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9thq

Crystal structure of the human serum transferrin with Fe(III) bound at the C-lobe only

Method: X-RAY DIFFRACTION D_max: 92.0 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9thq
deposition_date	2025-12-03
title	Crystal structure of the human serum transferrin with Fe(III) bound at the C-lobe only
keywords	protein metalation, vanadium compounds, METAL TRANSPORT; METAL TRANSPORT
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	29.37 Å
rg_electron	28.45 Å
i0	98073200.00
molecular_weight	75257.0 kDa
excluded_volume	92969 Å³
envelope_volume	115210 Å³
shell_volume	33967 Å³
envelope_diameter	95.4 Å
shell_rg	35.53 Å
envelope_rg	28.31 Å
shape_rg	28.45 Å
total_rg	29.11 Å
total_atoms	5265
n_residues	670
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	92.0 Å
rg_real	29.32 Å
rg_real_error	0.73 Å
i0_real	9.8070e+07
i0_real_error	1.4660e+06
rg_reciprocal	29.35 Å
i0_reciprocal	98080000.0000
total_estimate	0.9071
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	32.4 Å
skewness	0.242
kurtosis	-0.548
angular_range	— – 0.2700 Å⁻¹
current_alpha	0.0000
highest_alpha	21100000.0000
n_real_points	55
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.954; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.928

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Serotransferrin
formula_weight	75284.5 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	AAA
atom_count	5579

VPDKTVRWCAVSEHEATKCQSFRDHMKSVIPSDGPSVACVKKASYLDCIRAIAANEADAVTLDAGLVYDAYLAPNNLKPVVAEFYGSKEDPQTFYYAVAVVKKDSGFQMNQLRGKKSCHTGLGRSAGWNIPIGLLYCDLPEPRKPLEKAVANFFSGSCAPCADGTDFPQLCQLCPGCGCSTLNQYFGYSGAFKCLKDGAGDVAFVKHSTIFENLANKADRDQYELLCLDNTRKPVDEYKDCHLAQVPSHTVVARSMGGKEDLIWELLNQAQEHFGKDKSKEFQLFSSPHGKDLLFKDSAHGFLKVPPRMDAKMYLGYEYVTAIRNLREGTCPEAPTDECKPVKWCALSHHERLKCDEWSVNSVGKIECVSAETTEDCIAKIMNGEADAMSLDGGFVYIAGKCGLVPVLAENYNKSDNCEDTPEAGYFAVAVVKKSASDLTWDNLKGKKSCHTAVGRTAGWNIPMGLLYNKINHCRFDEFFSEGCAPGSKKDSSLCKLCMGSGLNLCEPNNKEGYYGYTGAFRCLVEKGDVAFVKHQTVPQNTGGKNPDPWAKNLNEKDYELLCLDGTRKPVEEYANCHLARAPNHAVVTRKDKEACVHKILRQQQHLFGSNVTDCSGNFCLFRSETKDLLFRDDTVCLAKLHDRNTYEKYLGEEYVKAVGNLRKCSTSSLLEACTFRRP

Entity 2 non-polymer

description	FE (III) ION
formula_weight	55.8 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	MALONIC ACID
formula_weight	104.1 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	BICARBONATE ION
formula_weight	61.0 kDa
src_method	syn
entity_count	9

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	249

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6. Citations (1)

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length_a	138.232 Å
length_b	158.132 Å
length_c	107.708 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 2 2 21
int_tables_number	20
crystal_system	—

resolution	2.440 Å
resolution_low	79.100 Å
r_factor	—
r_work	0.1878
r_free	0.2309

fit	/app/data/saxs_computation/th/9thq/9thq.fit
pddf	/app/data/pr_computation/th/9thq/9thq.pr.out
profile	/app/data/saxs_computation/th/9thq/9thq.dat