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9vfy

Crystal structure of Phaeodactylibacter sp. phosphoglucomutase in complex with glucose-6-phosphate

Method: X-RAY DIFFRACTION D_max: 76.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vfy
deposition_date	2025-06-12
last_revision	2026-04-15
title	Crystal structure of Phaeodactylibacter sp. phosphoglucomutase in complex with glucose-6-phosphate
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	23.70 Å
rg_electron	22.56 Å
i0	60670100.00
molecular_weight	59557.0 kDa
excluded_volume	74005 Å³
envelope_volume	84489 Å³
shell_volume	29987 Å³
envelope_diameter	76.0 Å
shell_rg	30.57 Å
envelope_rg	22.81 Å
shape_rg	22.54 Å
total_rg	23.48 Å
total_atoms	4198
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	76.6 Å
rg_real	23.54 Å
rg_real_error	0.28 Å
i0_real	6.0670e+07
i0_real_error	6.9750e+05
rg_reciprocal	23.58 Å
i0_reciprocal	60670000.0000
total_estimate	0.8893
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	29.9 Å
skewness	0.148
kurtosis	-0.472
angular_range	— – 0.3350 Å⁻¹
current_alpha	0.0001
highest_alpha	15110000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.854; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.999

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Phosphoglucomutase (Alpha-D-glucose-1,6-bisphosphate-dependent)
formula_weight	64126.9 kDa
ec_number	5.4.2.2
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4437

MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSMALHPQAGKTATPDQLVNIPRLITAYFTGQPDPSVREQRVSFGTSGHRGSSLNRSFNEQHILATTQAICLYRQKEGINGPVFMGIDSHALSEPAQATALEVLAANGVETMIAAGDEYTPTPAVSQAILAYNRGRAGGLADGIVITPSHNPPEDGGFKYNMTNGGPAESNVTAWIEAKANELLENGLREVKRIPFQRAMKASTTHRYDYLGAYVNGLGQVIDMDAIRSSGLEMGVDPLGGAGVHYWGHIADHYRLNLTVVDTEVDPTFRFMSLDWDGKIRMDPSSPYAMQRLIRLKDDYPVAFACDTDHDRHGIVTRSAGLMPPNHYLAVAIDYLFRHRPKWKPETGIGKTLVSSQMIDRVAARLGRKLVEVPVGFKWFVDGLFDGSLGFGGEESAGASFLDREGNAWSTDKDGIIAALLAGEITARTGKDPGEIYREFTREFGEPAYGRIDAPATPAQKDKLKKLSREQVTSSQLAGEKIEAILTEAPGNGASIGGLKAVTANGWFAARPSGTEDIYKIYAESFKGEEHLRQLQKEAQELVDRVIGLEHHHHHH

Source

organism	Phaeodactylibacter sp.
ncbi_taxonomy_id	1940289
host_organism	Escherichia coli

Entity 2 non-polymer

description	6-O-phosphono-alpha-D-glucopyranose
formula_weight	260.1 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	239

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6. Citations (1)

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length_a	108.904 Å
length_b	59.206 Å
length_c	99.542 Å
angle_alpha	90.00 °
angle_beta	118.05 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	1.970 Å
resolution_low	48.060 Å
r_factor	0.1766
r_work	0.1742
r_free	0.2222

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

Crystal structure of Phaeodactylibacter sp. phosphoglucomutase in complex with glucose-6-phosphate

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