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9vf5

Cryo-EM structure of apo form of Arthrobacter psychrolactophillus L-arabinose isomerase

Method: ELECTRON MICROSCOPY D_max: 129.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vf5
deposition_date	2025-06-10
last_revision	2026-05-27
title	Cryo-EM structure of apo form of Arthrobacter psychrolactophillus L-arabinose isomerase
keywords	Isomerase, Apo form, enzyme, Arthrobacter psychrolactophilus, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
method	ELECTRON MICROSCOPY

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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	42.38 Å
rg_electron	41.81 Å
i0	1587340000.00
molecular_weight	331570.0 kDa
excluded_volume	415280 Å³
envelope_volume	501030 Å³
shell_volume	93442 Å³
envelope_diameter	134.3 Å
shell_rg	51.40 Å
envelope_rg	41.64 Å
shape_rg	41.81 Å
total_rg	42.19 Å
total_atoms	23394
n_residues	3012
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	129.4 Å
rg_real	42.13 Å
rg_real_error	0.79 Å
i0_real	1.5870e+09
i0_real_error	2.8260e+07
rg_reciprocal	42.38 Å
i0_reciprocal	1588000000.0000
total_estimate	0.8273
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	56.0 Å
skewness	0.105
kurtosis	-0.531
angular_range	— – 0.1850 Å⁻¹
current_alpha	0.0000
highest_alpha	901100000.0000
n_real_points	38
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.929; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.963; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	L-arabinose isomerase
formula_weight	55668.9 kDa
ec_number	5.3.1.4
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F
atom_count	24583

MSSQLNNSLSEYEVWFLTGSQNLYGEETLRQVAEQSAEVAKTLQESTEIPVRVVFKDVLKDSESIRRAALDANADNKVIGLIAWMHTFSPAKMWIRGLSELNKPLLHLHTQANVALPWAEIDFDFMNLNQAAHGDREFGYMQSRMGISRKTVVGHVSNPLVREKIGTWTRAASAVAQIRTLKVARFGDNMRNVAVTEGDKTEAEIRFGVSVNSWSVNELAEAVDAASEADVDVLIAEYLRLYNVAPELLPGAARHDSLRYGAKIELGLRSFLEAGDFGAFTTNFEDLGGLRQLPGLAVQRLMADGYGFGAEGDWKTAILIRAAKVMGEGLPGGASLMEDYTYHLVPGQEKILGAHMLEVCPSLTTAKPSLEVHPLGIGGREDPVRLVFDADPGAGVVVALSDMRERFRLTANKVEVVPLDEPLPNLPVARAVWKPLPDFATSAAAWLEAGAAHHTVMSTAVGIEAFQDFADIFEAELLVIDEDTTQRGFVREIRWNQAYYRLAQGF

Source

organism	Arthrobacter psychrolactophilus
ncbi_taxonomy_id	92442
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
formula_weight	122.1 kDa
src_method	syn
entity_count	6

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1189

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	triclinic

resolution	1.520 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	1.52 Å
resolution_method	—
num_particles	1732769

fit	/app/data/saxs_computation/vf/9vf5/9vf5.fit
pddf	/app/data/pr_computation/vf/9vf5/9vf5.pr.out
profile	/app/data/saxs_computation/vf/9vf5/9vf5.dat

Cryo-EM structure of apo form of Arthrobacter psychrolactophillus L-arabinose isomerase

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

EM 3D