[English] 日本語
Yorodumi
- PDB-9hw9: Structural characterization of the type 3 fimbrial subunit MrkA f... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9hw9
TitleStructural characterization of the type 3 fimbrial subunit MrkA from Klebsiella pneumoniae by solution NMR spectroscopy
ComponentsFimbrial subunit type 3
KeywordsCELL ADHESION / Protein antigen / Klebsiella pneumoniae / Self-complemented MrkA monomer / Type 3 fimbriae / Solution NMR structure determination / biofilm formation
Function / homologyFimbrial-type adhesion domain / Fimbrial protein / : / Fimbrial-type adhesion domain superfamily / cell adhesion involved in single-species biofilm formation / Adhesion domain superfamily / pilus / Fimbrial subunit type 3
Function and homology information
Biological speciesKlebsiella pneumoniae (bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsMonaci, V. / Cantini, F.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Ministry of HealthPAN-HUB 2021-T4-AN-07-CUP B93C22000920001 Italy
Citation
Journal: Protein Sci. / Year: 2025
Title: Biological and structural characterization of the Type 3 fimbrial subunit MrkA from Klebsiella pneumoniae.
Authors: Monaci, V. / Oldrini, D. / Gasperini, G. / Banci, L. / Cantini, F. / Micoli, F.
#1: Journal: Biomol. NMR Assign / Year: 2024
Title: 1H, 13C and 15N assignment of self-complemented MrkA protein antigen from Klebsiella pneumoniae
Authors: Monaci, V. / Gasperini, G. / Banci, L. / Micoli, F. / Cantini, F.
History
DepositionJan 3, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fimbrial subunit type 3


Theoretical massNumber of molelcules
Total (without water)20,6391
Polymers20,6391
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200target function
RepresentativeModel #1target function

-
Components

#1: Protein Fimbrial subunit type 3


Mass: 20639.418 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The first 20 residues in the mature protein after leader sequence cleavage (donor strand, DS) present at the N-terminus is moved at the C-terminus and a hexaglycine linker is added. A 10 ...Details: The first 20 residues in the mature protein after leader sequence cleavage (donor strand, DS) present at the N-terminus is moved at the C-terminus and a hexaglycine linker is added. A 10 histidine tag is also added at N-terminus.
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: mrkA / Plasmid: pET29b / Details (production host): Kanamycin resistance / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P12267
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 1H-13C NOESY
121isotropic13D 1H-15N NOESY
131isotropic13D (H)CCH-TOCSY
141isotropic13D HNCA
151isotropic13D HNCO
161isotropic13D HN(CA)CO
171isotropic13D CBCA(CO)NH
181isotropic12D 1H-13C HSQC
191isotropic12D 1H-15N HSQC

-
Sample preparation

DetailsType: solution
Contents: 400 uM [U-99% 13C; U-99% 15N] 15N_13C_MrkA monomer, 50 mM sodium phosphate pH 7.0, 100 mM sodium chloride, 90% H2O/10% D2O
Details: 50 mM sodium phosphate, 100 mM NaCl pH 7.0 / Label: 15N_13C_MrkA monomer / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
400 uM15N_13C_MrkA monomer[U-99% 13C; U-99% 15N]1
50 mMsodium phosphate pH 7.0natural abundance1
100 mMsodium chloridenatural abundance1
Sample conditionsDetails: ionic strength: 150 mM; pH: 7; pressure: 1 atm; temperature: 298 K.
Ionic strength: 150 mM / Label: 15N_13C_MrkA monomer / pH: 7 / Pressure: 1 atm / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker Bruker Avance 950 / Manufacturer: Bruker / Model: Bruker Avance 950 / Field strength: 950 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert, Mumenthaler and Wuthrichstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
TopSpin4Bruker Biospincollection
RefinementMethod: molecular dynamics / Software ordinal: 2
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / 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://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