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- PDB-5uyc: YfeA from M9 minimal media supplemented with manganese - Mn wavelength -

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Basic information

Entry
Database: PDB / ID: 5uyc
TitleYfeA from M9 minimal media supplemented with manganese - 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: 1.959 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)36,1042
Polymers36,0491
Non-polymers551
Water4,125229
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)41.682, 52.174, 112.716
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.: 229 / 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: 1.7 Å3/Da / Density % sol: 27.65 % / 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% sodium azide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.89289 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: 1.89289 Å / Relative weight: 1
ReflectionResolution: 1.959→50 Å / Num. obs: 18167 / % possible obs: 98.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 26.003 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.036 / Net I/σ(I): 73.2
Reflection shellResolution: 1.959→1.99 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 13.3 / Num. unique obs: 784 / CC1/2: 0.747 / Rpim(I) all: 0.208 / % possible all: 88.3

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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: 5uya

5uya


Resolution: 1.959→38.286 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.07
RfactorNum. reflection% reflection
Rfree0.2029 3372 10.03 %
Rwork0.1683 --
obs0.1718 18116 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.959→38.286 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2153 0 1 229 2383
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072205
X-RAY DIFFRACTIONf_angle_d0.7993002
X-RAY DIFFRACTIONf_dihedral_angle_d3.1111331
X-RAY DIFFRACTIONf_chiral_restr0.056336
X-RAY DIFFRACTIONf_plane_restr0.006388
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9592-1.98710.33451150.29841062X-RAY DIFFRACTION83
1.9871-2.01680.28641350.26791212X-RAY DIFFRACTION95
2.0168-2.04830.31961430.21341260X-RAY DIFFRACTION99
2.0483-2.08190.2661470.20381280X-RAY DIFFRACTION97
2.0819-2.11780.28611330.18411228X-RAY DIFFRACTION99
2.1178-2.15630.22521450.16971269X-RAY DIFFRACTION99
2.1563-2.19780.22841400.18361249X-RAY DIFFRACTION98
2.1978-2.24260.221370.17661273X-RAY DIFFRACTION100
2.2426-2.29140.21911400.16731282X-RAY DIFFRACTION98
2.2914-2.34470.21251380.17391270X-RAY DIFFRACTION100
2.3447-2.40330.21591400.1721242X-RAY DIFFRACTION99
2.4033-2.46830.20331440.17481302X-RAY DIFFRACTION100
2.4683-2.54090.23111350.17261254X-RAY DIFFRACTION99
2.5409-2.62290.23041450.16951278X-RAY DIFFRACTION100
2.6229-2.71660.19921440.15671280X-RAY DIFFRACTION100
2.7166-2.82530.17951420.16671275X-RAY DIFFRACTION100
2.8253-2.95390.21791440.1771289X-RAY DIFFRACTION100
2.9539-3.10960.22511460.17871266X-RAY DIFFRACTION100
3.1096-3.30430.21751410.16971284X-RAY DIFFRACTION100
3.3043-3.55920.19041480.15921285X-RAY DIFFRACTION100
3.5592-3.91710.1721420.15441280X-RAY DIFFRACTION100
3.9171-4.48320.15591430.14291288X-RAY DIFFRACTION100
4.4832-5.64540.18181460.15721272X-RAY DIFFRACTION100
5.6454-38.29370.16931390.15781264X-RAY DIFFRACTION99

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