[English] 日本語
Yorodumi
- PDB-6xry: Intrinsically disordered bacterial polar organizing protein Z, Po... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6xry
TitleIntrinsically disordered bacterial polar organizing protein Z, PopZ, interacts with protein binding partners through an N-terminal Molecular Recognition Feature
ComponentsPolar organizing protein Z
KeywordsPROTEIN BINDING / Molecular Recognition Feature / MoRF / hub protein
Function / homologyProtein of unknown function DUF2497 / Protein of unknown function (DUF2497) / establishment of protein localization / identical protein binding / PopZ
Function and homology information
Biological speciesCaulobacter vibrioides (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsNordyke, C.T. / Ahmed, Y.M. / Puterbaugh, R.Z. / Bowman, G.R. / Varga, K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM118792-01 United States
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Intrinsically Disordered Bacterial Polar Organizing Protein Z, PopZ, Interacts with Protein Binding Partners Through an N-terminal Molecular Recognition Feature.
Authors: Nordyke, C.T. / Ahmed, Y.M. / Puterbaugh, R.Z. / Bowman, G.R. / Varga, K.
History
DepositionJul 14, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3May 15, 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: Polar organizing protein Z


Theoretical massNumber of molelcules
Total (without water)14,9881
Polymers14,9881
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1medoid

-
Components

#1: Protein Polar organizing protein Z / PopZ


Mass: 14988.290 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter vibrioides (strain ATCC 19089 / CB15) (bacteria)
Strain: ATCC 19089 / CB15 / Gene: popZ, CC_1319
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9A8N4

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D HNCO
131isotropic13D HN(CA)CO
141isotropic13D HNCA
151isotropic13D HN(CO)CA
161isotropic13D HN(CA)CB
171isotropic13D CBCA(CO)NH
181isotropic13D C(CO)NH
191isotropic13D HBHA(CO)NH
1101isotropic13D HBHANH
1111isotropic13D H(CCO)NH
1121isotropic13D 1H-15N NOESY
1131isotropic13D 1H-13C NOESY aliphatic
2142anisotropic12D 1H-15N HSQC
3153anisotropic12D 1H-15N HSQC
4164isotropic12D 1H-15N HSQC

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent systemDetails
solution1913 uM [U-99% 13C; U-99% 15N] Polar organizing protein Z, 95% H2O/5% D2O15N_13C_sample195% H2O/5% D2O
gel solid2142 uM [U-99% 15N] Polar organizing protein Z, 5.4% acrylamide gel with 5.4 mm outer diameter (OD),95% H2O/5% D2O15N_5.4mm_RDC_sample295% H2O/5% D2OPopZ sample is in a 5.4% acrylamide gel with 5.4 mm outer diameter (OD) axially stretched to 4.2 mm OD.
gel solid3142 uM [U-99% 15N] Polar organizing protein Z, 5.4% acrylamide gel with 6.0 mm outer diameter, 95% H2O/5% D2O15N_6.0mm_RDC_sample395% H2O/5% D2OPopZ sample is in a 5.4% acrylamide gel with 6.0 mm outer diameter (OD) axially stretched to 4.2 mm OD.
solution4142 uM [U-99% 15N] Polar organizing protein Z, 95% H2O/5% D2O15N_no_gel_RDC_sample495% H2O/5% D2OPopZ sample is in identical conditions as RDC gel samples but not in the presence of a gel.
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
913 uMPolar organizing protein Z[U-99% 13C; U-99% 15N]1
142 uMPolar organizing protein Z[U-99% 15N]2
142 uMPolar organizing protein Z[U-99% 15N]3
142 uMPolar organizing protein Z[U-99% 15N]4
5.4 %acrylamide gel with 5.4 mm outer diameternatural abundance2
5.4 %acrylamide gel with 6.0 mm outer diameternatural abundance3
Sample conditions
Conditions-IDDetailsIonic strengthLabelpHPressure (kPa)Temperature (K)
150 mM citrate-phosphate 20 mM NaCl 4 mM sodium azide 0.200 mM DSS 5% v/v deuterium oxide pH 5.5 298 K20 mM NaCl Not definedConditions_15.51.0 atm298 K
250 mM citrate-phosphate 20 mM NaCl 4 mM sodium azide 0.200 mM DSS 5% v/v deuterium oxide pH 5.5 298 K PopZ sample is in a 5.4% acrylamide gel with 5.4 mm outer diameter (OD) axially stretched to 4.2 mm OD.20 mM NaCl Not definedConditions_5.4mm_RDC_25.51 atm298 K
350 mM citrate-phosphate 20 mM NaCl 4 mM sodium azide 0.200 mM DSS 5% v/v deuterium oxide pH 5.5 298 K PopZ sample is in a 5.4% acrylamide gel with 6.0 mm outer diameter (OD) axially stretched to 4.2 mm OD.20 mM NaCl Not definedConditions_6.0mm_RDC_35.51 atm298 K
450 mM citrate-phosphate 20 mM NaCl 4 mM sodium azide 0.200 mM DSS 5% v/v deuterium oxide pH 5.5 298 K20 mM NaCl Not definedConditions_no_gel_RDC_45.51 atm298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III8001
Bruker AVANCE IIIBrukerAVANCE III7002

-
Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
I-PINELee, Bahrami, Dashti, Eghbalnia, Tonelli, Westler and Markleychemical shift assignment
NMRFAM-SPARKY1.41Lee, Tonelli, and Markleychemical shift assignment
PONDEROSA-C/SLee, Stark, and Markleystructure calculation
PONDEROSA-C/SLee, Stark, and Markleyrefinement
NMRFAM-SPARKYLee, Tonelli, and Markleypeak picking
PONDEROSA-C/SLee, Stark, and Markleydata analysis
RefinementMethod: simulated annealing / Software ordinal: 6
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: target function / 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