9xxu

Crystal structure of the chymotrypsin-cleaved iron-free C-lobe of bovine lactoferrin at 2.82 Angstrom resolution

Method: X-RAY DIFFRACTION Dmax: 101.9 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

Lactotransferrin

OrganismNot specified

UniProt P24627

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Homooligomer Protein × 2 其他Polymer 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 362–699 Chain C; UniProt 700–708 Not recorded ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 ;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 EDO 1,2-ETHANEDIOL × 2 GOL GLYCEROL × 1 ACT ACETATE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.6;298 K;0.1M Sodium acetate trihydrate (pH 4.6), 0.2M ammonium sulfate, 25% w/v PEG 2000 Resolution 2.82 Å R-free 0.269
2 Other combination Homooligomer Protein × 2 其他Polymer 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 362–699 Chain D; UniProt 700–708 Not recorded ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 ;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 GOL GLYCEROL × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.6;298 K;0.1M Sodium acetate trihydrate (pH 4.6), 0.2M ammonium sulfate, 25% w/v PEG 2000 Resolution 2.82 Å R-free 0.269

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.

86 other PDB entries and 88 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TRFL_BOVIN
Isoform
PDB entities 1, 2
Chains and sequence ranges Author chain A; PDBConstruct 1–338; UniProt 362–699 Author chain B; PDBConstruct 1–338; UniProt 362–699 Author chain C; PDBConstruct 1–9; UniProt 700–708 Author chain D; PDBConstruct 1–9; UniProt 700–708

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 9xxu

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9xxu
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9xxu
Deposition date deposition_date2025-12-01
最后修订 last_revision2025-12-31
Structure title titleCrystal structure of the chymotrypsin-cleaved iron-free C-lobe of bovine lactoferrin at 2.82 Angstrom resolution
Keywords keywordsC-LOBE, LACTOFERRIN, IRON BINDING, CLF, METAL BINDING PROTEIN; METAL BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier29.64
Radius of gyration Rg (electron density) rg_electron28.81
Forward intensity I(0) i0109952000.00
Molecular weight molecular_weight79036.0 kDa
Excluded volume excluded_volume97474 ų
Envelope volume envelope_volume124770 ų
Hydration-shell volume shell_volume36352 ų
Envelope diameter envelope_diameter106.5
Shell Rg shell_rg35.80
Envelope Rg envelope_rg28.81
Shape Rg shape_rg28.78
Total Rg total_rg29.56
Total atoms total_atoms5515
Residues n_residues682
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax101.9
Rg (real space) rg_real29.59
Rg uncertainty (real space) rg_real_error0.73
I(0) (real space) i0_real1.1000e+08
I(0) uncertainty (real space) i0_real_error1.8420e+06
Rg (reciprocal space) rg_reciprocal29.61
I(0) (reciprocal space) i0_reciprocal110000000.0000
Solution quality estimate total_estimate0.8747
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary36.5
Skewness Skewness skewness0.279
Kurtosis Kurtosis kurtosis-0.372
Angular range angular_range— – 0.2650 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha26320000.0000
Real-space data points n_real_points54
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.824; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.908

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (10)

8. Citations (1)

9. Files and Curves (10)