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- PDB-5uy0: YfeA from M9 minimal media supplemented with iron - Zn wavelength -

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Basic information

Entry
Database: PDB / ID: 5uy0
TitleYfeA from M9 minimal media supplemented with iron - 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: 1.709 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)36,1142
Polymers36,0491
Non-polymers651
Water5,098283
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)61.929, 66.472, 67.249
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.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 35.93 % / Description: tetragonal prism
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 6.3
Details: 30% PEG 4000, 50mM sodium chloride, 0.05% w/v sodium azide, 20mM Bis-tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.28215 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: 1.28215 Å / Relative weight: 1
ReflectionResolution: 1.709→50 Å / Num. obs: 30412 / % possible obs: 98.9 % / Redundancy: 8.1 % / Biso Wilson estimate: 27.603 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.032 / Net I/σ(I): 56
Reflection shellResolution: 1.709→1.74 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1478 / CC1/2: 0.938 / Rpim(I) all: 0.15 / % possible all: 97.7

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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: 1.709→30.965 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.34
RfactorNum. reflection% reflection
Rfree0.2124 3819 6.65 %
Rwork0.1785 --
obs0.1808 30366 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.709→30.965 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2133 0 1 283 2417
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072185
X-RAY DIFFRACTIONf_angle_d0.8082975
X-RAY DIFFRACTIONf_dihedral_angle_d3.1191320
X-RAY DIFFRACTIONf_chiral_restr0.059333
X-RAY DIFFRACTIONf_plane_restr0.007384
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7093-1.73090.23131530.23691947X-RAY DIFFRACTION97
1.7309-1.75370.25771510.22691943X-RAY DIFFRACTION98
1.7537-1.77770.22471390.22591938X-RAY DIFFRACTION98
1.7777-1.80310.26451400.22311968X-RAY DIFFRACTION98
1.8031-1.830.2361340.20981994X-RAY DIFFRACTION98
1.83-1.85860.2541430.20511976X-RAY DIFFRACTION98
1.8586-1.88910.2461390.20681953X-RAY DIFFRACTION98
1.8891-1.92170.26551390.2031972X-RAY DIFFRACTION98
1.9217-1.95660.2371580.20731977X-RAY DIFFRACTION99
1.9566-1.99420.21771420.18531971X-RAY DIFFRACTION99
1.9942-2.03490.21931430.19031967X-RAY DIFFRACTION99
2.0349-2.07920.20421380.18932012X-RAY DIFFRACTION99
2.0792-2.12750.23791350.19092005X-RAY DIFFRACTION99
2.1275-2.18070.24321270.19321970X-RAY DIFFRACTION99
2.1807-2.23970.21121560.19881999X-RAY DIFFRACTION99
2.2397-2.30550.21521310.18532028X-RAY DIFFRACTION100
2.3055-2.37990.18811360.18051979X-RAY DIFFRACTION100
2.3799-2.4650.23291350.1882018X-RAY DIFFRACTION100
2.465-2.56360.22331330.18742023X-RAY DIFFRACTION100
2.5636-2.68020.20861370.18482006X-RAY DIFFRACTION100
2.6802-2.82140.19571560.18171984X-RAY DIFFRACTION100
2.8214-2.99810.2651410.19471990X-RAY DIFFRACTION100
2.9981-3.22930.23731540.18922017X-RAY DIFFRACTION100
3.2293-3.55390.18261300.1651999X-RAY DIFFRACTION100
3.5539-4.06720.19671520.16052003X-RAY DIFFRACTION100
4.0672-5.12040.19511360.14392020X-RAY DIFFRACTION100
5.1204-30.96960.19061400.1731958X-RAY DIFFRACTION98

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