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- PDB-6q1c: Apo YfeA extracted from the E. coli periplasm -

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Basic information

Entry
Database: PDB / ID: 6q1c
TitleApo YfeA extracted from the E. coli periplasm
ComponentsPeriplasmic chelated iron-binding protein YfeA
KeywordsMETAL TRANSPORT / Yersinia pestis / substrate binding protein / SBP / YfeA
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: 1.76 Å
AuthorsRadka, C.D. / Labiuk, S.L. / DeLucas, L.J. / Aller, S.G.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Structures of the substrate-binding protein YfeA in apo and zinc-reconstituted holo forms.
Authors: Radka, C.D. / Labiuk, S.L. / DeLucas, L.J. / Aller, S.G.
History
DepositionAug 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Sep 25, 2019Group: Data collection / Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.3Oct 11, 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


Theoretical massNumber of molelcules
Total (without water)34,4251
Polymers34,4251
Non-polymers00
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.017, 52.426, 113.263
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Periplasmic chelated iron-binding protein YfeA


Mass: 34425.090 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 1.73 Å3/Da / Density % sol: 28.72 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 6.3
Details: 20 mM Bis-Tris, pH 6.3, 50 mM sodium chloride, 0.05% w/v sodium azide, 30% w/v PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.28242 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 7, 2017
RadiationMonochromator: Double crystal cryo-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28242 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 43178 / % possible obs: 98.5 % / Redundancy: 3.5 % / CC1/2: 0.923 / Net I/σ(I): 35.4
Reflection shellResolution: 1.76→1.79 Å / Num. unique obs: 2960 / CC1/2: 0.754

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-2000v712data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5UXS

5uxs


Resolution: 1.76→38.472 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 25.15
RfactorNum. reflection% reflection
Rfree0.2385 3592 8.32 %
Rwork0.1902 --
obs0.1941 43168 94.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 74.05 Å2 / Biso mean: 35.7979 Å2 / Biso min: 20.66 Å2
Refinement stepCycle: final / Resolution: 1.76→38.472 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 0 166 2208
Biso mean---45.3 -
Num. residues----259
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7602-1.78330.32911110.2855122576
1.7833-1.80780.30351240.262140786
1.8078-1.83360.32631270.2568149393
1.8336-1.8610.28411370.2616149095
1.861-1.890.27611400.2415158597
1.89-1.9210.3421440.2634159797
1.921-1.95410.35181420.2485155898
1.9541-1.98970.31761470.2393157097
1.9897-2.02790.25451370.2257151496
2.0279-2.06930.24541380.2245156296
2.0693-2.11430.29221370.2197154794
2.1143-2.16350.29721290.2232143792
2.1635-2.21760.25881410.2159150292
2.2176-2.27760.28461380.2064152293
2.2776-2.34460.24421370.1892152596
2.3446-2.42020.19981450.2096154498
2.4202-2.50670.22721470.1919158497
2.5067-2.60710.19871360.1998153497
2.6071-2.72570.24051420.1902155496
2.7257-2.86930.23181440.2061152895
2.8693-3.0490.21271340.2071153094
3.049-3.28430.25211410.199155396
3.2843-3.61460.22111500.1841158398
3.6146-4.13720.23281450.1638156698
4.1372-5.21030.18981400.1466152495
5.2103-38.40.25251390.1699154296

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