[English] 日本語
Yorodumi
- PDB-9ex3: Ferric-mycobactin receptor (FemA) in complex with dihydroaerugino... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9ex3
TitleFerric-mycobactin receptor (FemA) in complex with dihydroaeruginoic acid
ComponentsFerric-mycobactin receptor, FemA
KeywordsMEMBRANE PROTEIN / TonB-dependent transporter
Function / homology
Function and homology information


siderophore transport / siderophore uptake transmembrane transporter activity / sigma factor activity / cell outer membrane / regulation of iron ion transport / signaling receptor activity / cytosol
Similarity search - Function
Secretin and TonB N terminus short domain / Secretin/TonB, short N-terminal domain / Secretin and TonB N terminus short domain / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / TonB-dependent siderophore receptor / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / TonB-dependent receptor (TBDR) proteins profile. / Vitamin B12 transporter BtuB-like ...Secretin and TonB N terminus short domain / Secretin/TonB, short N-terminal domain / Secretin and TonB N terminus short domain / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / TonB-dependent siderophore receptor / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / TonB-dependent receptor (TBDR) proteins profile. / Vitamin B12 transporter BtuB-like / TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain / TonB-dependent Receptor Plug Domain / TonB-dependent receptor-like, beta-barrel domain superfamily
Similarity search - Domain/homology
: / Chem-J9F / : / Ferric-mycobactin receptor, FemA
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsMoynie, L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research Council United Kingdom
CitationJournal: Acs Chem.Biol. / Year: 2025
Title: Structure of the Outer Membrane Transporter FemA and Its Role in the Uptake of Ferric Dihydro-Aeruginoic Acid and Ferric Aeruginoic Acid in Pseudomonas aeruginosa .
Authors: Will, V. / Moynie, L. / Si Ahmed Charrier, E. / Le Bas, A. / Kuhn, L. / Volck, F. / Chicher, J. / Aksoy, H. / Madec, M. / Antheaume, C. / Mislin, G.L.A. / Schalk, I.J.
History
DepositionApr 5, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 2, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Ferric-mycobactin receptor, FemA
A: Ferric-mycobactin receptor, FemA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,73733
Polymers168,0972
Non-polymers3,64031
Water10,917606
1
B: Ferric-mycobactin receptor, FemA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,69915
Polymers84,0481
Non-polymers1,65114
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Ferric-mycobactin receptor, FemA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,03818
Polymers84,0481
Non-polymers1,99017
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.939, 86.308, 88.287
Angle α, β, γ (deg.)90.011, 61.634, 66.328
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

-
Components

-
Protein , 1 types, 2 molecules BA

#1: Protein Ferric-mycobactin receptor, FemA


Mass: 84048.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: femA, PA1910 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I2J4

-
Non-polymers , 6 types, 637 molecules

#2: Chemical
ChemComp-J9F / (4S)-2-(2-hydroxyphenyl)-4,5-dihydro-1,3-thiazole-4-carboxylic acid


Mass: 223.248 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H9NO3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#5: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 606 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.01 Å3/Da / Density % sol: 59.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: Mes, magnesium acetate, Peg 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.99992 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99992 Å / Relative weight: 1
ReflectionResolution: 2.15→71.63 Å / Num. obs: 103043 / % possible obs: 96.1 % / Redundancy: 3.5 % / Biso Wilson estimate: 25.67 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.142 / Net I/σ(I): 10.9
Reflection shellResolution: 2.15→2.18 Å / Rmerge(I) obs: 0.782 / Num. unique obs: 3006 / CC1/2: 0.707

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→44.07 Å / SU ML: 0.2699 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 31.1862 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2637 1950 1.9 %
Rwork0.2289 100770 -
obs0.2296 102720 95.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.59 Å2
Refinement stepCycle: LAST / Resolution: 2.15→44.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10282 0 194 606 11082
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008510694
X-RAY DIFFRACTIONf_angle_d0.942214479
X-RAY DIFFRACTIONf_chiral_restr0.05841560
X-RAY DIFFRACTIONf_plane_restr0.00561933
X-RAY DIFFRACTIONf_dihedral_angle_d7.72918668
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.20.33661100.27995181X-RAY DIFFRACTION68.49
2.2-2.260.33831390.26367244X-RAY DIFFRACTION96.81
2.26-2.330.29141410.25567298X-RAY DIFFRACTION96.79
2.33-2.40.29561450.24937297X-RAY DIFFRACTION97.17
2.4-2.490.27391190.24337310X-RAY DIFFRACTION97.29
2.49-2.590.29411150.24217342X-RAY DIFFRACTION97.44
2.59-2.70.28491490.23297349X-RAY DIFFRACTION97.58
2.7-2.850.29561440.23617348X-RAY DIFFRACTION97.69
2.85-3.030.26971290.2377341X-RAY DIFFRACTION97.89
3.03-3.260.25591480.23187384X-RAY DIFFRACTION98.15
3.26-3.590.25931370.22797386X-RAY DIFFRACTION98.49
3.59-4.110.24571510.21927419X-RAY DIFFRACTION98.76
4.11-5.170.23431530.20097444X-RAY DIFFRACTION99.07
5.17-44.070.23861700.21867427X-RAY DIFFRACTION99.26

+
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