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9thr

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

Method: X-RAY DIFFRACTION D_max: 91.9 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9thr
deposition_date	2025-12-03
title	Crystal structure of the human serum transferrin with Fe(III) bound at the C-lobe only (treated with DMSO)
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	29.18 Å
rg_electron	28.26 Å
i0	93565200.00
molecular_weight	73895.0 kDa
excluded_volume	91496 Å³
envelope_volume	112190 Å³
shell_volume	33389 Å³
envelope_diameter	94.8 Å
shell_rg	35.22 Å
envelope_rg	28.11 Å
shape_rg	28.26 Å
total_rg	28.92 Å
total_atoms	5172
n_residues	662
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	91.9 Å
rg_real	29.13 Å
rg_real_error	0.69 Å
i0_real	9.3570e+07
i0_real_error	1.5320e+06
rg_reciprocal	29.15 Å
i0_reciprocal	93570000.0000
total_estimate	0.9064
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	0
r_peak_primary	— Å
skewness	0.242
kurtosis	-0.540
angular_range	— – 0.2700 Å⁻¹
current_alpha	0.0000
highest_alpha	20830000.0000
n_real_points	55
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.951; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.927

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

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	5228

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	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	BICARBONATE ION
formula_weight	61.0 kDa
src_method	syn
entity_count	5

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	39

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6. Citations (1)

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length_a	137.098 Å
length_b	156.774 Å
length_c	107.108 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	3.200 Å
resolution_low	74.320 Å
r_factor	—
r_work	0.1797
r_free	0.2491

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