[English] 日本語
Yorodumi
- PDB-2k4x: Solution structure of 30S ribosomal protein S27A from Thermoplasm... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2k4x
TitleSolution structure of 30S ribosomal protein S27A from Thermoplasma acidophilum
Components30S ribosomal protein S27ae
KeywordsRIBOSOMAL PROTEIN / 30S ribosomal protein S27A / Metal-binding / Ribonucleoprotein / Zinc-finger / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Ontario Centre for Structural Proteomics / OCSP
Function / homology
Function and homology information


ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / zinc ion binding
Similarity search - Function
N-terminal domain of TfIIb - #180 / Ribosomal protein S27ae / N-terminal domain of TfIIb / Other non-globular / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Special / Zinc-binding ribosomal protein
Similarity search - Domain/homology
Small ribosomal subunit protein eS31
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
MethodSOLUTION NMR / simulated annealing
AuthorsWu, B. / Yee, A. / Fares, C. / Lemak, A. / Semest, A. / Arrowsmith, C. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG) / Ontario Centre for Structural Proteomics (OCSP)
Citation
Journal: To be Published
Title: Solution structure of 30S ribosomal protein S27A from Thermoplasma acidophilum/Northeast Structural Genomics Consortium Target TaT88/Ontario Center for Structural Proteomics target ta1093
Authors: Wu, B. / Yee, A. / Fares, C. / Lemak, A. / Semest, A. / Arrowsmith, C.
#1: Journal: J.Biomol.Nmr / Year: 2011
Title: A novel strategy for NMR resonance assignment and protein structure determination.
Authors: Lemak, A. / Gutmanas, A. / Chitayat, S. / Karra, M. / Fares, C. / Sunnerhagen, M. / Arrowsmith, C.H.
History
DepositionJun 20, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 23, 2012Group: Database references
Revision 1.3Feb 19, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4Jun 14, 2023Group: Database references / Derived calculations / Other / Category: database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 30S ribosomal protein S27ae
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,4632
Polymers6,3981
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein 30S ribosomal protein S27ae


Mass: 6397.507 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Species: acidophilum / Gene: rps27ae, Ta1093 / Plasmid: p11 / Species (production host): coli / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HJ78
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCO
1213D CBCA(CO)NH
1313D HN(CA)CB
1413D HN(CO)CA
1513D HNCA
1613D C(CO)NH
1713D H(CCO)NH
1813D HBHA(CO)NH
1913D (H)CCH-TOCSY
11013D CCH-TOCSY
11113D 1H-15N NOESY
11213D 1H-13C NOESY
11323D 1H-13C NOESY
11413D 1H-13C NOESY aromatic

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-100% 13C; U-100% 15N] 30S ribosomal protein S27A, 10 mM [U-100% 2H] TRIS, 300 mM sodium chloride, 10 uM ZnSO4, 10 mM [U-100% 2H] DTT, 0.01 % sodium azide, 10 mM benzamidine, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-100% 13C; U-100% 15N] 30S ribosomal protein S27A, 10 mM [U-100% 2H] TRIS, 300 mM sodium chloride, 10 uM ZnSO4, 10 mM [U-100% 2H] DTT, 0.01 % sodium azide, 10 mM benzamidine, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mM30S ribosomal protein S27A[U-100% 13C; U-100% 15N]1
10 mMTRIS[U-100% 2H]1
300 mMsodium chloride1
10 uMZnSO41
10 mMDTT[U-100% 2H]1
0.01 %sodium azide1
10 mMbenzamidine1
0.5 mM30S ribosomal protein S27A[U-100% 13C; U-100% 15N]2
10 mMTRIS[U-100% 2H]2
300 mMsodium chloride2
10 uMZnSO42
10 mMDTT[U-100% 2H]2
0.01 %sodium azide2
10 mMbenzamidine2
Sample conditionsIonic strength: 300 / pH: 7 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE8002

-
Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3.95Goddarddata analysis
Sparky3.95Goddardpeak picking
AutoAssignZimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CNS1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
AutoStructureHuang, Tejero, Powers and Montelionenmr structure quality assessment
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

+
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