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- PDB-8xf8: High-resolution structure of the siderophore periplasmic binding ... -

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Basic information

Entry
Database: PDB / ID: 8xf8
TitleHigh-resolution structure of the siderophore periplasmic binding protein FtsB from Streptococcus pyogenes with ferrioxamine B
ComponentsIron-hydroxamate ABC transporter substrate-binding protein FtsB
KeywordsMETAL BINDING PROTEIN / Streptococcus pyogenes / siderophore / hydroxamate / FtsB / ABC transporter / alanine scanning / antibiotic strategy / ferrioxamine B
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
methanesulfonic acid / Ferrioxamine B / Iron-hydroxamate ABC transporter substrate-binding protein
Similarity search - Component
Biological speciesStreptococcus pyogenes SSI-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 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)32,92910
Polymers31,8491
Non-polymers1,0799
Water7,476415
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)76.223, 76.223, 102.502
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 6 types, 424 molecules

#2: Chemical ChemComp-0UE / Ferrioxamine B


Mass: 613.505 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H45FeN6O8 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-03S / methanesulfonic acid


Mass: 96.106 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4O3S
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.7 Å3/Da / Density % sol: 54.43 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 50 mM zinc sulfate 25% PEG 550-MME 100 mM MES pH 6.5

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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: Oct 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.15→40.5 Å / Num. obs: 113334 / % possible obs: 94.9 % / Redundancy: 10.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.019 / Net I/σ(I): 20.9
Reflection shellResolution: 1.15→1.17 Å / Rmerge(I) obs: 0.928 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4502 / CC1/2: 0.721 / Rpim(I) all: 0.319 / % possible all: 76.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSJan 10, 2022 BUILT=20220120data reduction
Aimless0.7.9data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8XEU

8xeu


Resolution: 1.15→40.5 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.932 / SU ML: 0.019 / Cross valid method: FREE R-VALUE / ESU R: 0.029 / ESU R Free: 0.029
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1529 2277 2.009 %
Rwork0.1353 111053 -
all0.136 --
obs-113330 94.947 %
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: 13.327 Å2
Baniso -1Baniso -2Baniso -3
1-0.099 Å20.05 Å20 Å2
2--0.099 Å20 Å2
3----0.322 Å2
Refinement stepCycle: LAST / Resolution: 1.15→40.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2222 0 55 415 2692
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0122458
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162444
X-RAY DIFFRACTIONr_angle_refined_deg1.6691.8593363
X-RAY DIFFRACTIONr_angle_other_deg0.5271.7685695
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1435319
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.179534
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg1.46654
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.08610467
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.0781096
X-RAY DIFFRACTIONr_chiral_restr0.0790.2379
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022778
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02498
X-RAY DIFFRACTIONr_nbd_refined0.2330.2470
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.22221
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21185
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21159
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.2248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0610.22
X-RAY DIFFRACTIONr_metal_ion_refined0.2290.27
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2630.224
X-RAY DIFFRACTIONr_nbd_other0.2230.247
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2070.233
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1320.25
X-RAY DIFFRACTIONr_mcbond_it2.3681.3061168
X-RAY DIFFRACTIONr_mcbond_other2.3511.3061168
X-RAY DIFFRACTIONr_mcangle_it3.612.3531471
X-RAY DIFFRACTIONr_mcangle_other3.6162.3551472
X-RAY DIFFRACTIONr_scbond_it3.4081.5221290
X-RAY DIFFRACTIONr_scbond_other3.4021.521288
X-RAY DIFFRACTIONr_scangle_it5.2862.7021873
X-RAY DIFFRACTIONr_scangle_other5.2852.7031874
X-RAY DIFFRACTIONr_lrange_it9.07318.2262969
X-RAY DIFFRACTIONr_lrange_other8.1716.0352835
X-RAY DIFFRACTIONr_rigid_bond_restr2.11334902
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.15-1.180.2121390.2076937X-RAY DIFFRACTION80.5923
1.18-1.2120.2031750.1857813X-RAY DIFFRACTION92.6575
1.212-1.2470.1681390.177667X-RAY DIFFRACTION93.5186
1.247-1.2860.1971410.1647479X-RAY DIFFRACTION94.1322
1.286-1.3280.1751570.1467264X-RAY DIFFRACTION94.523
1.328-1.3740.1571510.1337071X-RAY DIFFRACTION95.0013
1.374-1.4260.1441500.1196826X-RAY DIFFRACTION95.2225
1.426-1.4840.1391290.1136659X-RAY DIFFRACTION95.8216
1.484-1.550.1221450.1056379X-RAY DIFFRACTION96.2242
1.55-1.6260.1271100.1036172X-RAY DIFFRACTION96.6164
1.626-1.7130.1421260.1065807X-RAY DIFFRACTION96.739
1.713-1.8170.1461220.1115596X-RAY DIFFRACTION97.4272
1.817-1.9420.1431160.1185213X-RAY DIFFRACTION97.6723
1.942-2.0980.122980.1194931X-RAY DIFFRACTION98.1843
2.098-2.2970.133870.1174537X-RAY DIFFRACTION98.5087
2.297-2.5670.127780.1264128X-RAY DIFFRACTION98.7324
2.567-2.9630.178880.143648X-RAY DIFFRACTION99.2561
2.963-3.6240.186710.1483110X-RAY DIFFRACTION99.5618
3.624-5.1040.159300.1492446X-RAY DIFFRACTION99.7985
5.104-40.50.158250.2111370X-RAY DIFFRACTION99.8568

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