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- PDB-5uy5: YfeA from M9 minimal media supplemented with iron - Mn wavelength -

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Basic information

Entry
Database: PDB / ID: 5uy5
TitleYfeA from M9 minimal media supplemented with iron - Mn 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: 2.144 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

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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)36,1042
Polymers36,0491
Non-polymers551
Water3,243180
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)61.968, 66.489, 67.208
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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 35.95 % / 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.89174 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: 1.89174 Å / Relative weight: 1
ReflectionResolution: 2.144→50 Å / Num. obs: 15410 / % possible obs: 97.5 % / Redundancy: 7.8 % / Biso Wilson estimate: 33.109 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.025 / Net I/σ(I): 67.4
Reflection shellResolution: 2.144→2.19 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 14 / Num. unique obs: 654 / CC1/2: 0.954 / Rpim(I) all: 0.099 / % possible all: 85.4

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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: 5uy0

5uy0


Resolution: 2.144→37.582 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.1
RfactorNum. reflection% reflection
Rfree0.204 2891 10.05 %
Rwork0.1634 --
obs0.1675 15376 97.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.144→37.582 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2133 0 1 180 2314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082185
X-RAY DIFFRACTIONf_angle_d0.8322975
X-RAY DIFFRACTIONf_dihedral_angle_d3.4271320
X-RAY DIFFRACTIONf_chiral_restr0.057333
X-RAY DIFFRACTIONf_plane_restr0.007384
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1436-2.17870.23831300.18191034X-RAY DIFFRACTION83
2.1787-2.21630.21861370.18211234X-RAY DIFFRACTION95
2.2163-2.25660.2121300.1851193X-RAY DIFFRACTION97
2.2566-2.29990.24981400.17981228X-RAY DIFFRACTION96
2.2999-2.34690.19891330.17471224X-RAY DIFFRACTION98
2.3469-2.39790.27021390.17031220X-RAY DIFFRACTION96
2.3979-2.45370.22611190.1711255X-RAY DIFFRACTION99
2.4537-2.5150.2411150.16711250X-RAY DIFFRACTION97
2.515-2.5830.22981450.17061209X-RAY DIFFRACTION98
2.583-2.6590.22591450.16521246X-RAY DIFFRACTION99
2.659-2.74480.20831450.17131231X-RAY DIFFRACTION98
2.7448-2.84290.21831500.17211243X-RAY DIFFRACTION99
2.8429-2.95670.25521220.19621257X-RAY DIFFRACTION99
2.9567-3.09120.25181560.19071226X-RAY DIFFRACTION99
3.0912-3.2540.20951310.17751283X-RAY DIFFRACTION99
3.254-3.45780.24451350.17091247X-RAY DIFFRACTION100
3.4578-3.72450.20371620.1671241X-RAY DIFFRACTION100
3.7245-4.09890.20851400.14651249X-RAY DIFFRACTION100
4.0989-4.69110.14391480.13351262X-RAY DIFFRACTION100
4.6911-5.90660.15631310.14531266X-RAY DIFFRACTION100
5.9066-37.58780.16551380.15281263X-RAY DIFFRACTION99

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