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

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Basic information

Entry
Database: PDB / ID: 21zd
TitleCrystal structure of the petrobactin-binding protein FatB from Bacillus cereus in the apo-form
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
Ferric anguibactin-binding protein
Similarity search - Component
Biological speciesBacillus cereus ATCC 14579 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 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


Theoretical massNumber of molelcules
Total (without water)32,7401
Polymers32,7401
Non-polymers00
Water3,099172
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.425, 57.796, 100.934
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Ferric anguibactin-binding protein


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. Although the full construct was used for crystallization, residues 281-288 are disordered and were therefore not modeled due to lack of interpretable electron density.
Source: (gene. exp.) Bacillus cereus ATCC 14579 (bacteria) / Gene: BC_5106 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q815N5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O
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: 1.62 Å3/Da / Density % sol: 24.19 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.15M Potassium thiocyanate, 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: Feb 26, 2025
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: 1.91→38.01 Å / Num. obs: 16974 / % possible obs: 94.9 % / Redundancy: 5.5 % / Biso Wilson estimate: 27.05 Å2 / CC1/2: 0.968 / CC star: 0.992 / Net I/σ(I): 13.47
Reflection shellResolution: 1.91→1.978 Å / Mean I/σ(I) obs: 2.18 / Num. unique obs: 1430 / CC1/2: 0.294 / CC star: 0.674 / % possible all: 85.58

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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: 1.91→38.01 Å / SU ML: 0.2334 / Cross valid method: FREE R-VALUE / σ(F): 0.1 / Phase error: 26.7206
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2578 1607 9.85 %
Rwork0.2148 14764 -
obs0.2194 16323 94.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.73 Å2
Refinement stepCycle: LAST / Resolution: 1.91→38.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2203 0 0 172 2375
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00282244
X-RAY DIFFRACTIONf_angle_d0.60423044
X-RAY DIFFRACTIONf_chiral_restr0.0438351
X-RAY DIFFRACTIONf_plane_restr0.0062393
X-RAY DIFFRACTIONf_dihedral_angle_d15.8116827
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.960.3691180.26311061X-RAY DIFFRACTION84.64
1.96-2.030.30041230.25271125X-RAY DIFFRACTION88.26
2.03-2.10.27431240.24921110X-RAY DIFFRACTION88.14
2.1-2.180.28351290.23671186X-RAY DIFFRACTION93.33
2.18-2.280.28131310.22741235X-RAY DIFFRACTION95.13
2.28-2.40.28431340.22751225X-RAY DIFFRACTION96.45
2.4-2.550.30751370.22191227X-RAY DIFFRACTION96.53
2.55-2.750.26891390.21831285X-RAY DIFFRACTION98.14
2.75-3.030.2251410.21191281X-RAY DIFFRACTION99.09
3.03-3.460.25731410.19891297X-RAY DIFFRACTION99.38
3.47-4.360.20271440.18591325X-RAY DIFFRACTION99.93
4.37-38.010.26341530.21981407X-RAY DIFFRACTION99.49

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