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9var

Crystal structure of Cu-bound artificial metalloprotein incorporating a TP ligand

Method: X-RAY DIFFRACTION D_max: 102.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9var
deposition_date	2025-06-04
title	Crystal structure of Cu-bound artificial metalloprotein incorporating a TP ligand
keywords	noncanonical amino acids, 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	30.12 Å
rg_electron	29.56 Å
i0	232445000.00
molecular_weight	81735.0 kDa
excluded_volume	79279 Å³
envelope_volume	134590 Å³
shell_volume	37659 Å³
envelope_diameter	107.8 Å
shell_rg	36.86 Å
envelope_rg	29.60 Å
shape_rg	29.55 Å
total_rg	30.06 Å
total_atoms	6185
n_residues	736
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	102.1 Å
rg_real	30.11 Å
rg_real_error	0.73 Å
i0_real	2.3240e+08
i0_real_error	3.4470e+06
rg_reciprocal	30.12 Å
i0_reciprocal	232400000.0000
total_estimate	0.8824
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	32.8 Å
skewness	0.322
kurtosis	-0.405
angular_range	— – 0.2650 Å⁻¹
current_alpha	0.0000
highest_alpha	90410000.0000
n_real_points	54
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.840; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.969

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	dTDP-4-dehydrorhamnose 3,5-epimerase
formula_weight	22118.7 kDa
ec_number	5.1.3.13
mutation	R79 mutation
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	6352

GSHMAEFRFIKTSLDGAIIIEPEVYTDERGYFMETFNEAIFQENGLEVRFVQDNESMSVRGVLRGLHFQREKPQGKLVRVIXGEIFDVAVDLRKNSDTYGEWTGVRLSDENRREFFIPEGFAHGFLALSDECIVNYKCTELYHPEYDSGIPWDDPDIGIDWPLEMVDDLIISEKDRNWKPLRENPVYL

Source

organism	Methanothermobacter thermautotrophicus
ncbi_taxonomy_id	145262
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	COPPER (II) ION
formula_weight	63.5 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	nat
entity_count	2

Entity 4 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	167

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6. Citations (1)

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length_a	51.582 Å
length_b	72.741 Å
length_c	63.520 Å
angle_alpha	90.05 °
angle_beta	113.49 °
angle_gamma	89.89 °
z_pdb	4

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.862 Å
resolution_low	29.130 Å
r_factor	0.2272
r_work	0.2248
r_free	0.2736

fit	/app/data/saxs_computation/va/9var/9var.fit
pddf	/app/data/pr_computation/va/9var/9var.pr.out
profile	/app/data/saxs_computation/va/9var/9var.dat