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9xs9

Crystal structure of a cupin protein (tm1459, R39K/H52A/H54A/H92A/C106E mutant) in ruthenium(p-cymene) bound form

Method: X-RAY DIFFRACTION D_max: 63.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9xs9
deposition_date	2025-11-20
last_revision	2026-04-29
title	Crystal structure of a cupin protein (tm1459, R39K/H52A/H54A/H92A/C106E mutant) in ruthenium(p-cymene) bound form
keywords	Artificial metalloenzymes, Biocatalysis, Ruthenium(p-cymene), 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	18.84 Å
rg_electron	17.27 Å
i0	11473200.00
molecular_weight	26357.0 kDa
excluded_volume	33442 Å³
envelope_volume	37459 Å³
shell_volume	17999 Å³
envelope_diameter	62.1 Å
shell_rg	23.59 Å
envelope_rg	17.57 Å
shape_rg	17.26 Å
total_rg	18.32 Å
total_atoms	3690
n_residues	232
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	63.1 Å
rg_real	18.74 Å
rg_real_error	0.30 Å
i0_real	1.1470e+07
i0_real_error	1.3850e+05
rg_reciprocal	18.76 Å
i0_reciprocal	11470000.0000
total_estimate	0.8755
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	23.7 Å
skewness	0.212
kurtosis	-0.349
angular_range	— – 0.4200 Å⁻¹
current_alpha	0.0000
highest_alpha	3090000.0000
n_real_points	73
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.794; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.996

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Cupin type-2 domain-containing protein
formula_weight	13224.1 kDa
mutation	R39K/H52A/H54A/H92A/C106E
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	4106

GPSGMILKRAYDVTPQKISTDKVRGVRKRVLIGLKDAPNFVMKLFTVEPGGLIDRASAPWEHEIFVLKGKLTVLKEQGEETVEEGFYIFVEPNEIAGFRNDTDSEVEFLELIPKEGGE

Source

organism	Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)
ncbi_taxonomy_id	243274
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	1-methyl-4-(1-methylethyl)benzene
formula_weight	134.2 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	RUTHENIUM ION
formula_weight	101.1 kDa
src_method	nat
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	294

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6. Citations (1)

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length_a	50.148 Å
length_b	58.096 Å
length_c	74.539 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	1.087 Å
resolution_low	50.000 Å
r_factor	0.1331
r_work	0.1317
r_free	0.1605

fit	/app/data/saxs_computation/xs/9xs9/9xs9.fit
pddf	/app/data/pr_computation/xs/9xs9/9xs9.pr.out
profile	/app/data/saxs_computation/xs/9xs9/9xs9.dat

Crystal structure of a cupin protein (tm1459, R39K/H52A/H54A/H92A/C106E mutant) in ruthenium(p-cymene) bound form

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