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21zd

Crystal structure of the petrobactin-binding protein FatB from Bacillus cereus in the apo-form

Method: X-RAY DIFFRACTION Dmax: 69.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ferric anguibactin-binding protein

Bacillus cereus ATCC 14579

UniProt Q815N5

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 40–338 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；289 K；0.15M Potassium thiocyanate, 30% (w/v) PEG monomethyl ether 2000 Resolution 1.91 Å R-free 0.258

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 21ZD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
21ZE Crystal structure of the petrobactin-binding protein FatB from Bacillus cereus complexed with ferric petrobactin Deposited 2026-01-04 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 40–338（299 aa）
Not recorded 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 × 1 FE FE (III) ION × 1 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；10% (v/v) 2-propanol, 0.1 M BICINE, pH 8.5, 36% (w/v) PEG 1000
Resolution 1.78 Å R-free 0.217
21ZF Crystal structure of the petrobactin-binding protein FatB from Bacillus cereus complexed with ferric petrobactin photoproduct, FePBv Deposited 2026-01-04 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 40–338（299 aa）
Not recorded A1MDH ~{N}-[3-[4-[[5-[4-[3-[[3,4-bis(oxidanyl)phenyl]carbonylamino]propylamino]butylamino]-5-oxidanyl-3-oxidanylidene-pent-4-enoyl]amino]butylamino]propyl]-3,4-bis(oxidanyl)benzamide × 1 FE FE (III) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；10% (v/v) 2-propanol, 0.1 M BICINE, pH 8.5, 28% (w/v) PEG 1000
Resolution 1.58 Å R-free 0.188
21ZG Crystal structure of the petrobactin-binding protein FatB from Bacillus cereus complexed with ferric siderophore mimic, Fe(3,4-DHB)2 Deposited 2026-01-04 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 40–338（299 aa）
Not recorded DHB 3,4-DIHYDROXYBENZOIC ACID × 2 FE FE (III) ION × 1 EDO 1,2-ETHANEDIOL × 1 IPA ISOPROPYL ALCOHOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；15% (v/v) 2-propanol, 0.1 M MES monohydrate, pH 6.0, 30% (w/v) PEG monomethyl ether 2000
Resolution 1.40 Å R-free 0.173

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q815N5_BACCR
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 4–302； UniProt 40–338

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 21zd

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 21zd
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2. Structure Basics 2. Structure Basics

Entry ID entry_id21zd
Deposition date deposition_date2026-01-04
Structure title titleCrystal structure of the petrobactin-binding protein FatB from Bacillus cereus in the apo-form
Keywords keywordssiderophore-binding protein, substrate-binding protein, ABC transporter, METAL TRANSPORT PROTEIN; METAL TRANSPORT PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier21.50 Å
Radius of gyration Rg (electron density) rg_electron20.65 Å
Forward intensity I(0) i016661900.00
Molecular weight molecular_weight31235.0 kDa
Excluded volume excluded_volume39328 ų
Envelope volume envelope_volume47538 ų
Hydration-shell volume shell_volume19776 ų
Envelope diameter envelope_diameter70.1 Å
Shell Rg shell_rg26.45 Å
Envelope Rg envelope_rg20.69 Å
Shape Rg shape_rg20.61 Å
Total Rg total_rg21.59 Å
Total atoms total_atoms4415
Residues n_residues287
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax69.9 Å
Rg (real space) rg_real21.50 Å
Rg uncertainty (real space) rg_real_error0.40 Å
I(0) (real space) i0_real1.6660e+07
I(0) uncertainty (real space) i0_real_error2.1520e+05
Rg (reciprocal space) rg_reciprocal21.50 Å
I(0) (reciprocal space) i0_reciprocal16660000.0000
Solution quality estimate total_estimate0.8887
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary23.6 Å
Skewness Skewness skewness0.355
Kurtosis Kurtosis kurtosis-0.383
Angular range angular_range— – 0.3700 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4139000.0000
Real-space data points n_real_points69
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.861; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.976
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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9. Files and Curves (10)