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9uod

Crystal structure of pHBMT1 from Populus trichocarpa

Method: X-RAY DIFFRACTION D_max: 70.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9uod
deposition_date	2025-04-25
last_revision	2026-04-29
title	Crystal structure of pHBMT1 from Populus trichocarpa
keywords	Transferase, Structural Genomics, PSI-Biology; TRANSFERASE
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	23.17 Å
rg_electron	21.87 Å
i0	36598700.00
molecular_weight	47666.0 kDa
excluded_volume	60080 Å³
envelope_volume	69597 Å³
shell_volume	26074 Å³
envelope_diameter	71.9 Å
shell_rg	29.05 Å
envelope_rg	21.94 Å
shape_rg	21.85 Å
total_rg	22.78 Å
total_atoms	3352
n_residues	426
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	70.9 Å
rg_real	23.03 Å
rg_real_error	0.41 Å
i0_real	3.6600e+07
i0_real_error	5.1330e+05
rg_reciprocal	23.06 Å
i0_reciprocal	36600000.0000
total_estimate	0.8333
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	28.4 Å
skewness	0.126
kurtosis	-0.554
angular_range	— – 0.3450 Å⁻¹
current_alpha	0.0000
highest_alpha	7380000.0000
n_real_points	66
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.946; Stabil: 1.000; 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 (5)

Entity 1 polymer

description	BEBT-like acyltransferase
formula_weight	49772.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3704

AFNVRRCEPELVAPAKATPHESKPLSDIDRQLYLQFQSPHYNFYAHNPSMQGKDPVKVIREGIAQALVYYYPYAGRIRQEPENKLVVDCTGEGVLFIEADADGTLEQFGDPIQPPFPCAEELLYNVPGSAGIINTPLLIIQITRLKCGGFILGFRLNHPMSDAIGLVQLLSAIGEISRGAQAPSILPVWQRELLCARNPPRVTCTHNEYGDHHDLVVDPSELNVPEFRGSTDGAAHRCFIIGPKELSNIRKWIPPHLHPCSKFEIITACLWRCHAIASQANPNEEMRICMLVNARSKFNPPLPKGYYGNVLALPAAITSARKLCLNSLGYALELIRQAKNKITEEYIRSLADFIEITKGLPKGLQSYVVSDLTSVGFDQVDYGWGKPVYTGPSKAMPDDINNSGTYYLPYRNKKGERGVMVLISLRAPVMARFAMLFEELTKHDPD

Source

organism	Populus trichocarpa
common_name	black cottonwood
ncbi_taxonomy_id	3694
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	ETHANOL
formula_weight	46.1 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	281

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6. Citations (1)

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length_a	102.007 Å
length_b	53.153 Å
length_c	103.430 Å
angle_alpha	90.00 °
angle_beta	105.51 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	1.820 Å
resolution_low	99.660 Å
r_factor	0.1793
r_work	0.1774
r_free	0.2157

fit	/app/data/saxs_computation/uo/9uod/9uod.fit
pddf	/app/data/pr_computation/uo/9uod/9uod.pr.out
profile	/app/data/saxs_computation/uo/9uod/9uod.dat