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- PDB-5uyw: YfeA ancillary sites that co-load with site 2 -

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Basic information

Entry
Database: PDB / ID: 5uyw
TitleYfeA ancillary sites that co-load with site 2
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: 1.954 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)36,4417
Polymers36,0491
Non-polymers3926
Water3,387188
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)62.277, 66.358, 67.086
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.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 1.92 Å3/Da / Density % sol: 36.03 % / 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% w/v sodium azide, 10mM manganese chloride SOAKING: Fiber used to streak 1.5uL droplet of 10mM zinc chloride into ...Details: "30% PEG 4000, 20mM Bis-tris propane, 50mM sodium chloride, 0.05% w/v sodium azide, 10mM manganese chloride SOAKING: Fiber used to streak 1.5uL droplet of 10mM zinc chloride into crystallization drop. Mixture incubated 4-hrs prior to freezing."

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / 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: 1.95→50 Å / Num. obs: 20672 / % possible obs: 99.6 % / Redundancy: 4.8 % / Biso Wilson estimate: 27.528 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.036 / Net I/σ(I): 44.9
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.421 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 998 / CC1/2: 0.974 / Rpim(I) all: 0.207 / % possible all: 98.4

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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: 5uyg

5uyg


Resolution: 1.954→31.138 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.73
RfactorNum. reflection% reflection
Rfree0.2239 3742 9.67 %
Rwork0.1866 --
obs0.1903 20628 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.954→31.138 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2140 0 6 188 2334
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082192
X-RAY DIFFRACTIONf_angle_d0.9072985
X-RAY DIFFRACTIONf_dihedral_angle_d3.2831324
X-RAY DIFFRACTIONf_chiral_restr0.062335
X-RAY DIFFRACTIONf_plane_restr0.007385
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9539-1.97860.32421170.26281236X-RAY DIFFRACTION95
1.9786-2.00460.27611540.25141292X-RAY DIFFRACTION100
2.0046-2.03210.34191400.23781280X-RAY DIFFRACTION98
2.0321-2.06110.29741330.21471293X-RAY DIFFRACTION100
2.0611-2.09190.25881210.22091324X-RAY DIFFRACTION99
2.0919-2.12460.25421260.22451291X-RAY DIFFRACTION100
2.1246-2.15940.28091510.2151287X-RAY DIFFRACTION99
2.1594-2.19660.26031300.20961289X-RAY DIFFRACTION100
2.1966-2.23650.24781260.20831334X-RAY DIFFRACTION99
2.2365-2.27950.26651630.20031271X-RAY DIFFRACTION100
2.2795-2.32610.24851290.20131287X-RAY DIFFRACTION99
2.3261-2.37660.21561290.19671301X-RAY DIFFRACTION100
2.3766-2.43190.27281530.18921285X-RAY DIFFRACTION100
2.4319-2.49270.25851170.19611345X-RAY DIFFRACTION100
2.4927-2.560.24511440.19711292X-RAY DIFFRACTION100
2.56-2.63530.25291440.19841284X-RAY DIFFRACTION100
2.6353-2.72030.24251180.18051314X-RAY DIFFRACTION100
2.7203-2.81750.19741430.18071303X-RAY DIFFRACTION100
2.8175-2.93020.25351330.20291328X-RAY DIFFRACTION100
2.9302-3.06350.21561510.21631294X-RAY DIFFRACTION100
3.0635-3.22480.21981350.18171302X-RAY DIFFRACTION100
3.2248-3.42670.22091450.18621293X-RAY DIFFRACTION100
3.4267-3.69080.21471620.17851270X-RAY DIFFRACTION100
3.6908-4.06150.19381470.16891288X-RAY DIFFRACTION100
4.0615-4.64760.17531330.14671305X-RAY DIFFRACTION100
4.6476-5.84910.17971510.17041300X-RAY DIFFRACTION100
5.8491-31.14240.21081490.16751273X-RAY DIFFRACTION98

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