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- PDB-8xf4: Structure of the siderophore periplasmic binding protein FtsB fro... -

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Basic information

Entry
Database: PDB / ID: 8xf4
TitleStructure of the siderophore periplasmic binding protein FtsB from Streptococcus pyogenes with Bisucaberin bound
ComponentsIron-hydroxamate ABC transporter substrate-binding protein FtsB
KeywordsMETAL BINDING PROTEIN / Streptococcus pyogenes / siderophore / hydroxamate / FtsB / ABC transporter / alanine scanning / antibiotic strategy / Bisucaberin
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-OX8 / Iron-hydroxamate ABC transporter substrate-binding protein
Similarity search - Component
Biological speciesStreptococcus pyogenes SSI-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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)32,7625
Polymers31,8491
Non-polymers9134
Water1,60389
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)59.974, 62.099, 67.926
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-OX8 / 1,12-bis(oxidanyl)-1,6,12,17-tetrazacyclodocosane-2,5,13,16-tetrone


Mass: 400.470 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H32N4O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 38.06 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 150 mM KSCN 30% PEG-MME 2000

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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: May 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→45.8 Å / Num. obs: 17418 / % possible obs: 98.6 % / Redundancy: 13.2 % / CC1/2: 1 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.021 / Net I/σ(I): 25.2
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.996 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 1236 / CC1/2: 0.817 / Rpim(I) all: 0.281

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSJan 10, 2022 BUILT=20220120data reduction
Aimless0.7.13data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8XEU

8xeu


Resolution: 2→45.8 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.946 / SU B: 6.084 / SU ML: 0.158 / Cross valid method: FREE R-VALUE / ESU R: 0.231 / ESU R Free: 0.179
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.234 829 4.768 %
Rwork0.1991 16557 -
all0.201 --
obs-17386 98.259 %
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: 35.564 Å2
Baniso -1Baniso -2Baniso -3
1--1.529 Å20 Å2-0 Å2
2---0.303 Å20 Å2
3---1.832 Å2
Refinement stepCycle: LAST / Resolution: 2→45.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2183 0 58 89 2330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0122286
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162243
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.8693086
X-RAY DIFFRACTIONr_angle_other_deg0.5151.8115203
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.335273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.68256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.41810413
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.3931090
X-RAY DIFFRACTIONr_chiral_restr0.0670.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022548
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02468
X-RAY DIFFRACTIONr_nbd_refined0.2230.2482
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.22099
X-RAY DIFFRACTIONr_nbtor_refined0.1850.21148
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21150
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2104
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0310.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0570.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2660.29
X-RAY DIFFRACTIONr_nbd_other0.2160.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1320.25
X-RAY DIFFRACTIONr_mcbond_it2.3883.3851095
X-RAY DIFFRACTIONr_mcbond_other2.3883.3851095
X-RAY DIFFRACTIONr_mcangle_it3.4156.0711367
X-RAY DIFFRACTIONr_mcangle_other3.4156.0721368
X-RAY DIFFRACTIONr_scbond_it3.3173.8851191
X-RAY DIFFRACTIONr_scbond_other3.3153.8861192
X-RAY DIFFRACTIONr_scangle_it5.316.9241719
X-RAY DIFFRACTIONr_scangle_other5.3096.9251720
X-RAY DIFFRACTIONr_lrange_it6.69835.3882638
X-RAY DIFFRACTIONr_lrange_other6.6935.4442625
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0520.292560.291175X-RAY DIFFRACTION97.3892
2.052-2.1080.37560.2621176X-RAY DIFFRACTION97.7778
2.108-2.1690.308610.2611107X-RAY DIFFRACTION97.4958
2.169-2.2360.357590.241087X-RAY DIFFRACTION97.0364
2.236-2.3090.329580.2281073X-RAY DIFFRACTION97.416
2.309-2.3890.256550.2281047X-RAY DIFFRACTION98.2175
2.389-2.4790.274520.2191001X-RAY DIFFRACTION98.2276
2.479-2.580.318510.21960X-RAY DIFFRACTION98.3463
2.58-2.6950.259480.222948X-RAY DIFFRACTION98.5163
2.695-2.8260.293370.237903X-RAY DIFFRACTION98.5325
2.826-2.9780.314380.22859X-RAY DIFFRACTION98.14
2.978-3.1580.233400.214808X-RAY DIFFRACTION98.1481
3.158-3.3750.241320.219779X-RAY DIFFRACTION99.0232
3.375-3.6430.276280.207736X-RAY DIFFRACTION99.3498
3.643-3.9890.175330.178668X-RAY DIFFRACTION99.1513
3.989-4.4550.149420.142598X-RAY DIFFRACTION99.2248
4.455-5.1360.181280.154548X-RAY DIFFRACTION99.1394
5.136-6.2710.172200.174477X-RAY DIFFRACTION99.7992
6.271-8.7870.179240.154373X-RAY DIFFRACTION99.7487
8.787-45.80.165110.151234X-RAY DIFFRACTION98.7903

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