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9vga

Crystal structure of Phaeodactylibacter sp. phosphoglucomutase in complex with manganese ion

Method: X-RAY DIFFRACTION D_max: 74.1 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vga
deposition_date	2025-06-13
last_revision	2026-05-13
title	Crystal structure of Phaeodactylibacter sp. phosphoglucomutase in complex with manganese ion
keywords	Metal-binding, Phosphoserine, Isomerase; ISOMERASE
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	23.89 Å
rg_electron	22.74 Å
i0	60069300.00
molecular_weight	59328.0 kDa
excluded_volume	73767 Å³
envelope_volume	84884 Å³
shell_volume	30001 Å³
envelope_diameter	77.2 Å
shell_rg	30.68 Å
envelope_rg	22.94 Å
shape_rg	22.71 Å
total_rg	23.65 Å
total_atoms	4182
n_residues	545
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	74.1 Å
rg_real	23.73 Å
rg_real_error	0.38 Å
i0_real	6.0070e+07
i0_real_error	7.1600e+05
rg_reciprocal	23.77 Å
i0_reciprocal	60070000.0000
total_estimate	0.9005
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	30.1 Å
skewness	0.137
kurtosis	-0.492
angular_range	— – 0.3300 Å⁻¹
current_alpha	0.0000
highest_alpha	12910000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.913; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.975

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Phosphoglucomutase (Alpha-D-glucose-1,6-bisphosphate-dependent)
formula_weight	59502.8 kDa
ec_number	5.4.2.2
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4478

MALHPQAGKTATPDQLVNIPRLITAYFTGQPDPSVREQRVSFGTSGHRGSSLNRSFNEQHILATTQAICLYRQKEGINGPVFMGIDSHALSEPAQATALEVLAANGVETMIAAGDEYTPTPAVSQAILAYNRGRAGGLADGIVITPSHNPPEDGGFKYNMTNGGPAESNVTAWIEAKANELLENGLREVKRIPFQRAMKASTTHRYDYLGAYVNGLGQVIDMDAIRSSGLEMGVDPLGGAGVHYWGHIADHYRLNLTVVDTEVDPTFRFMSLDWDGKIRMDPSSPYAMQRLIRLKDDYPVAFACDTDHDRHGIVTRSAGLMPPNHYLAVAIDYLFRHRPKWKPETGIGKTLVSSQMIDRVAARLGRKLVEVPVGFKWFVDGLFDGSLGFGGEESAGASFLDREGNAWSTDKDGIIAALLAGEITARTGKDPGEIYREFTREFGEPAYGRIDAPATPAQKDKLKKLSREQVTSSQLAGEKIEAILTEAPGNGASIGGLKAVTANGWFAARPSGTEDIYKIYAESFKGEEHLRQLQKEAQELVDRVIG

Source

organism	Phaeodactylibacter sp.
ncbi_taxonomy_id	1940289
host_organism	Escherichia coli

Entity 2 non-polymer

description	MANGANESE (II) ION
formula_weight	54.9 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	296

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6. Citations (1)

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length_a	61.657 Å
length_b	101.706 Å
length_c	168.361 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 2 2 21
int_tables_number	20
crystal_system	orthorhombic

resolution	1.820 Å
resolution_low	52.730 Å
r_factor	0.2521
r_work	0.2494
r_free	0.3097

fit	/app/data/saxs_computation/vg/9vga/9vga.fit
pddf	/app/data/pr_computation/vg/9vga/9vga.pr.out
profile	/app/data/saxs_computation/vg/9vga/9vga.dat

Crystal structure of Phaeodactylibacter sp. phosphoglucomutase in complex with manganese ion

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