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9t0v

Crystal structure of H416C NikA mutant from Escherichia coli in complex with Fe(III)-EDTA

Method: X-RAY DIFFRACTION D_max: 94.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9t0v
deposition_date	2025-10-20
last_revision	2026-06-10
title	Crystal structure of H416C NikA mutant from Escherichia coli in complex with Fe(III)-EDTA
keywords	Nickel importer Fe(III)-EDTA binding His416Cys mutation, 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	30.46 Å
rg_electron	29.17 Å
i0	194844000.00
molecular_weight	112670.0 kDa
excluded_volume	141690 Å³
envelope_volume	170480 Å³
shell_volume	46812 Å³
envelope_diameter	100.2 Å
shell_rg	37.82 Å
envelope_rg	29.02 Å
shape_rg	29.14 Å
total_rg	30.06 Å
total_atoms	7951
n_residues	993
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	94.5 Å
rg_real	30.27 Å
rg_real_error	0.52 Å
i0_real	1.9480e+08
i0_real_error	2.9610e+06
rg_reciprocal	30.35 Å
i0_reciprocal	194900000.0000
total_estimate	0.8938
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	41.8 Å
skewness	0.134
kurtosis	-0.412
angular_range	— – 0.2600 Å⁻¹
current_alpha	0.0000
highest_alpha	85710000.0000
n_real_points	53
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.899; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.936

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	Nickel-binding periplasmic protein
formula_weight	56325.7 kDa
mutation	H416C
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	8188

AAPDEITTAWPVNVGPLNPHLYTPNQMFAQSMVYEPLVKYQADGSVIPWLAKSWTHSEDGKTWTFTLRDDVKFSNGEPFDAEAAAENFRAVLDNRQRHAWLELANQIVDVKALSKTELQITLKSAYYPFLQELALPRPFRFIAPSQFKNHETMNGIKAPIGTGPWILQESKLNQYDVFVRNENYWGEKPAIKKITFNVIPDPTTRAVAFETGDIDLLYGNEGLLPLDTFARFSQNPAYHTQLSQPIETVMLALNTAKAPTNELAVREALNYAVNKKSLIDNALYGTQQVADTLFAPSVPYANLGLKPSQYDPQKAKALLEKAGWTLPAGKDIREKNGQPLRIELSFIGTDALSKSMAEIIQADMRQIGADVSLIGEEESSIYARQRDGRFGMIFHRTWGAPYDPHAFLSSMRVPSCADFQAQQGLADKPLIDKEIGEVLATHDETQRQALYRDILTRLHDEAVYLPISYISMMVVSKPELGNIPYAPIATEIPFEQIKPVKP

Source

organism	Escherichia coli K-12
ncbi_taxonomy_id	83333
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	FE (III) ION
formula_weight	55.8 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	{[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID
formula_weight	292.2 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	3

Entity 6 non-polymer

description	ACETATE ION
formula_weight	59.0 kDa
src_method	syn
entity_count	2

Entity 7 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	1

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	178

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6. Citations (1)

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length_a	86.688 Å
length_b	94.924 Å
length_c	124.183 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	2.542 Å
resolution_low	44.569 Å
r_factor	0.2064
r_work	0.2037
r_free	0.2562

fit	/app/data/saxs_computation/t0/9t0v/9t0v.fit
pddf	/app/data/pr_computation/t0/9t0v/9t0v.pr.out
profile	/app/data/saxs_computation/t0/9t0v/9t0v.dat