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9uyw

Crystal structure of apo-form artificial metalloprotein incorporating a TP ligand

Method: X-RAY DIFFRACTION D_max: 76.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9uyw
deposition_date	2025-05-15
title	Crystal structure of apo-form 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	22.43 Å
rg_electron	21.72 Å
i0	59933600.00
molecular_weight	40751.0 kDa
excluded_volume	39620 Å³
envelope_volume	63880 Å³
shell_volume	24605 Å³
envelope_diameter	81.9 Å
shell_rg	28.73 Å
envelope_rg	22.04 Å
shape_rg	21.70 Å
total_rg	22.40 Å
total_atoms	3090
n_residues	368
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	76.9 Å
rg_real	22.44 Å
rg_real_error	0.58 Å
i0_real	5.9930e+07
i0_real_error	8.0460e+05
rg_reciprocal	22.43 Å
i0_reciprocal	59930000.0000
total_estimate	0.7809
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	25.6 Å
skewness	0.452
kurtosis	-0.097
angular_range	— – 0.3550 Å⁻¹
current_alpha	0.0000
highest_alpha	18260000.0000
n_real_points	67
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.721; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

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	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	3237

GSHMAEFRFIKTSLDGAIIIEPEVYTDERGYFMETFNEAIFQENGLEVRFVQDNESMSVRGVLRGLHFQREKPQGKLVRVIXGEIFDVAVDLRKNSDTYGEWTGVRLSDENRREFFIPEGFAHGFLALSDECIVNYKCTELYHPEYDSGIPWDDPDIGIDWPLEMVDDLIISEKDRNWKPLRENPVYL

Source

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

Entity 2 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	nat
entity_count	2

Entity 3 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	147

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6. Citations (1)

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length_a	51.678 Å
length_b	72.428 Å
length_c	63.509 Å
angle_alpha	90.00 °
angle_beta	113.84 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.480 Å
resolution_low	29.040 Å
r_factor	0.2220
r_work	0.2196
r_free	0.2668

fit	/app/data/saxs_computation/uy/9uyw/9uyw.fit
pddf	/app/data/pr_computation/uy/9uyw/9uyw.pr.out
profile	/app/data/saxs_computation/uy/9uyw/9uyw.dat

Crystal structure of apo-form artificial metalloprotein incorporating a TP ligand

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