[English] 日本語
Yorodumi
- PDB-2ghj: Crystal structure of folded and partially unfolded forms of Aquif... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ghj
TitleCrystal structure of folded and partially unfolded forms of Aquifex aeolicus ribosomal protein L20
Components50S ribosomal protein L20
KeywordsSTRUCTURAL PROTEIN / folding intermediate / ribosomal protein extension
Function / homology
Function and homology information


cytosolic large ribosomal subunit / rRNA binding / structural constituent of ribosome / translation
Similarity search - Function
Ribosomal protein L20, C-terminal domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1450 / c-terminal domain of poly(a) binding protein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Ribosomal protein L20 signature. / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Large ribosomal subunit protein bL20
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsTimsit, Y. / Allemand, F. / Chiaruttini, C. / Springer, M.
CitationJournal: Embo Rep. / Year: 2006
Title: Coexistence of two protein folding states in the crystal structure of ribosomal protein L20
Authors: Timsit, Y. / Allemand, F. / Chiaruttini, C. / Springer, M.
History
DepositionMar 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 50S ribosomal protein L20
B: 50S ribosomal protein L20
D: 50S ribosomal protein L20
E: 50S ribosomal protein L20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,29010
Polymers56,7134
Non-polymers5766
Water90150
1
A: 50S ribosomal protein L20
D: 50S ribosomal protein L20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7416
Polymers28,3572
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-67 kcal/mol
Surface area13700 Å2
MethodPISA
2
B: 50S ribosomal protein L20
E: 50S ribosomal protein L20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5494
Polymers28,3572
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-56 kcal/mol
Surface area12290 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10730 Å2
ΔGint-166 kcal/mol
Surface area22240 Å2
MethodPISA
4
B: 50S ribosomal protein L20
D: 50S ribosomal protein L20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6455
Polymers28,3572
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-62 kcal/mol
Surface area14660 Å2
MethodPISA
5
A: 50S ribosomal protein L20
E: 50S ribosomal protein L20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6455
Polymers28,3572
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-65 kcal/mol
Surface area14760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.914, 45.217, 67.060
Angle α, β, γ (deg.)104.06, 106.20, 97.76
Int Tables number1
Space group name H-MP1
DetailsThe asymetric unit consists of 2 dimers related by the same non crystallographic axis. One dimer (A,D) is formed by two folded monomers One dimer (B,E) is formed by two partially unfolded monomers

-
Components

#1: Protein
50S ribosomal protein L20


Mass: 14178.334 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: dimer A,D is formed by folded, dimer B,E by unfolded monomers
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: rplT / Production host: Escherichia coli (E. coli) / References: UniProt: O67086
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 43.65 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 50 mM Tris pH 7; 200 mM ammonium sulfate; 25 % PEG monomethyl ether, VAPOR DIFFUSION, HANGING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97961 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 24, 2001 / Details: mirrors
RadiationMonochromator: Sagittaly bent Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97961 Å / Relative weight: 1
ReflectionResolution: 2.53→30 Å / Num. all: 26849 / Num. obs: 21490 / % possible obs: 96.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 1.9 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 10.6

-
Processing

Software
NameClassification
MOSFLMdata reduction
CNSrefinement
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.9→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.292 1884 18.4 %random
Rwork0.22 ---
all0.22 10246 --
obs0.22 10246 --
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.745 Å2-2.643 Å2-11.009 Å2
2--1.677 Å2-10.359 Å2
3----2.422 Å2
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3238 0 30 50 3318

+
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