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- PDB-8xfa: Structure of the siderophore periplasmic binding protein FtsB mut... -

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Basic information

Entry
Database: PDB / ID: 8xfa
TitleStructure of the siderophore periplasmic binding protein FtsB mutant Y137A from Streptococcus pyogenes with ferrioxamine E bound
ComponentsIron-hydroxamate ABC transporter substrate-binding protein FtsB
KeywordsMETAL BINDING PROTEIN / Streptococcus pyogenes / siderophore / hydroxamate / FtsB / ABC transporter / alanine scanning / antibiotic strategy / ferrioxamine E
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
Chem-6L0 / : / Iron-hydroxamate ABC transporter substrate-binding protein
Similarity search - Component
Biological speciesStreptococcus pyogenes SSI-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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)32,5044
Polymers31,7571
Non-polymers7473
Water3,369187
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)58.817, 61.723, 69.590
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


Mass: 31757.389 Da / Num. of mol.: 1 / Mutation: Y137A
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-6L0 / (8E)-6,17,28-trihydroxy-1,6,12,17,23,28-hexaazacyclotritriacont-8-ene-2,5,13,16,24,27-hexone


Mass: 598.689 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46N6O9 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 1.99 Å3/Da / Density % sol: 38.15 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 100 mM KSCN 30% PEG MME-550

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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 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→46.2 Å / Num. obs: 22069 / % possible obs: 99.1 % / Redundancy: 12.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.03 / Net I/σ(I): 18.6
Reflection shellResolution: 1.85→1.89 Å / Rmerge(I) obs: 0.851 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1187 / CC1/2: 0.729 / Rpim(I) all: 0.292

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSFeb 5, 2021 BUILT=20210323data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8XEU

8xeu


Resolution: 1.85→46.177 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.126 / SU ML: 0.093 / Cross valid method: FREE R-VALUE / ESU R: 0.149 / ESU R Free: 0.14
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2203 817 3.71 %
Rwork0.1714 21205 -
all0.173 --
obs-22022 98.944 %
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: 22.272 Å2
Baniso -1Baniso -2Baniso -3
1--1.253 Å20 Å2-0 Å2
2--0.152 Å2-0 Å2
3---1.101 Å2
Refinement stepCycle: LAST / Resolution: 1.85→46.177 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2191 0 49 187 2427
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0122296
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162256
X-RAY DIFFRACTIONr_angle_refined_deg1.3931.8613103
X-RAY DIFFRACTIONr_angle_other_deg0.4931.8025234
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0455279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.76856
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.48710418
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.5561091
X-RAY DIFFRACTIONr_chiral_restr0.0710.2348
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022567
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02469
X-RAY DIFFRACTIONr_nbd_refined0.2160.2429
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.22070
X-RAY DIFFRACTIONr_nbtor_refined0.1780.21129
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.21125
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2150
X-RAY DIFFRACTIONr_metal_ion_refined0.0640.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1580.211
X-RAY DIFFRACTIONr_nbd_other0.1790.251
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1350.211
X-RAY DIFFRACTIONr_mcbond_it1.3392.1851107
X-RAY DIFFRACTIONr_mcbond_other1.3372.1851107
X-RAY DIFFRACTIONr_mcangle_it1.9733.9211383
X-RAY DIFFRACTIONr_mcangle_other1.9723.9231384
X-RAY DIFFRACTIONr_scbond_it2.3782.4841189
X-RAY DIFFRACTIONr_scbond_other2.3772.4841190
X-RAY DIFFRACTIONr_scangle_it3.7844.421718
X-RAY DIFFRACTIONr_scangle_other3.7834.421719
X-RAY DIFFRACTIONr_lrange_it4.66723.8542628
X-RAY DIFFRACTIONr_lrange_other4.63923.5852601
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.85-1.8980.245640.22813980.22816560.9520.96288.2850.196
1.898-1.950.257560.22414440.22515330.960.96497.84740.191
1.95-2.0060.206630.19414510.19515220.9740.97599.47440.159
2.006-2.0680.265470.18714730.18915200.9630.9771000.158
2.068-2.1360.224540.17413780.17614320.9620.9791000.142
2.136-2.210.176500.16313550.16414050.9810.9831000.14
2.21-2.2940.212410.1613190.16113600.9710.9831000.133
2.294-2.3870.184380.14812580.14912960.9750.9861000.123
2.387-2.4930.205480.15112040.15312520.9750.9851000.127
2.493-2.6140.22450.16211510.16411960.9810.9841000.136
2.614-2.7550.24500.16811000.17111500.9650.9821000.142
2.755-2.9220.21510.17210440.17410950.9710.9811000.147
2.922-3.1220.241390.1769850.17910240.9680.981000.155
3.122-3.3710.212380.1849240.1859620.9750.981000.164
3.371-3.6910.236270.1768730.1779000.9680.9831000.164
3.691-4.1240.187220.1557790.1568010.9740.9871000.146
4.124-4.7550.221310.1446950.1477260.9720.9871000.136
4.755-5.8080.291300.1815940.1866240.9650.9851000.17
5.808-8.150.188160.2034730.2024890.9750.981000.188
8.15-46.1770.10270.163070.1593140.9880.9741000.159

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