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- PDB-5uyf: YfeA from M9 minimal media supplemented with zinc - Mn wavelength -

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Basic information

Entry
Database: PDB / ID: 5uyf
TitleYfeA from M9 minimal media supplemented with zinc - 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: 2.057 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
Water3,261181
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)41.859, 52.191, 112.762
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.: 181 / 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: 1.71 Å3/Da / Density % sol: 28 % / Description: tetragonal prism
Crystal growTemperature: 295.15 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: 1.89289 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: 2.057→50 Å / Num. obs: 15986 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 34.315 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.037 / Net I/σ(I): 67.3
Reflection shellResolution: 2.057→2.1 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.411 / Mean I/σ(I) obs: 13.5 / Num. unique obs: 800 / CC1/2: 0.883 / Rpim(I) all: 0.171 / % possible all: 99.9

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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: 5uyd

5uyd


Resolution: 2.057→38.3 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.5
RfactorNum. reflection% reflection
Rfree0.2004 2957 10.01 %
Rwork0.1624 --
obs0.1662 15934 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.057→38.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2153 0 1 181 2335
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062205
X-RAY DIFFRACTIONf_angle_d0.7663002
X-RAY DIFFRACTIONf_dihedral_angle_d3.0021331
X-RAY DIFFRACTIONf_chiral_restr0.054336
X-RAY DIFFRACTIONf_plane_restr0.005388
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0567-2.09040.2321340.22291213X-RAY DIFFRACTION93
2.0904-2.12640.26821320.1941237X-RAY DIFFRACTION100
2.1264-2.16510.21551410.18731283X-RAY DIFFRACTION100
2.1651-2.20670.23031440.17841276X-RAY DIFFRACTION100
2.2067-2.25180.24651390.1851239X-RAY DIFFRACTION100
2.2518-2.30070.23571440.17371305X-RAY DIFFRACTION100
2.3007-2.35420.23141400.17431247X-RAY DIFFRACTION100
2.3542-2.41310.23891470.16811277X-RAY DIFFRACTION100
2.4131-2.47830.21781390.181300X-RAY DIFFRACTION100
2.4783-2.55120.25711360.17171214X-RAY DIFFRACTION100
2.5512-2.63360.2111460.17331310X-RAY DIFFRACTION100
2.6336-2.72770.19051380.16171258X-RAY DIFFRACTION100
2.7277-2.83680.23071390.16551262X-RAY DIFFRACTION100
2.8368-2.96590.22241480.1821274X-RAY DIFFRACTION100
2.9659-3.12220.26271370.17691289X-RAY DIFFRACTION100
3.1222-3.31770.23191370.17911269X-RAY DIFFRACTION100
3.3177-3.57370.20871420.16611250X-RAY DIFFRACTION100
3.5737-3.9330.18041390.1531288X-RAY DIFFRACTION100
3.933-4.50140.12951430.13261270X-RAY DIFFRACTION100
4.5014-5.66830.18191480.13931265X-RAY DIFFRACTION100
5.6683-38.30690.15991440.15161259X-RAY DIFFRACTION100

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