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9t0x

Crystal structure of H416C NikA mutant from Escherichia coli covalently bound to a modified Mn(salen) complex

Method: X-RAY DIFFRACTION D_max: 97.7 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9t0x
deposition_date	2025-10-20
last_revision	2026-06-10
title	Crystal structure of H416C NikA mutant from Escherichia coli covalently bound to a modified Mn(salen) complex
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	30.16 Å
rg_electron	28.88 Å
i0	190051000.00
molecular_weight	112000.0 kDa
excluded_volume	141130 Å³
envelope_volume	167150 Å³
shell_volume	46352 Å³
envelope_diameter	99.5 Å
shell_rg	37.59 Å
envelope_rg	28.70 Å
shape_rg	28.85 Å
total_rg	29.76 Å
total_atoms	7916
n_residues	996
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	97.7 Å
rg_real	29.97 Å
rg_real_error	0.44 Å
i0_real	1.9010e+08
i0_real_error	2.7030e+06
rg_reciprocal	30.05 Å
i0_reciprocal	190100000.0000
total_estimate	0.6837
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	40.6 Å
skewness	0.127
kurtosis	-0.414
angular_range	— – 0.2650 Å⁻¹
current_alpha	0.0001
highest_alpha	68920000.0000
n_real_points	54
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.834; Stabil: 1.000; Sysdev: 0.135; Positv: 1.000; Valcen: 0.986; Smooth: 0.991

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

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

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	8424

AAPDEITTAWPVNVGPLNPHLYTPNQMFAQSMVYEPLVKYQADGSVIPWLAKSWTHSEDGKTWTFTLRDDVKFSNGEPFDAEAAAENFRAVLDNRQRHAWLELANQIVDVKALSKTELQITLKSAYYPFLQELALPRPFRFIAPSQFKNHETMNGIKAPIGTGPWILQESKLNQYDVFVRNENYWGEKPAIKKITFNVIPDPTTRAVAFETGDIDLLYGNEGLLPLDTFARFSQNPAYHTQLSQPIETVMLALNTAKAPTNELAVREALNYAVNKKSLIDNALYGTQQVADTLFAPSVPYANLGLKPSQYDPQKAKALLEKAGWTLPAGKDIREKNGQPLRIELSFIGTDALSKSMAEIIQADMRQIGADVSLIGEEESSIYARQRDGRFGMIFHRTWGAPYDPHAFLSSMRVPSCADFQAQQGLADKPLIDKEIGEVLATHDETQRQALYRDILTRLHDEAVYLPISYISMMVVSKPELGNIPYAPIATEIPFEQIKPVKP

Source

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

Entity 2 non-polymer

description	1-methylpyrrolidine-2,5-dione
formula_weight	113.1 kDa
src_method	syn
entity_count	2

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	321

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6. Citations (1)

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length_a	85.799 Å
length_b	93.229 Å
length_c	123.489 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	1.810 Å
resolution_low	46.610 Å
r_factor	0.2178
r_work	0.2171
r_free	0.2761

fit	/app/data/saxs_computation/t0/9t0x/9t0x.fit
pddf	/app/data/pr_computation/t0/9t0x/9t0x.pr.out
profile	/app/data/saxs_computation/t0/9t0x/9t0x.dat

Crystal structure of H416C NikA mutant from Escherichia coli covalently bound to a modified Mn(salen) complex

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