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9uly

crystal structure of AbGHMP in complex with L-Ara and AMPPNP

Method: X-RAY DIFFRACTION D_max: 114.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9uly
deposition_date	2025-04-21
last_revision	2026-04-29
title	crystal structure of AbGHMP in complex with L-Ara and AMPPNP
keywords	arabinokinase, TRANSFERASE; 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	34.56 Å
rg_electron	34.52 Å
i0	179429000.00
molecular_weight	104860.0 kDa
excluded_volume	130070 Å³
envelope_volume	161800 Å³
shell_volume	40947 Å³
envelope_diameter	121.2 Å
shell_rg	38.59 Å
envelope_rg	34.96 Å
shape_rg	34.55 Å
total_rg	34.69 Å
total_atoms	7371
n_residues	966
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	114.8 Å
rg_real	34.86 Å
rg_real_error	1.05 Å
i0_real	1.7940e+08
i0_real_error	3.2240e+06
rg_reciprocal	34.68 Å
i0_reciprocal	179400000.0000
total_estimate	0.8169
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	32.4 Å
skewness	0.611
kurtosis	-0.124
angular_range	— – 0.2300 Å⁻¹
current_alpha	0.0000
highest_alpha	81610000.0000
n_real_points	47
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.775; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.925; Smooth: 0.369

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	AbGHMP
formula_weight	53874.7 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	7371

MFRITHGSTLGLPDVEAFLHTLNTVEQNPATRGLFDPAGEIIVARAPGRLDVMGGIADYSGSLVLEMPIREATFVALQRASDRQLKLVSLSEDSTEALHFEMPLADFDHAGEPISYETARSYFKRDPAQHWAAYVAGVFLVLMRERGAQFTEGARLLIASRVPQGKGVSSSAALEVATMNAVANAFGISLAPRETALLCQKVENLVAGAPCGVMDQMTSVWGETNQLLALLCQPAELQSAVSIPDEISFWGIDSGIRHAVTGSDYGSVRVGAFMGYRMIAELAGLPVTDGDPVQIVDLRWSGYLSNLTPSQFEQMYAEKLPERISGAEFLARYGGTTDAITRVEPDRSYAVRVPTGHPIYEHHRVRLFAELLSARITERQLAERGLACLGELMYQSHASYSACGLGSTATDRLVELAREAGPSEGIYGAKITGGGSGGTVAVFGRREAAPAIVRIAERYAGEAGYQPYIFSGSSPGGATFGHLRLRPNEFLEHHHHHH

Source

organism	Acidobacteriota
ncbi_taxonomy_id	57723
host_organism	Escherichia coli

Entity 2 non-polymer

description	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
formula_weight	506.2 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	beta-L-arabinopyranose
formula_weight	150.1 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

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6. Citations (1)

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length_a	57.356 Å
length_b	112.146 Å
length_c	89.922 Å
angle_alpha	90.00 °
angle_beta	93.17 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.600 Å
resolution_low	41.680 Å
r_factor	0.2103
r_work	0.2076
r_free	0.2588

fit	/app/data/saxs_computation/ul/9uly/9uly.fit
pddf	/app/data/pr_computation/ul/9uly/9uly.pr.out
profile	/app/data/saxs_computation/ul/9uly/9uly.dat

crystal structure of AbGHMP in complex with L-Ara and AMPPNP

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