[English] 日本語
Yorodumi
- PDB-1l2x: Atomic Resolution Crystal Structure of a Viral RNA Pseudoknot -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1l2x
TitleAtomic Resolution Crystal Structure of a Viral RNA Pseudoknot
ComponentsRNA pseudoknot
KeywordsRNA / Pseudoknot / frameshifting / atomic resolution / viral RNA / metal ions / flexibility
Function / homology: / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsEgli, M. / Minasov, G. / Su, L. / Rich, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Metal ions and flexibility in a viral RNA pseudoknot at atomic resolution.
Authors: Egli, M. / Minasov, G. / Su, L. / Rich, A.
History
DepositionFeb 25, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id / _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: RNA pseudoknot
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,49911
Polymers9,2451
Non-polymers25410
Water3,243180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.160, 30.160, 140.278
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-66-

HOH

21A-134-

HOH

31A-173-

HOH

-
Components

#1: RNA chain RNA pseudoknot


Mass: 9245.484 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: RNA SEQUENCE TAKEN FROM BEET WESTERN YELLOW VIRUS
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 1.99 Å3/Da / Density % sol: 38.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: potassium MOPS, spermidine, magnesium chloride, sec-butanol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1potassium MOPS11
2spermidine11
3MgCl211
4sec-butanol11
Crystal grow
*PLUS
Temperature: 25 ℃ / Details: Su, L., (1999) Nature Struct. Biol., 6, 285.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14 mg/mlRNA1drop
25 mM1dropMgCl2
35 %sec-butanol1drop
4100 mMpotassium MOPS1drop
52 mMspermidine1drop
618 %sec-butanol1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 12, 1998 / Details: mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→25 Å / Num. all: 21462 / Num. obs: 21462 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 29.8 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 21.4
Reflection shellResolution: 1.25→1.29 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 4.1 / Num. unique all: 2048 / % possible all: 98.4
Reflection
*PLUS

-
Processing

Software
NameClassification
AMoREphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 437D

437d


Resolution: 1.25→20 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
Stereochemistry target values: G. Parkinson et al., Acta Cryst. (1996) D52, 57-64
Details: Konnert-Hendrickson conjugate-gradient algorithm used in refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.207 2131 -RANDOM
Rwork0.142 ---
all-21348 --
obs-21348 99.1 %-
Displacement parametersBiso mean: 23.2 Å2
Baniso -1Baniso -2Baniso -3
1-19.29 Å29.64 Å20 Å2
2--19.29 Å20 Å2
3---3.44 Å2
Refinement stepCycle: LAST / Resolution: 1.25→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 709 10 200 919
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.005
X-RAY DIFFRACTIONs_angle_d1.3
LS refinement shellResolution: 1.25→1.29 Å
RfactorNum. reflection% reflection
Rwork0.243 --
Rfree-243 -
obs--88.5 %
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor obs: 0.142
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg1.3

+
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