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9vfz

Crystal structure of Phaeodactylibacter sp. phosphoglucomutase in complex with glucose-1-phosphate

Method: X-RAY DIFFRACTION D_max: 70.0 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vfz
deposition_date	2025-06-12
last_revision	2026-05-13
title	Crystal structure of Phaeodactylibacter sp. phosphoglucomutase in complex with glucose-1-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	23.76 Å
rg_electron	22.61 Å
i0	60759500.00
molecular_weight	59557.0 kDa
excluded_volume	74005 Å³
envelope_volume	85598 Å³
shell_volume	30282 Å³
envelope_diameter	77.2 Å
shell_rg	30.67 Å
envelope_rg	22.87 Å
shape_rg	22.59 Å
total_rg	23.54 Å
total_atoms	8304
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	70.0 Å
rg_real	23.59 Å
rg_real_error	0.10 Å
i0_real	5.8640e+07
i0_real_error	5.5640e+05
rg_reciprocal	23.64 Å
i0_reciprocal	60760000.0000
total_estimate	0.7182
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	29.5 Å
skewness	0.157
kurtosis	-0.465
angular_range	— – 0.3350 Å⁻¹
current_alpha	8.1850
highest_alpha	14880000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.960; Stabil: 0.914; Sysdev: 0.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.746

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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	8357

MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSMALHPQAGKTATPDQLVNIPRLITAYFTGQPDPSVREQRVSFGTSGHRGSSLNRSFNEQHILATTQAICLYRQKEGINGPVFMGIDSHALSEPAQATALEVLAANGVETMIAAGDEYTPTPAVSQAILAYNRGRAGGLADGIVITPSHNPPEDGGFKYNMTNGGPAESNVTAWIEAKANELLENGLREVKRIPFQRAMKASTTHRYDYLGAYVNGLGQVIDMDAIRSSGLEMGVDPLGGAGVHYWGHIADHYRLNLTVVDTEVDPTFRFMSLDWDGKIRMDPSSPYAMQRLIRLKDDYPVAFACDTDHDRHGIVTRSAGLMPPNHYLAVAIDYLFRHRPKWKPETGIGKTLVSSQMIDRVAARLGRKLVEVPVGFKWFVDGLFDGSLGFGGEESAGASFLDREGNAWSTDKDGIIAALLAGEITARTGKDPGEIYREFTREFGEPAYGRIDAPATPAQKDKLKKLSREQVTSSQLAGEKIEAILTEAPGNGASIGGLKAVTANGWFAARPSGTEDIYKIYAESFKGEEHLRQLQKEAQELVDRVIGLEHHHHHH

Source

organism	Phaeodactylibacter sp.
ncbi_taxonomy_id	1940289
host_organism	Escherichia coli

Entity 2 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

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

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	53

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6. Citations (1)

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length_a	108.970 Å
length_b	58.966 Å
length_c	99.517 Å
angle_alpha	90.00 °
angle_beta	118.22 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	1.950 Å
resolution_low	49.160 Å
r_factor	0.2769
r_work	0.2724
r_free	0.3586

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

Crystal structure of Phaeodactylibacter sp. phosphoglucomutase in complex with glucose-1-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