[English] 日本語
Yorodumi
- PDB-5aym: Crystal structure of a bacterial homologue of iron transporter fe... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5aym
TitleCrystal structure of a bacterial homologue of iron transporter ferroportin in outward-facing state with soaked iron
ComponentsSolute carrier family 39 (Iron-regulated transporter)
KeywordsTRANSPORT PROTEIN / alpha helical
Function / homologyFerroportin-1 / Ferroportin1 (FPN1) / iron ion transmembrane transporter activity / MFS transporter superfamily / metal ion binding / plasma membrane / : / Ferreportin
Function and homology information
Biological speciesBdellovibrio bacteriovorus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsTaniguchi, R. / Kato, H.E. / Font, J. / Deshpande, C.N. / Ishitani, R. / Jormakka, M. / Nureki, O.
CitationJournal: Nat Commun / Year: 2015
Title: Outward- and inward-facing structures of a putative bacterial transition-metal transporter with homology to ferroportin
Authors: Taniguchi, R. / Kato, H.E. / Font, J. / Deshpande, C.N. / Wada, M. / Ito, K. / Ishitani, R. / Jormakka, M. / Nureki, O.
History
DepositionAug 25, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 20, 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: Solute carrier family 39 (Iron-regulated transporter)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6572
Polymers48,6011
Non-polymers561
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area17610 Å2
Unit cell
Length a, b, c (Å)57.080, 86.170, 96.710
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Solute carrier family 39 (Iron-regulated transporter) / membrane transporter


Mass: 48600.785 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bdellovibrio bacteriovorus (bacteria) / Strain: ATCC 15356 / DSM 50701 / NCIB 9529 / HD100 / Gene: slc39, Bd2019 / Plasmid: pET variant / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: Q6MLJ0
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.73 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 7.5
Details: 100 mM Tris, pH 7.5, 50-200 mM K-formate, 50-100 mM (NH4)2HPO4, and 26-32% PEG550MME, 5 mM FeSO4 soaked

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1.45 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45 Å / Relative weight: 1
ReflectionResolution: 3→49.2 Å / Num. obs: 18454 / % possible obs: 100 % / Redundancy: 7.5 % / Net I/σ(I): 10.4
Reflection shellRejects: 0

-
Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
PHASERphasing
RefinementResolution: 3→49.157 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.86 / Stereochemistry target values: ML
Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2689 1839 9.97 %
Rwork0.2237 16615 -
obs0.2283 18454 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.37 Å2 / Biso mean: 26.7089 Å2 / Biso min: 7.95 Å2
Refinement stepCycle: final / Resolution: 3→49.157 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3014 0 1 0 3015
Biso mean--26.05 --
Num. residues----398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023090
X-RAY DIFFRACTIONf_angle_d0.6044217
X-RAY DIFFRACTIONf_chiral_restr0.019508
X-RAY DIFFRACTIONf_plane_restr0.002511
X-RAY DIFFRACTIONf_dihedral_angle_d10.4721034
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.0001-3.08120.30331390.247712971436
3.0812-3.17190.25841420.238212891431
3.1719-3.27420.30291340.22312481382
3.2742-3.39120.2451430.224313071450
3.3912-3.5270.28241400.205212671407
3.527-3.68740.2291440.19512791423
3.6874-3.88180.24511420.214612751417
3.8818-4.12490.23371460.225312721418
4.1249-4.44320.35631410.233812791420
4.4432-4.88990.27241420.22112791421
4.8899-5.59670.30721350.256112771412
5.5967-7.04790.3061480.25112741422
7.0479-49.16310.21011430.195812721415

+
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