[English] 日本語
Yorodumi
- PDB-5uyb: YfeA from M9 minimal media supplemented with manganese - Fe wavelength -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5uyb
TitleYfeA from M9 minimal media supplemented with manganese - Fe wavelength
ComponentsPeriplasmic chelated iron-binding protein YfeA
KeywordsMETAL TRANSPORT / polyspecific / transition metal / transport
Function / homology
Function and homology information


cellular response to iron ion / iron ion transport / periplasmic space / cell adhesion / metal ion binding
Similarity search - Function
Adhesin B / Adhesion lipoprotein / : / Periplasmic solute binding protein, ZnuA-like / Zinc-uptake complex component A periplasmic / Nitrogenase molybdenum iron protein domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Iron-binding protein YfeA
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsRadka, C.D. / DeLucas, L.J. / Aller, S.G.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2017
Title: Crystal structure of Yersinia pestis virulence factor YfeA reveals two polyspecific metal-binding sites.
Authors: Radka, C.D. / DeLucas, L.J. / Wilson, L.S. / Lawrenz, M.B. / Perry, R.D. / Aller, S.G.
History
DepositionFeb 23, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 9, 2017Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Periplasmic chelated iron-binding protein YfeA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1052
Polymers36,0491
Non-polymers561
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.746, 52.186, 112.744
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Periplasmic chelated iron-binding protein YfeA


Mass: 36048.809 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: yfeA, YPO2439, y1897, YP_2227 / Production host: Escherichia coli (E. coli) / References: UniProt: Q56952
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.7 Å3/Da / Density % sol: 27.79 % / Description: tetragonal prism
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 6.3
Details: 30% PEG 4000, 20mM Bis-tris propane, 50mM sodium chloride, 0.005% w/v sodium azide

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.74013 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jan 10, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.74013 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 18617 / % possible obs: 99.7 % / Redundancy: 7.6 % / Biso Wilson estimate: 22.293 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.035 / Net I/σ(I): 52.7
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 5.2 / Num. unique obs: 921 / CC1/2: 0.941 / Rpim(I) all: 0.158 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000v712data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5uya

5uya


Resolution: 1.95→39.149 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.48
RfactorNum. reflection% reflection
Rfree0.2017 3457 10.01 %
Rwork0.1651 --
obs0.1688 21444 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.95→39.149 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2153 0 1 230 2384
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062205
X-RAY DIFFRACTIONf_angle_d0.7643002
X-RAY DIFFRACTIONf_dihedral_angle_d3.0071331
X-RAY DIFFRACTIONf_chiral_restr0.057336
X-RAY DIFFRACTIONf_plane_restr0.006388
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9503-1.9770.30771370.23261242X-RAY DIFFRACTION97
1.977-2.00520.27531380.20871220X-RAY DIFFRACTION97
2.0052-2.03520.24891290.17831212X-RAY DIFFRACTION100
2.0352-2.0670.21571410.18621247X-RAY DIFFRACTION99
2.067-2.10090.22031380.18211246X-RAY DIFFRACTION98
2.1009-2.13710.19031380.16431218X-RAY DIFFRACTION100
2.1371-2.17590.21911360.18381249X-RAY DIFFRACTION98
2.1759-2.21780.20491400.17121265X-RAY DIFFRACTION100
2.2178-2.2630.21871340.17271224X-RAY DIFFRACTION100
2.263-2.31220.22061390.16761250X-RAY DIFFRACTION99
2.3122-2.3660.17881390.17221235X-RAY DIFFRACTION100
2.366-2.42520.20821390.16311236X-RAY DIFFRACTION100
2.4252-2.49080.23391380.16931256X-RAY DIFFRACTION100
2.4908-2.5640.24171400.17181256X-RAY DIFFRACTION100
2.564-2.64680.23291340.17371244X-RAY DIFFRACTION100
2.6468-2.74130.22571430.16331266X-RAY DIFFRACTION100
2.7413-2.85110.19141380.17051210X-RAY DIFFRACTION100
2.8511-2.98080.24041430.17781261X-RAY DIFFRACTION100
2.9808-3.13790.20061410.1751232X-RAY DIFFRACTION100
3.1379-3.33440.22681390.17331268X-RAY DIFFRACTION100
3.3344-3.59170.21340.15691237X-RAY DIFFRACTION100
3.5917-3.95280.18631410.15151259X-RAY DIFFRACTION100
3.9528-4.52410.15491420.141246X-RAY DIFFRACTION100
4.5241-5.6970.16341390.14741253X-RAY DIFFRACTION100
5.697-39.15640.1621370.15531247X-RAY DIFFRACTION100

+
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