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- PDB-5uxu: YfeA from Yersinia pestis treated with EDTA during purification a... -

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Basic information

Entry
Database: PDB / ID: 5uxu
TitleYfeA from Yersinia pestis treated with EDTA during purification and crystallization
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: 1.839 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)36,1142
Polymers36,0491
Non-polymers651
Water7,278404
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)55.319, 66.875, 81.693
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.: 404 / 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: 2.1 Å3/Da / Density % sol: 41.31 % / Description: tetragonal prism
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 2mM EDTA, 30% PEG4000, 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: APS / Beamline: 23-ID-B / Wavelength: 1.28229 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 15, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28229 Å / Relative weight: 1
ReflectionResolution: 1.839→50 Å / Num. obs: 26517 / % possible obs: 98 % / Redundancy: 3.3 % / Biso Wilson estimate: 19.045 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.042 / Net I/σ(I): 48.9
Reflection shellResolution: 1.84→1.87 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.171 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 1199 / CC1/2: 0.924 / Rpim(I) all: 0.122 / % possible all: 90.6

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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: 1.839→40.846 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 19.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.203 3659 7.61 %
Rwork0.1703 --
obs0.1728 48112 94.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.839→40.846 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2161 0 1 404 2566
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072214
X-RAY DIFFRACTIONf_angle_d0.8753015
X-RAY DIFFRACTIONf_dihedral_angle_d3.1781339
X-RAY DIFFRACTIONf_chiral_restr0.063338
X-RAY DIFFRACTIONf_plane_restr0.007389
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8386-1.86280.23161250.23631494X-RAY DIFFRACTION81
1.8628-1.88830.23591300.22851568X-RAY DIFFRACTION87
1.8883-1.91530.21941310.2081586X-RAY DIFFRACTION88
1.9153-1.94380.23921370.18851661X-RAY DIFFRACTION94
1.9438-1.97420.22381430.1861728X-RAY DIFFRACTION94
1.9742-2.00660.21131370.1821719X-RAY DIFFRACTION95
2.0066-2.04120.21561390.18051713X-RAY DIFFRACTION95
2.0412-2.07830.23431430.17151728X-RAY DIFFRACTION95
2.0783-2.11830.19751420.18411681X-RAY DIFFRACTION94
2.1183-2.16150.21741380.17531707X-RAY DIFFRACTION94
2.1615-2.20850.21231460.18791765X-RAY DIFFRACTION96
2.2085-2.25990.24361390.17741660X-RAY DIFFRACTION93
2.2599-2.31640.22111410.17681691X-RAY DIFFRACTION94
2.3164-2.3790.21961430.17531723X-RAY DIFFRACTION95
2.379-2.4490.21371400.17911735X-RAY DIFFRACTION96
2.449-2.5280.21761470.17711778X-RAY DIFFRACTION97
2.528-2.61840.21691450.17281738X-RAY DIFFRACTION97
2.6184-2.72320.20071450.16121767X-RAY DIFFRACTION97
2.7232-2.84710.19521450.17231759X-RAY DIFFRACTION97
2.8471-2.99720.19281380.18841752X-RAY DIFFRACTION96
2.9972-3.18490.22641360.17521716X-RAY DIFFRACTION94
3.1849-3.43070.21511490.17091715X-RAY DIFFRACTION96
3.4307-3.77570.20771500.16341796X-RAY DIFFRACTION99
3.7757-4.32150.1651450.1421786X-RAY DIFFRACTION99
4.3215-5.44260.16471450.14811749X-RAY DIFFRACTION96
5.4426-40.85660.17211400.14991738X-RAY DIFFRACTION96

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