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9xxu

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

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

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9xxu
deposition_date	2025-12-01
last_revision	2025-12-31
title	Crystal structure of the chymotrypsin-cleaved iron-free C-lobe of bovine lactoferrin at 2.82 Angstrom resolution
keywords	C-LOBE, LACTOFERRIN, IRON BINDING, CLF, METAL BINDING PROTEIN; METAL BINDING PROTEIN
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	29.64 Å
rg_electron	28.81 Å
i0	109952000.00
molecular_weight	79036.0 kDa
excluded_volume	97474 Å³
envelope_volume	124770 Å³
shell_volume	36352 Å³
envelope_diameter	106.5 Å
shell_rg	35.80 Å
envelope_rg	28.81 Å
shape_rg	28.78 Å
total_rg	29.56 Å
total_atoms	5515
n_residues	682
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	101.9 Å
rg_real	29.59 Å
rg_real_error	0.73 Å
i0_real	1.1000e+08
i0_real_error	1.8420e+06
rg_reciprocal	29.61 Å
i0_reciprocal	110000000.0000
total_estimate	0.8747
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	36.5 Å
skewness	0.279
kurtosis	-0.372
angular_range	— – 0.2650 Å⁻¹
current_alpha	0.0000
highest_alpha	26320000.0000
n_real_points	54
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.824; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.908

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4. Crystallography & Experiment

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5. Entities & Polymer Info (10)

Entity 1 polymer

description	Lactotransferrin
formula_weight	36842.6 kDa
ec_number	3.4.21.-
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	5564

TRVVWCAVGPEEQKKCQQWSQQSGQNVTCATASTTDDCIVLVLKGEADALNLDGGYIYTAGKCGLVPVLAENRKSSKHSSLDCVLRPTEGYLAVAVVKKANEGLTWNSLKDKKSCHTAVDRTAGWNIPMGLIVNQTGSCAFDEFFSQSCAPGADPKSRLCALCAGDDQGLDKCVPNSKEKYYGYTGAFRCLAEDVGDVAFVKNDTVWENTNGESTADWAKNLNREDFRLLCLDGTRKPVTEAQSCHLAVAPNHAVVSRSDRAAHVKQVLLHQQALFGKNGKNCPDKFCLFKSETKNLLFNDNTECLAKLGGRPTYEEYLGTEYVTAIANLKKCSTSPL

Entity 2 polymer

description	C-terminal fragment of Lactotransferrin
formula_weight	1024.2 kDa
ec_number	3.4.21.-
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,D

LEACAFLTR

Entity 3 branched

description	;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 ;
formula_weight	910.8 kDa
src_method	syn
entity_count	2

Entity 4 branched

description	;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 ;
formula_weight	1073.0 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	2

Entity 7 non-polymer

description	ACETATE ION
formula_weight	59.0 kDa
src_method	nat
entity_count	1

Entity 8 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	2

Entity 9 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	3

Entity 10 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	41

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6. Citations (1)

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length_a	92.684 Å
length_b	139.060 Å
length_c	120.741 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	C 2 2 21
int_tables_number	20
crystal_system	—

resolution	2.820 Å
resolution_low	47.583 Å
r_factor	—
r_work	0.2114
r_free	0.2686

fit	/app/data/saxs_computation/xx/9xxu/9xxu.fit
pddf	/app/data/pr_computation/xx/9xxu/9xxu.pr.out
profile	/app/data/saxs_computation/xx/9xxu/9xxu.dat

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

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction

5. Entities & Polymer Info (10)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 branched

Entity 4 branched

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)