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- PDB-5uyd: YfeA from M9 minimal media supplemented with zinc - Zn wavelength -

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Basic information

Entry
Database: PDB / ID: 5uyd
TitleYfeA from M9 minimal media supplemented with zinc - 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: 1.927 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 1.2Oct 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
Water5,116284
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)41.786, 52.174, 112.796
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.: 284 / 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: 27.88 % / 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% 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: 1.927→50 Å / Num. obs: 19305 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 22.727 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.038 / Net I/σ(I): 54.8
Reflection shellResolution: 1.927→1.96 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 6.4 / Num. unique obs: 937 / CC1/2: 0.937 / Rpim(I) all: 0.169 / % 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: 5uxs

5uxs


Resolution: 1.927→39.184 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.33
RfactorNum. reflection% reflection
Rfree0.2011 3599 10.04 %
Rwork0.1619 --
obs0.1659 19252 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.927→39.184 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2153 0 1 284 2438
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072205
X-RAY DIFFRACTIONf_angle_d0.7743002
X-RAY DIFFRACTIONf_dihedral_angle_d3.1651331
X-RAY DIFFRACTIONf_chiral_restr0.058336
X-RAY DIFFRACTIONf_plane_restr0.006388
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9272-1.95260.28451210.22621111X-RAY DIFFRACTION92
1.9526-1.97930.31221400.20171276X-RAY DIFFRACTION100
1.9793-2.00760.24021400.17851272X-RAY DIFFRACTION100
2.0076-2.03760.22971370.17441210X-RAY DIFFRACTION100
2.0376-2.06940.23461390.16191246X-RAY DIFFRACTION100
2.0694-2.10340.22051410.16141276X-RAY DIFFRACTION100
2.1034-2.13960.20691330.16111221X-RAY DIFFRACTION100
2.1396-2.17850.20491410.16371259X-RAY DIFFRACTION100
2.1785-2.22040.2021400.16581249X-RAY DIFFRACTION100
2.2204-2.26570.21151410.17551242X-RAY DIFFRACTION100
2.2657-2.3150.22271350.16791232X-RAY DIFFRACTION100
2.315-2.36880.24071380.1751253X-RAY DIFFRACTION100
2.3688-2.42810.18921380.16231224X-RAY DIFFRACTION100
2.4281-2.49370.22281470.17271245X-RAY DIFFRACTION100
2.4937-2.56710.18641440.17541263X-RAY DIFFRACTION100
2.5671-2.64990.21961340.1671220X-RAY DIFFRACTION100
2.6499-2.74460.19191360.15411266X-RAY DIFFRACTION100
2.7446-2.85450.22151350.16431221X-RAY DIFFRACTION100
2.8545-2.98430.20721440.16641268X-RAY DIFFRACTION100
2.9843-3.14160.19671320.16751226X-RAY DIFFRACTION100
3.1416-3.33830.21031430.16281255X-RAY DIFFRACTION100
3.3383-3.59590.17971420.15651234X-RAY DIFFRACTION100
3.5959-3.95750.19071390.14951249X-RAY DIFFRACTION100
3.9575-4.52940.19541410.14271244X-RAY DIFFRACTION100
4.5294-5.70380.16291340.14731256X-RAY DIFFRACTION100
5.7038-39.19180.17711440.1621235X-RAY DIFFRACTION100

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