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

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Basic information

Entry
Database: PDB / ID: 21zg
TitleCrystal structure of the petrobactin-binding protein FatB from Bacillus cereus complexed with ferric siderophore mimic, Fe(3,4-DHB)2
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
3,4-DIHYDROXYBENZOIC ACID / : / ISOPROPYL ALCOHOL / Ferric anguibactin-binding protein
Similarity search - Component
Biological speciesBacillus cereus ATCC 14579 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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

Downloads & links

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Assembly

Deposited unit
A: Ferric anguibactin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2266
Polymers32,7401
Non-polymers4865
Water9,044502
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-7 kcal/mol
Surface area13780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.443, 66.743, 50.504
Angle α, β, γ (deg.)90.000, 90.400, 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

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 507 molecules

#2: Chemical ChemComp-DHB / 3,4-DIHYDROXYBENZOIC ACID


Mass: 154.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O4 / 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.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 502 / 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: 2.13 Å3/Da / Density % sol: 42.34 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 15% (v/v) 2-propanol, 0.1 M MES monohydrate, pH 6.0, 30% (w/v) PEG monomethyl ether 2000

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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: Dec 6, 2022
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: 1.4→41.44 Å / Num. obs: 53132 / % possible obs: 97.63 % / Redundancy: 6.6 % / Biso Wilson estimate: 13.15 Å2 / CC1/2: 0.995 / CC star: 0.999 / Net I/σ(I): 20.16
Reflection shellResolution: 1.4→1.45 Å / Mean I/σ(I) obs: 3.77 / Num. unique obs: 4938 / CC1/2: 0.785 / CC star: 0.938

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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: 1.4→41.44 Å / SU ML: 0.1334 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.2382
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1732 2647 5 %
Rwork0.1394 50416 -
obs0.1407 52846 97.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.08 Å2
Refinement stepCycle: LAST / Resolution: 1.4→41.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2253 0 31 502 2786
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00582325
X-RAY DIFFRACTIONf_angle_d0.84223155
X-RAY DIFFRACTIONf_chiral_restr0.0749360
X-RAY DIFFRACTIONf_plane_restr0.0075408
X-RAY DIFFRACTIONf_dihedral_angle_d5.7277309
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.25881240.20192154X-RAY DIFFRACTION79.48
1.42-1.450.24231210.16452550X-RAY DIFFRACTION94.31
1.45-1.480.21991280.15242688X-RAY DIFFRACTION96.87
1.48-1.510.19811520.13432621X-RAY DIFFRACTION98.12
1.51-1.540.16791470.1252682X-RAY DIFFRACTION97.89
1.54-1.580.1621420.12222651X-RAY DIFFRACTION97.08
1.58-1.630.17761630.12962645X-RAY DIFFRACTION98.42
1.63-1.670.22591330.13362714X-RAY DIFFRACTION98.55
1.67-1.730.22771560.14632679X-RAY DIFFRACTION98.81
1.73-1.790.20211030.1472725X-RAY DIFFRACTION98.92
1.79-1.860.20971320.13752708X-RAY DIFFRACTION98.37
1.86-1.950.16981560.1292657X-RAY DIFFRACTION98.32
1.95-2.050.15051250.1322706X-RAY DIFFRACTION98.88
2.05-2.180.15321390.12932722X-RAY DIFFRACTION98.76
2.18-2.350.16711690.13042638X-RAY DIFFRACTION98.18
2.35-2.580.16461360.13992696X-RAY DIFFRACTION97.89
2.58-2.960.14771610.14952718X-RAY DIFFRACTION99.38
2.96-3.720.16571230.14252701X-RAY DIFFRACTION97.55
3.72-41.440.16371460.13872761X-RAY DIFFRACTION98.38

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