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- PDB-7wqu: FeoC from Klebsiella pneumoniae -

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Basic information

Entry
Database: PDB / ID: 7wqu
TitleFeoC from Klebsiella pneumoniae
Components
  • Ferrous iron transport protein B
  • Probable [Fe-S]-dependent transcriptional repressor
KeywordsMETAL BINDING PROTEIN / FeoC / sulfur cluster / channel
Function / homology
Function and homology information


: / ferrous iron transmembrane transporter activity / iron-sulfur cluster binding / iron ion binding / GTP binding / DNA binding / plasma membrane
Similarity search - Function
Probable [Fe-S]-dependent transcriptional repressor / Transcriptional regulator HTH-type, FeoC / FeoC like transcriptional regulator / FeoB, cytosolic helical domain / FeoB cytosolic helical domain / Ferrous iron transport protein B / FeoB-type guanine nucleotide-binding (G) domain / Ferrous iron transport protein B / FeoB-type guanine nucleotide-binding (G) domain profile. / GTP binding domain ...Probable [Fe-S]-dependent transcriptional repressor / Transcriptional regulator HTH-type, FeoC / FeoC like transcriptional regulator / FeoB, cytosolic helical domain / FeoB cytosolic helical domain / Ferrous iron transport protein B / FeoB-type guanine nucleotide-binding (G) domain / Ferrous iron transport protein B / FeoB-type guanine nucleotide-binding (G) domain profile. / GTP binding domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Ferrous iron transport protein B / Probable [Fe-S]-dependent transcriptional repressor
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.202 Å
AuthorsHsueh, K.L. / Yu, L.K. / Hsieh, Y.C. / Hsiao, Y.Y. / Chen, C.J.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan) Taiwan
CitationJournal: Biochim Biophys Acta Proteins Proteom / Year: 2023
Title: FeoC from Klebsiella pneumoniae uses its iron sulfur cluster to regulate the GTPase activity of the ferrous iron channel.
Authors: Hsueh, K.L. / Yu, L.K. / Hsieh, Y.C. / Hsiao, Y.Y. / Chen, C.J.
History
DepositionJan 26, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1May 3, 2023Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferrous iron transport protein B
B: Probable [Fe-S]-dependent transcriptional repressor


Theoretical massNumber of molelcules
Total (without water)38,4702
Polymers38,4702
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-9 kcal/mol
Surface area14830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.292, 176.292, 176.292
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23

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Components

#1: Protein Ferrous iron transport protein B


Mass: 29133.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: feoB_3, NCTC13465_06046 / Production host: Escherichia (bacteria) / References: UniProt: A0A2X3IBQ3
#2: Protein Probable [Fe-S]-dependent transcriptional repressor


Mass: 9336.975 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: feoC, feoC_1, feoC_2, feoC_3, B4U61_05105, B5L96_23940, BANRA_00013, BANRA_02115, BANRA_03104, BANRA_05041, BANRA_05068, BL124_00007660, BN49_0337, BS595_00310, BVX91_21775, C3F39_16835, DBX64_ ...Gene: feoC, feoC_1, feoC_2, feoC_3, B4U61_05105, B5L96_23940, BANRA_00013, BANRA_02115, BANRA_03104, BANRA_05041, BANRA_05068, BL124_00007660, BN49_0337, BS595_00310, BVX91_21775, C3F39_16835, DBX64_03020, DD583_06240, DDJ63_18885, DRB11_11255, EAO24_26705, EHZ17_14310, FXN67_10090, G5637_14020, G7Z27_01710, GJJ08_001695, GNG14_19045, GTH21_21045, H7U16_01300, NCTC11679_00389, NCTC13443_06889, NCTC13635_04158, NCTC3279_04123, NCTC5052_03367, NCTC5053_04698, NCTC9128_00574, NCTC9140_07590, NCTC9617_03741, NCTC9645_02373, NCTC9661_01156, SAMEA3499874_04074, SAMEA3499901_00641, SAMEA3512100_03353, SAMEA3515130_02436, SAMEA3538828_03100, SAMEA3649466_04175, SAMEA3649648_02635, SAMEA3649733_05023, SAMEA3649758_02179, SAMEA3720909_02087, SAMEA3727643_02153, SAMEA3727679_02629, SAMEA3729663_01240, SAMEA4364603_03689
Production host: Escherichia (bacteria) / References: UniProt: W9BMW4

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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: 5.93 Å3/Da / Density % sol: 79.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 2 M ammonium sulfate and 0.1 M sodium acetate trihydrate pH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.2→30 Å / Num. obs: 6774 / % possible obs: 100 % / Redundancy: 12 % / CC1/2: 0.98 / Net I/σ(I): 2
Reflection shellResolution: 4.2→4.39 Å / Num. unique obs: 845 / CC1/2: 0.952

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0135refinement
PHENIX1.10.1refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AWX

4awx


Resolution: 4.202→29.382 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2323 275 10.01 %
Rwork0.2192 --
obs0.2205 6774 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 261.42 Å2 / Biso mean: 133.8716 Å2 / Biso min: 78.77 Å2
Refinement stepCycle: final / Resolution: 4.202→29.382 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2395 0 0 0 2395
Num. residues----312
LS refinement shellResolution: 4.2022→4.5256 Å
RfactorNum. reflection% reflection
Rfree0.2415 135 -
Rwork0.213 --
obs-1198 100 %

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