[English] 日本語
Yorodumi
- PDB-2kfw: Solution structure of full-length SlyD from E.coli -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2kfw
TitleSolution structure of full-length SlyD from E.coli
ComponentsFKBP-type peptidyl-prolyl cis-trans isomerase slyD
KeywordsISOMERASE / Protein / SlyD / Cobalt / Copper / Cytoplasm / Metal-binding / Nickel / Rotamase / Zinc
Function / homology
Function and homology information


protein maturation by protein folding / cobalt ion binding / nickel cation binding / protein maturation / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / unfolded protein binding / response to heat / protein refolding / protein stabilization ...protein maturation by protein folding / cobalt ion binding / nickel cation binding / protein maturation / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / unfolded protein binding / response to heat / protein refolding / protein stabilization / copper ion binding / zinc ion binding / cytosol
Similarity search - Function
Thrombin, subunit H - #330 / : / Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / Thrombin, subunit H / Roll ...Thrombin, subunit H - #330 / : / Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / Thrombin, subunit H / Roll / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
FKBP-type peptidyl-prolyl cis-trans isomerase SlyD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsclosest to the average, model 1
AuthorsMartino, L. / He, Y. / Hands-Taylor, K.L. / Valentine, E.R. / Kelly, G. / Giancola, C. / Conte, M.R.
CitationJournal: Febs J. / Year: 2009
Title: The interaction of the Escherichia coli protein SlyD with nickel ions illuminates the mechanism of regulation of its peptidyl-prolyl isomerase activity.
Authors: Martino, L. / He, Y. / Hands-Taylor, K.L. / Valentine, E.R. / Kelly, G. / Giancola, C. / Conte, M.R.
History
DepositionFeb 28, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FKBP-type peptidyl-prolyl cis-trans isomerase slyD


Theoretical massNumber of molelcules
Total (without water)20,8831
Polymers20,8831
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

-
Components

#1: Protein FKBP-type peptidyl-prolyl cis-trans isomerase slyD / PPIase / Rotamase / Histidine-rich protein / WHP


Mass: 20882.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: slyD, b3349, JW3311 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: P0A9K9, peptidylprolyl isomerase

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCA
1413D HN(CO)CA
1513D HN(CA)CB
1613D CBCA(CO)NH
1713D (H)CCH-TOCSY
1813D HNCO
1913D 1H-15N NOESY
11013D 1H-13C NOESY
11113D HNHA
11213D HN(CO)CA

-
Sample preparation

DetailsContents: 20 mM TRIS, 100 mM potassium chloride, 1 mM DTT, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
20 mMTRIS-11
100 mMpotassium chloride-21
1 mMDTT-31
Sample conditionsIonic strength: 100 / pH: 7.25 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AvanceBrukerAVANCE6002
Varian INOVAVarianINOVA8003
Varian INOVAVarianINOVA6004

-
Processing

NMR software
NameDeveloperClassification
X-PLORBrungerstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOSCornilescu, Delaglio and Baxdata analysis
MOLMOLKoradi, Billeter and Wuthrichdata analysis
XEASYBartels et al.data analysis
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.peak picking
ProcheckNMRLaskowski and MacArthurdata analysis
VNMRVariancollection
TopSpinBruker Biospincollection
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
X-PLORBrungerrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
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