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- PDB-5uyg: YfeA with metal bound to site 2 - Zn wavelength -

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Basic information

Entry
Database: PDB / ID: 5uyg
TitleYfeA with metal bound to site 2 - Zn 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: 1.859 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 24, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)36,1803
Polymers36,0491
Non-polymers1312
Water4,504250
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)62.356, 66.036, 66.827
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 1.91 Å3/Da / Density % sol: 35.55 % / 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, 0.05% sodium azide, 10mM manganese chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.28281 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Nov 26, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28281 Å / Relative weight: 1
ReflectionResolution: 1.859→50 Å / Num. obs: 23851 / % possible obs: 99.8 % / Redundancy: 4.8 % / Biso Wilson estimate: 28.509 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.035 / Net I/σ(I): 46.6
Reflection shellResolution: 1.859→1.89 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 1183 / CC1/2: 0.903 / Rpim(I) all: 0.188 / % possible all: 99.9

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Processing

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

5uxs


Resolution: 1.859→46.972 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.44
RfactorNum. reflection% reflection
Rfree0.218 3772 8.43 %
Rwork0.1892 --
obs0.1916 23804 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.859→46.972 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2140 0 2 250 2392
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082192
X-RAY DIFFRACTIONf_angle_d0.8872985
X-RAY DIFFRACTIONf_dihedral_angle_d3.271324
X-RAY DIFFRACTIONf_chiral_restr0.059335
X-RAY DIFFRACTIONf_plane_restr0.007385
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8588-1.88230.29361830.24741495X-RAY DIFFRACTION99
1.8823-1.90710.3532980.25851543X-RAY DIFFRACTION100
1.9071-1.93320.33261220.24441533X-RAY DIFFRACTION100
1.9332-1.96080.25091640.25671515X-RAY DIFFRACTION100
1.9608-1.99010.29891330.24831506X-RAY DIFFRACTION100
1.9901-2.02120.26111530.21631523X-RAY DIFFRACTION100
2.0212-2.05430.25691420.22831516X-RAY DIFFRACTION100
2.0543-2.08980.27441480.21671525X-RAY DIFFRACTION100
2.0898-2.12780.2231480.20861500X-RAY DIFFRACTION100
2.1278-2.16870.22021220.21191555X-RAY DIFFRACTION100
2.1687-2.2130.25411550.19831499X-RAY DIFFRACTION100
2.213-2.26110.25191280.20781504X-RAY DIFFRACTION100
2.2611-2.31370.31151170.2021562X-RAY DIFFRACTION100
2.3137-2.37150.25531460.20531504X-RAY DIFFRACTION100
2.3715-2.43570.21781180.19611543X-RAY DIFFRACTION100
2.4357-2.50730.19951540.19431528X-RAY DIFFRACTION100
2.5073-2.58820.22841540.19261496X-RAY DIFFRACTION100
2.5882-2.68070.251280.19431554X-RAY DIFFRACTION100
2.6807-2.78810.18781480.18611492X-RAY DIFFRACTION100
2.7881-2.91490.22011320.2021528X-RAY DIFFRACTION100
2.9149-3.06860.24181320.22341534X-RAY DIFFRACTION100
3.0686-3.26080.24061390.18731521X-RAY DIFFRACTION100
3.2608-3.51250.17871280.19111546X-RAY DIFFRACTION100
3.5125-3.86580.21361410.16861511X-RAY DIFFRACTION100
3.8658-4.42480.1841600.15611512X-RAY DIFFRACTION100
4.4248-5.57340.18211680.15571486X-RAY DIFFRACTION100
5.5734-46.98660.18461150.16611501X-RAY DIFFRACTION97

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