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- PDB-21ze: Crystal structure of the petrobactin-binding protein FatB from Ba... -

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Basic information

Entry
Database: PDB / ID: 21ze
TitleCrystal structure of the petrobactin-binding protein FatB from Bacillus cereus complexed with ferric petrobactin
ComponentsFerric anguibactin-binding protein
KeywordsMETAL TRANSPORT PROTEIN / siderophore-binding protein / substrate-binding protein / ABC transporter
Function / homology
Function and homology information


iron coordination entity transport / outer membrane-bounded periplasmic space / plasma membrane
Similarity search - Function
FatB domain / : / 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-F8W / : / Ferric anguibactin-binding protein
Similarity search - Component
Biological speciesBacillus cereus ATCC 14579 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsLee, H. / Kim, S.O. / You, S. / Noh, T. / Ihee, H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Institute for Basic Science (IBS)IBS-R033 Korea, Republic Of
CitationJournal: Nat Commun / Year: 2026
Title: Structural basis of FatB-mediated iron uptake via tyrosine/histidine direct coordination accompanying long-distance domain reorganization.
Authors: Lee, H. / Kim, S.O. / You, S. / Segalina, A. / Noh, T. / Ihee, H.
History
DepositionJan 4, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2026Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferric anguibactin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7637
Polymers32,7401
Non-polymers1,0236
Water5,567309
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.684, 67.990, 50.631
Angle α, β, γ (deg.)90.000, 92.110, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Ferric anguibactin-binding protein / Petrobactin-binding protein FatB


Mass: 32739.895 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The construct corresponds to residues 40-338 of Bacillus cereus FatB (UniProt Q815N5). Three additional residues, Ser-Asn-Ala (SNA), are present at the N-terminus as a remnant of the His6- ...Details: The construct corresponds to residues 40-338 of Bacillus cereus FatB (UniProt Q815N5). Three additional residues, Ser-Asn-Ala (SNA), are present at the N-terminus as a remnant of the His6-tag following TEV protease cleavage.
Source: (gene. exp.) Bacillus cereus ATCC 14579 (bacteria) / Gene: BC_5106 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q815N5
#2: Chemical ChemComp-F8W / 4-[4-[3-[[3,4-bis(oxidanyl)phenyl]carbonylamino]propylamino]butylamino]-2-[2-[4-[3-[[3,4-bis(oxidanyl)phenyl]carbonylamino]propylamino]butylamino]-2-oxidanylidene-ethyl]-2-oxidanyl-4-oxidanylidene-butanoic acid


Mass: 718.794 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H50N6O11 / 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 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 2.08 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 10% (v/v) 2-propanol, 0.1 M BICINE, pH 8.5, 36% (w/v) PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 27, 2024
RadiationMonochromator: DCM Si (111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.78→40.59 Å / Num. obs: 25529 / % possible obs: 98 % / Redundancy: 21.2 % / Biso Wilson estimate: 20.75 Å2 / CC1/2: 0.825 / CC star: 0.951 / Net I/σ(I): 41.1
Reflection shellResolution: 1.785→1.849 Å / Mean I/σ(I) obs: 11.12 / Num. unique obs: 2448 / CC1/2: 0.903 / CC star: 0.974

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000v722data reduction
HKL-2000v722data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→40.59 Å / SU ML: 0.1597 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 25.7304
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2173 1226 4.88 %
Rwork0.1685 23896 -
obs0.1711 25121 97.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.43 Å2
Refinement stepCycle: LAST / Resolution: 1.78→40.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2262 0 68 309 2639
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00922405
X-RAY DIFFRACTIONf_angle_d1.00813258
X-RAY DIFFRACTIONf_chiral_restr0.0614366
X-RAY DIFFRACTIONf_plane_restr0.0074419
X-RAY DIFFRACTIONf_dihedral_angle_d14.8775346
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.860.25881030.19342612X-RAY DIFFRACTION96.41
1.86-1.940.27511090.19882696X-RAY DIFFRACTION98.59
1.94-2.040.25381380.19532639X-RAY DIFFRACTION98.2
2.04-2.170.25511370.1822672X-RAY DIFFRACTION98.56
2.17-2.340.23011630.18462660X-RAY DIFFRACTION99.09
2.34-2.570.2531430.17992622X-RAY DIFFRACTION98.19
2.57-2.950.24051400.18252685X-RAY DIFFRACTION98.88
2.95-3.710.19031410.16222657X-RAY DIFFRACTION97.36
3.71-40.590.18651520.14242653X-RAY DIFFRACTION96.49
Refinement TLS params.Method: refined / Origin x: 10.1002790111 Å / Origin y: 6.0579931464 Å / Origin z: 8.59473762943 Å
111213212223313233
T0.112502640205 Å20.0170557944374 Å20.0166510775656 Å2-0.121788168857 Å2-0.0235109795164 Å2--0.133999093149 Å2
L1.59105626829 °2-0.314322204814 °20.51089454225 °2-0.861700350955 °20.0193466432535 °2--2.06109151222 °2
S-0.0750683511876 Å °-0.177019108145 Å °0.0701080258153 Å °0.106926591884 Å °0.080467071525 Å °-0.0919205744165 Å °0.0367917189419 Å °0.0439294558338 Å °0.00273446348575 Å °
Refinement TLS groupSelection details: all

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