[English] 日本語
Yorodumi
- PDB-5t1n: Solution-state NMR structural ensemble of NPr (1-85) refined with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5t1n
TitleSolution-state NMR structural ensemble of NPr (1-85) refined with RDCs and PCS
ComponentsPhosphocarrier protein NPr
KeywordsTRANSFERASE / PTSNtr / phosphotransfer / HPr-like / bacterial
Function / homology
Function and homology information


transferase activity, transferring phosphorus-containing groups / phosphoenolpyruvate-dependent sugar phosphotransferase system / : / cytoplasm
Similarity search - Function
Phosphotransferase system, HPr histidine phosphorylation site / PTS HPR domain histidine phosphorylation site signature. / Phosphotransferase system, HPr serine phosphorylation site / PTS HPR domain serine phosphorylation site signature. / HPr-like / Histidine-containing Protein; Chain: A; / Phosphocarrier protein HPr-like / HPr-like superfamily / PTS HPr component phosphorylation site / PTS HPR domain profile. ...Phosphotransferase system, HPr histidine phosphorylation site / PTS HPR domain histidine phosphorylation site signature. / Phosphotransferase system, HPr serine phosphorylation site / PTS HPR domain serine phosphorylation site signature. / HPr-like / Histidine-containing Protein; Chain: A; / Phosphocarrier protein HPr-like / HPr-like superfamily / PTS HPr component phosphorylation site / PTS HPR domain profile. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphocarrier protein NPr / Phosphocarrier protein NPr
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsStrickland, M. / Wang, G. / Peterkofsky, A. / Tjandra, N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI) United States
CitationJournal: Structure / Year: 2016
Title: Structure of the NPr:EIN(Ntr) Complex: Mechanism for Specificity in Paralogous Phosphotransferase Systems.
Authors: Strickland, M. / Stanley, A.M. / Wang, G. / Botos, I. / Schwieters, C.D. / Buchanan, S.K. / Peterkofsky, A. / Tjandra, N.
History
DepositionAug 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2016Group: Database references
Revision 1.2Dec 21, 2016Group: Database references
Revision 1.3Jul 26, 2017Group: Author supporting evidence / Database references / Structure summary
Category: entity / pdbx_audit_support / pdbx_database_related
Item: _entity.pdbx_number_of_molecules / _pdbx_audit_support.funding_organization
Revision 1.4Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Dec 4, 2019Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.6May 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: Phosphocarrier protein NPr


Theoretical massNumber of molelcules
Total (without water)9,2551
Polymers9,2551
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy
DetailsMonomer according to Gel filtration

-
Components

#1: Protein Phosphocarrier protein NPr / Nitrogen-related HPr


Mass: 9254.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: ptsO, Z4569, ECs4085 / Plasmid: pETDuet1 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566
References: UniProt: P0A9N2, UniProt: P0A9N0*PLUS, Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic33D 1H-15N NOESY
121isotropic33D 1H-13C NOESY
131isotropic34D HNHC NOESY
143isotropic13D HN(CA)CB
2153isotropic12D IPAP
2162anisotropic12D IPAP
2173isotropic13D HN(CA)CB
2204isotropic22D 1H-15N HSQC
2185anisotropic22D 1H-15N HSQC

-
Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution11 mM [U-13C; U-15N] NPr, 25 mM Tris, 93% H2O/7% D2OUsed for NOE and hydrogen bond restraints.NPr_Wang93% H2O/7% D2O
filamentous virus20.6 mM [U-13C; U-15N; U-2H] NPr, 10 mM TRIS, 100 mM sodium chloride, 0.5 mM EDTA, 93% H2O/7% D2OPf1 filamentous phage was used to induce partial alignment.NPr_rdc93% H2O/7% D2O
solution30.6 mM [U-13C; U-15N; U-2H] NPr, 10 mM TRIS, 100 mM sodium chloride, 0.5 mM EDTA, 93% H2O/7% D2OUsed for assignment and for RDC isotropic sample.NPr_assign93% H2O/7% D2O
solution40.6 mM [U-15N; U-2H] NPr, 10 mM TRIS, 100 mM sodium chloride, 0.5 mM EDTA, 93% H2O/7% D2OThe sample was mutated (E45C) to accommodate a Lu-M8-SPy tag, which was the control sample for pseudocontact shifts.NPr_PCSiso93% H2O/7% D2O
solution50.6 mM [U-15N; U-2H] NPr, 10 mM TRIS, 100 mM sodium chloride, 0.5 mM EDTA, 93% H2O/7% D2OThe sample was mutated (E45C) to accommodate a Yb-M8-SPy tag, which was used to induce pseudocontact shifts.NPr_PCSaniso93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMNPr[U-13C; U-15N]1
25 mMTrisnatural abundance1
0.6 mMNPr[U-13C; U-15N; U-2H]2
10 mMTRISnatural abundance2
100 mMsodium chloridenatural abundance2
0.5 mMEDTAnatural abundance2
0.6 mMNPr[U-13C; U-15N; U-2H]3
10 mMTRISnatural abundance3
100 mMsodium chloridenatural abundance3
0.5 mMEDTAnatural abundance3
0.6 mMNPr[U-15N; U-2H]4
10 mMTRISnatural abundance4
100 mMsodium chloridenatural abundance4
0.5 mMEDTAnatural abundance4
0.6 mMNPr[U-15N; U-2H]5
10 mMTRISnatural abundance5
100 mMsodium chloridenatural abundance5
0.5 mMEDTAnatural abundance5
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
125 mMconditions_17 1 atm308 K
2108 mMconditions_27.5 1 atm300 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCEBrukerAVANCE6001Cryoprobe
Bruker AVANCEBrukerAVANCE8002Cryoprobe
Varian INOVAVarianINOVA6003

-
Processing

NMR software
NameVersionDeveloperClassification
Analysis2.4.2CCPNchemical shift assignment
PIPPGarrettchemical shift assignment
PIPPGarrettpeak picking
Analysis2.4.2CCPNpeak picking
VNMRVariancollection
TopSpin3Bruker Biospincollection
NMRPipe8.2Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
X-PLOR NIH2.37.7Schwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIH2.37.7Schwieters, Kuszewski, Tjandra and Clorerefinement
TALOS-N4.12Cornilescu, Delaglio and Baxdata analysis
Gaussian9Gaussian, Inc.geometry optimization
RefinementMethod: torsion angle dynamics / Software ordinal: 8
Details: Structure was refined using PDB ID 5T17 as a starting structure.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / 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://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