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9t29

Jumonji domain-containing protein 2D with crystallization epitope mutation Q41R

Method: X-RAY DIFFRACTION D_max: 66.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9t29
deposition_date	2025-10-22
last_revision	2025-11-26
title	Jumonji domain-containing protein 2D with crystallization epitope mutation Q41R
keywords	Substrate Complex, Oxidoreductase, GDP-L-Fucose, L-Fucose; OXIDOREDUCTASE
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	20.84 Å
rg_electron	19.66 Å
i0	24840900.00
molecular_weight	37827.0 kDa
excluded_volume	47149 Å³
envelope_volume	54658 Å³
shell_volume	22682 Å³
envelope_diameter	68.6 Å
shell_rg	26.83 Å
envelope_rg	20.02 Å
shape_rg	19.62 Å
total_rg	20.70 Å
total_atoms	2667
n_residues	331
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	66.6 Å
rg_real	20.71 Å
rg_real_error	0.39 Å
i0_real	2.4840e+07
i0_real_error	3.5290e+05
rg_reciprocal	20.73 Å
i0_reciprocal	24840000.0000
total_estimate	0.8907
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	26.1 Å
skewness	0.163
kurtosis	-0.367
angular_range	— – 0.3800 Å⁻¹
current_alpha	0.0000
highest_alpha	5482000.0000
n_real_points	70
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.862; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.998

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Lysine-specific demethylase 4D
formula_weight	39607.9 kDa
ec_number	1.14.11.66
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2759

SMETMKSKANCAQNPNCNIMIFHPTKEEFNDFDKYIAYMESRGAHRAGLAKIIPPKEWKARETYDNISEILIATPLQQVASGRAGVFTQYHKKKKAMTVGEYRHLANSKKYQTPPHQNFEDLERKYWKNRIYNSPIYGADISGSLFDENTKQWNLGHLGTIQDLLEKECGVVIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHLGEPKTWYVVPPEHGQRLERLARELFPGSSRGCGAFLRHKVALISPTVLKENGIPFNRITQEAGEFMVTFPYGYHAGFNHGFNCAEAINFATPRWIDYGKMASQCSCGEARVTFSMDAFVRILQPERYDLWKRGQDR

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	NICKEL (II) ION
formula_weight	58.7 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	92

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6. Citations (1)

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length_a	73.167 Å
length_b	73.167 Å
length_c	134.440 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 32 2 1
int_tables_number	154
crystal_system	—

resolution	2.013 Å
resolution_low	57.320 Å
r_factor	0.2263
r_work	0.2251
r_free	0.2501

fit	/app/data/saxs_computation/t2/9t29/9t29.fit
pddf	/app/data/pr_computation/t2/9t29/9t29.pr.out
profile	/app/data/saxs_computation/t2/9t29/9t29.dat

Jumonji domain-containing protein 2D with crystallization epitope mutation Q41R

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