[English] 日本語
Yorodumi
- PDB-5xv9: Solution Structure of Cold Shock Protein from Colwellia psychrery... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xv9
TitleSolution Structure of Cold Shock Protein from Colwellia psychrerythraea
ComponentsCold-shock DNA-binding domain family protein
KeywordsRNA BINDING PROTEIN / Cold-shock protein / Psychrophile / NMR spectroscopy / solution structure
Function / homology
Function and homology information


DNA binding / cytoplasm
Similarity search - Function
Cold shock, CspA / Cold-shock (CSD) domain / Cold-shock (CSD) domain signature. / Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / Cold shock domain / Cold shock protein domain / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold ...Cold shock, CspA / Cold-shock (CSD) domain / Cold-shock (CSD) domain signature. / Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / Cold shock domain / Cold shock protein domain / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Cold-shock DNA-binding domain family protein
Similarity search - Component
Biological speciesColwellia psychrerythraea (bacteria)
MethodSOLUTION NMR / na
AuthorsLee, Y. / Kim, Y.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation of KoreaMSIP- 2016R1A2B2008543 Korea, Republic Of
Citation
Journal: Biochemistry / Year: 2018
Title: Tyr51: Key Determinant of the Low Thermostability of the Colwellia psychrerythraea Cold-Shock Protein.
Authors: Lee, Y. / Kwak, C. / Jeong, K.W. / Durai, P. / Ryu, K.S. / Kim, E.H. / Cheong, C. / Ahn, H.C. / Kim, H.J. / Kim, Y.
#1: Journal: Biochem. Biophys. Res. Commun. / Year: 2014
Title: Structure and flexibility of the thermophilic cold-shock protein of Thermus aquaticus
Authors: Jin, B. / Jeong, K.W. / Kim, Y.
#2: Journal: Biochemistry / Year: 2013
Title: Structural and dynamic features of cold-shock proteins of Listeria monocytogenes, a psychrophilic bacterium
Authors: Lee, J. / Jeong, K.W. / Jin, B. / Ryu, K.S. / Kim, E.H. / Ahn, J.H. / Kim, Y.
History
DepositionJun 27, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.id ..._citation.country / _citation.id / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
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 / _pdbx_nmr_spectrometer.model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cold-shock DNA-binding domain family protein


Theoretical massNumber of molelcules
Total (without water)7,2991
Polymers7,2991
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis, no assembly
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4820 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20all calculated structures submitted
RepresentativeModel #1lowest energy

-
Components

#1: Protein Cold-shock DNA-binding domain family protein


Mass: 7299.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Colwellia psychrerythraea (strain 34H / ATCC BAA-681) (bacteria)
Strain: 34H / ATCC BAA-681 / Gene: CPS_0718 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q488P6

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic52D 1H-15N HSQC
122isotropic52D 1H-13C HSQC
132isotropic53D HN(CA)CB
142isotropic53D CBCA(CO)NH
152isotropic53D HNCO
162isotropic53D C(CO)NH
172isotropic53D HBHA(CO)NH
182isotropic53D H(CCO)NH
192isotropic53D (H)CCH-TOCSY
1104isotropic52D 1H-1H TOCSY
1114isotropic52D 1H-1H NOESY
1121isotropic53D 1H-15N NOESY
1132isotropic53D 1H-13C NOESY aliphatic
1141isotropic52D 1H-15N HSQC-DSSE(IPAP)
1153anisotropic52D 1H-15N HSQC-DSSE(IPAP)

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent systemDetails
solution10.5 mM [U-99% 15N] Colwellia psychrerythraea Cold Shock Protein, 50 mM potassium phosphate, 100 mM potassium chloride, 0.1 mM EDTA, 2 mM DTT, 50 nM DSS, 0.5 mg/mL sodium azide, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution20.5 mM [U-99% 13C; U-99% 15N] Colwellia psychrerythraea Cold Shock Protein, 50 mM potassium phosphate, 100 mM potassium chloride, 0.1 mM EDTA, 2 mM DTT, 50 nM DSS, 0.5 mg/mL sodium azide, 90% H2O/10% D2O13C&15N_sample90% H2O/10% D2O
gel solution30.5 mM [U-99% 15N] Colwellia psychrerythraea Cold Shock Protein, 50 mM potassium phosphate, 100 mM potassium chloride, 0.1 mM EDTA, 2 mM DTT, 50 nM DSS, 0.5 mg/mL sodium azide, 90% H2O/10% D2O15N_sample_in_gel90% H2O/10% D2O15N-labeled protein soaked into 5% acrylamide gel(4.87% acrylamide, 0.13% bis-acrylamide)
solution40.5 mM Colwellia psychrerythraea Cold Shock Protein, 50 mM potassium phosphate, 100 mM potassium chloride, 0.1 mM EDTA, 2 mM DTT, 50 nM DSS, 0.5 mg/mL sodium azide, 90% H2O/10% D2ONon-label90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMColwellia psychrerythraea Cold Shock Protein[U-99% 15N]1
50 mMpotassium phosphatenatural abundance1
100 mMpotassium chloridenatural abundance1
0.1 mMEDTAnatural abundance1
2 mMDTTnatural abundance1
50 nMDSSnatural abundance1
0.5 mg/mLsodium azidenatural abundance1
0.5 mMColwellia psychrerythraea Cold Shock Protein[U-99% 13C; U-99% 15N]2
50 mMpotassium phosphatenatural abundance2
100 mMpotassium chloridenatural abundance2
0.1 mMEDTAnatural abundance2
2 mMDTTnatural abundance2
50 nMDSSnatural abundance2
0.5 mg/mLsodium azidenatural abundance2
0.5 mMColwellia psychrerythraea Cold Shock Protein[U-99% 15N]3
50 mMpotassium phosphatenatural abundance3
100 mMpotassium chloridenatural abundance3
0.1 mMEDTAnatural abundance3
2 mMDTTnatural abundance3
50 nMDSSnatural abundance3
0.5 mg/mLsodium azidenatural abundance3
0.5 mMColwellia psychrerythraea Cold Shock Proteinnatural abundance4
50 mMpotassium phosphatenatural abundance4
100 mMpotassium chloridenatural abundance4
0.1 mMEDTAnatural abundance4
2 mMDTTnatural abundance4
50 nMDSSnatural abundance4
0.5 mg/mLsodium azidenatural abundance4
Sample conditionsIonic strength: 100 mM / Label: standard / pH: 6.0 / Pressure: 1 atm / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

-
Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRFAM-SPARKYLee, Tonelli and Markleychemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
PONDEROSA-C/SLee, Cornilescu, Dashti, Eghbalnia, Tonelli, Westler, Butcher, Wildman-Henzler and Markleyrefinement
RefinementMethod: na / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / 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