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- PDB-5uya: YfeA from M9 minimal media supplemented with manganese - Zn wavelength -

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Basic information

Entry
Database: PDB / ID: 5uya
TitleYfeA from M9 minimal media supplemented with manganese - 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: 1.719 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
Water5,278293
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)41.793, 52.127, 113.006
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.: 293 / 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: 27.96 % / 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: 1.28215 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: 1.719→50 Å / Num. obs: 26994 / % possible obs: 99.8 % / Redundancy: 7.4 % / Biso Wilson estimate: 20.66 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.037 / Net I/σ(I): 59.1
Reflection shellResolution: 1.719→1.75 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 7.9 / Num. unique obs: 1320 / CC1/2: 0.965 / Rpim(I) all: 0.154 / % possible all: 98.7

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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: 1.719→38.313 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.78
RfactorNum. reflection% reflection
Rfree0.1922 3763 7.45 %
Rwork0.1645 --
obs0.1665 26936 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.719→38.313 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2153 0 1 293 2447
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062205
X-RAY DIFFRACTIONf_angle_d0.7753002
X-RAY DIFFRACTIONf_dihedral_angle_d3.041331
X-RAY DIFFRACTIONf_chiral_restr0.057336
X-RAY DIFFRACTIONf_plane_restr0.006388
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7191-1.74080.21571320.1841662X-RAY DIFFRACTION94
1.7408-1.76370.24991380.17171718X-RAY DIFFRACTION100
1.7637-1.78790.23981380.18271734X-RAY DIFFRACTION100
1.7879-1.81340.2781370.19021753X-RAY DIFFRACTION99
1.8134-1.84050.1991390.19761705X-RAY DIFFRACTION100
1.8405-1.86930.26931420.18311744X-RAY DIFFRACTION99
1.8693-1.89990.241410.19161757X-RAY DIFFRACTION100
1.8999-1.93270.25161380.19691683X-RAY DIFFRACTION100
1.9327-1.96780.23141450.18291777X-RAY DIFFRACTION100
1.9678-2.00570.23061380.16661722X-RAY DIFFRACTION100
2.0057-2.04660.20791410.16681707X-RAY DIFFRACTION100
2.0466-2.09110.21771380.16461782X-RAY DIFFRACTION100
2.0911-2.13970.20251370.16311689X-RAY DIFFRACTION100
2.1397-2.19320.21411430.17521776X-RAY DIFFRACTION100
2.1932-2.25250.18081370.16331692X-RAY DIFFRACTION100
2.2525-2.31880.18911420.1611751X-RAY DIFFRACTION99
2.3188-2.39360.21341370.17341750X-RAY DIFFRACTION100
2.3936-2.47920.21271380.17341756X-RAY DIFFRACTION100
2.4792-2.57840.21711430.17841710X-RAY DIFFRACTION100
2.5784-2.69570.18351380.16621722X-RAY DIFFRACTION100
2.6957-2.83780.20141420.17181745X-RAY DIFFRACTION100
2.8378-3.01560.2011360.17711748X-RAY DIFFRACTION100
3.0156-3.24830.23561420.16671742X-RAY DIFFRACTION100
3.2483-3.5750.1911350.15741725X-RAY DIFFRACTION100
3.575-4.09180.14091430.14081746X-RAY DIFFRACTION100
4.0918-5.15320.14521440.13821758X-RAY DIFFRACTION100
5.1532-38.32260.15431390.16421707X-RAY DIFFRACTION99

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