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- PDB-8xeu: Structure of the siderophore periplasmic binding protein FtsB fro... -

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Basic information

Entry
Database: PDB / ID: 8xeu
TitleStructure of the siderophore periplasmic binding protein FtsB from Streptococcus pyogenes with ferrichrome bound
ComponentsIron-hydroxamate ABC transporter substrate-binding protein FtsB
KeywordsMETAL BINDING PROTEIN / Streptococcus pyogenes / siderophore / hydroxamate / FtsB / ABC transporter / alanine scanning / antibiotic strategy / ferrichrome
Function / homology
Function and homology information


iron coordination entity transport / outer membrane-bounded periplasmic space / metal ion binding
Similarity search - Function
: / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
FERRICHROME / Iron-hydroxamate ABC transporter substrate-binding protein
Similarity search - Component
Biological speciesStreptococcus pyogenes SSI-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsCaaveiro, J.M.M. / Fernandez-Perez, J. / Tsumoto, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)20H02531 Japan
CitationJournal: Structure / Year: 2024
Title: Structural basis for the ligand promiscuity of the hydroxamate siderophore binding protein FtsB from Streptococcus pyogenes.
Authors: Fernandez-Perez, J. / Senoo, A. / Caaveiro, J.M.M. / Nakakido, M. / de Vega, S. / Nakagawa, I. / Tsumoto, K.
History
DepositionDec 13, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 18, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Iron-hydroxamate ABC transporter substrate-binding protein FtsB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5902
Polymers31,8491
Non-polymers7411
Water4,630257
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.490, 62.916, 67.064
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 Iron-hydroxamate ABC transporter substrate-binding protein FtsB / FtsB


Mass: 31849.482 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes SSI-1 (bacteria)
Gene: E0F66_02370 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A5S4TPK8
#2: Chemical ChemComp-FCE / FERRICHROME


Mass: 740.520 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H42FeN9O12 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2 Å3/Da / Density % sol: 38.6 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 100 mM BIS-TRIS pH 6.5 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Mar 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→42.9 Å / Num. obs: 24183 / % possible obs: 99.4 % / Redundancy: 13 % / CC1/2: 0.999 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.027 / Net I/σ(I): 20.4
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 13.6 % / Rmerge(I) obs: 0.983 / Mean I/σ(I) obs: 3 / Num. unique obs: 1373 / CC1/2: 0.82 / Rpim(I) all: 0.283 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSJan 31, 2020 BUILT=20200417data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HXP

3hxp


Resolution: 1.8→33.555 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.644 / SU ML: 0.1 / Cross valid method: FREE R-VALUE / ESU R: 0.144 / ESU R Free: 0.137
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2265 1161 4.809 %
Rwork0.1795 22980 -
all0.182 --
obs-24141 99.207 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 24.395 Å2
Baniso -1Baniso -2Baniso -3
1--0.634 Å20 Å20 Å2
2--0.733 Å20 Å2
3----0.099 Å2
Refinement stepCycle: LAST / Resolution: 1.8→33.555 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2183 0 49 257 2489
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132291
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172198
X-RAY DIFFRACTIONr_angle_refined_deg1.7461.6833113
X-RAY DIFFRACTIONr_angle_other_deg1.4271.6115120
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9215275
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.20724.12497
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.82515415
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.434156
X-RAY DIFFRACTIONr_chiral_restr0.0910.2298
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022459
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02439
X-RAY DIFFRACTIONr_nbd_refined0.2120.2451
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1720.22161
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21137
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21105
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2184
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2150.211
X-RAY DIFFRACTIONr_nbd_other0.2280.239
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.230.219
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1380.21
X-RAY DIFFRACTIONr_mcbond_it0.8741.5091097
X-RAY DIFFRACTIONr_mcbond_other0.871.5081096
X-RAY DIFFRACTIONr_mcangle_it1.3442.2581370
X-RAY DIFFRACTIONr_mcangle_other1.3442.2591371
X-RAY DIFFRACTIONr_scbond_it1.3641.7321194
X-RAY DIFFRACTIONr_scbond_other1.3641.7321195
X-RAY DIFFRACTIONr_scangle_it2.192.5131742
X-RAY DIFFRACTIONr_scangle_other2.1892.5131743
X-RAY DIFFRACTIONr_lrange_it4.2819.1322666
X-RAY DIFFRACTIONr_lrange_other4.27919.1342667
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8470.299660.2311644X-RAY DIFFRACTION98.1067
1.847-1.8970.244870.2051612X-RAY DIFFRACTION98.4357
1.897-1.9520.263740.1991595X-RAY DIFFRACTION98.8159
1.952-2.0120.305760.2021527X-RAY DIFFRACTION99.0117
2.012-2.0780.272720.1981503X-RAY DIFFRACTION99.0566
2.078-2.1510.243690.1771456X-RAY DIFFRACTION99.1547
2.151-2.2320.259580.181410X-RAY DIFFRACTION99.2563
2.232-2.3230.188620.1651342X-RAY DIFFRACTION98.8732
2.323-2.4260.265530.181333X-RAY DIFFRACTION99.2126
2.426-2.5440.199390.1651256X-RAY DIFFRACTION99.386
2.544-2.6810.278600.191186X-RAY DIFFRACTION99.8397
2.681-2.8430.261530.1931136X-RAY DIFFRACTION99.5812
2.843-3.0380.241510.1871079X-RAY DIFFRACTION99.5595
3.038-3.2810.276500.201986X-RAY DIFFRACTION100
3.281-3.5920.224620.187916X-RAY DIFFRACTION99.8979
3.592-4.0130.197560.162827X-RAY DIFFRACTION100
4.013-4.6280.181750.145718X-RAY DIFFRACTION100
4.628-5.6530.2550.161631X-RAY DIFFRACTION100
5.653-7.9350.219220.18515X-RAY DIFFRACTION99.6289
7.935-33.50.178210.156308X-RAY DIFFRACTION97.6261
Refinement TLS params.Method: refined / Origin x: 9.3972 Å / Origin y: -8.0777 Å / Origin z: -19.06 Å
111213212223313233
T0.0668 Å2-0.0138 Å2-0.0189 Å2-0.0111 Å20.0038 Å2--0.0068 Å2
L2.6652 °20.159 °2-0.217 °2-1.0825 °2-0.0931 °2--0.5567 °2
S-0.0317 Å °0.1281 Å °-0.0266 Å °-0.1491 Å °0.0542 Å °0.043 Å °0.0339 Å °-0.0379 Å °-0.0225 Å °
Refinement TLS groupSelection: ALL

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