Structure of Domain A of Thermus flavus 5S rRNA at 2.3 A Resolution. Comparison of Nearest Neighbor Parameters for Mismatches and the Influence of Solvent
Authors: Perbandt, M. / Lorenz, S. / Betzel, C. / Erdmann, V.A.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1993
Title: Crystallization and Preliminary Diffraction Studies of the Chemically Synthesized Domain A of Thermus flavus 5S rRNA: An Dodecamer Double Helix
Authors: Lorenz, S. / Furste, J. / Bald, R. / Zhang, M. / Raderschall, E. / Betzel, C. / Dauter, Z. / Wilson, K.
History
DepositionSep 29, 1997Deposition site: NDB / Processing site: NDB
Revision 1.0Nov 10, 1997Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2018Group: Data collection / Experimental preparation / Category: diffrn / exptl_crystal_grow
Item: _diffrn.ambient_temp / _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Aug 2, 2023Group: Data collection / Database references / Refinement description
Category: database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA (5'-R(*AP*UP*CP*CP*CP*CP*CP*GP*UP*GP*CP*C)-3')
B: RNA (5'-R(*GP*GP*UP*GP*CP*GP*GP*GP*GP*GP*AP*U)-3')


Theoretical massNumber of molelcules
Total (without water)7,6872
Polymers7,6872
Non-polymers00
Water2,846158
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.100, 30.100, 86.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

-
Components

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


Mass: 3723.264 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: RNA chain RNA (5'-R(*GP*GP*UP*GP*CP*GP*GP*GP*GP*GP*AP*U)-3')


Mass: 3963.408 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.6 Å3/Da / Density % sol: 51.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3MGCL211
4NA CACODYLATE11
5WATER12
6MPD12
7MGCL212
8NA CACODYLATE12
Crystal grow
*PLUS
Temperature: 45 ℃ / pH: 6.5
Details: Lorenz, S., (1993) Acta Crystallogr.,Sect.D, 49, 418.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlRNA1drop
25 %1drop
3200 mM1dropMgCl2
420 mMsodium cacodylate1drop
530 %MPD1reservoir
6400 mM1reservoirMgCl2
740 mMsodium cacodylate1reservoir
81

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11531
21531
Diffraction source
SourceSiteBeamlineTypeIDWavelengthWavelength (Å)
SEALED TUBECONVENTIONAL Mo10.71070.7107
SYNCHROTRONEMBL/DESY, HAMBURG X1120.920.92
Detector
TypeIDDetector
MARRESEARCH1IMAGE PLATE
MARRESEARCH2IMAGE PLATE
Radiation
IDMonochromatorMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GRAPHITEMx-ray1
2Mx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.71071
20.921
ReflectionHighest resolution: 2.4 Å / Num. obs: 2477 / % possible obs: 83.5 %
Reflection
*PLUS
Highest resolution: 2.4 Å / % possible obs: 83.5 %

-
Processing

Software
NameClassification
AMoREphasing
NUCLSQrefinement
XDSdata reduction
DENZOdata reduction
RefinementStarting model: NDB ENTRY ARN035 (PDB ENTRY 1RNA)

1rna


Resolution: 2.4→8 Å / σ(F): 0 / Details: X-PLOR (BRUNGER) ALSO WAS USED. /
RfactorNum. reflection
obs0.18 2477
Displacement parametersBiso mean: 23.9 Å2
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 508 0 158 666
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONn_bond_d0.025
X-RAY DIFFRACTIONn_angle_d0.068
X-RAY DIFFRACTIONn_planar_d0.014
X-RAY DIFFRACTIONn_hb_or_metal_coord
X-RAY DIFFRACTIONn_sugar_bond_it
X-RAY DIFFRACTIONn_sugar_angle_it
X-RAY DIFFRACTIONn_phos_bond_it
X-RAY DIFFRACTIONn_phos_angle_it
X-RAY DIFFRACTIONn_bond_angle_restr
X-RAY DIFFRACTIONn_dihedral_angle_restr
X-RAY DIFFRACTIONn_impr_tor
X-RAY DIFFRACTIONn_sugar_bond_d
X-RAY DIFFRACTIONn_sugar_bond_angle_d
X-RAY DIFFRACTIONn_phos_bond_d
X-RAY DIFFRACTIONn_phos_bond_angle_d
X-RAY DIFFRACTIONn_plane_restr
X-RAY DIFFRACTIONn_chiral_restr0.036
X-RAY DIFFRACTIONn_singtor_nbd
X-RAY DIFFRACTIONn_multtor_nbd
X-RAY DIFFRACTIONn_xhyhbond_nbd
LS refinement shellResolution: 2.3→2.4 Å / % reflection obs: 50 %
Software
*PLUS
Name: NUCLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 8 Å / σ(F): 0 / Rfactor obs: 0.18 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 23.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONn_bond_d0.025
X-RAY DIFFRACTIONn_angle_d0.068

+
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://pdbjlvh1.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