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9v68

Crystal structure of Phaeodactylibacter sp. Phosphoglucomutase

Method: X-RAY DIFFRACTION D_max: 73.2 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9v68
deposition_date	2025-05-27
last_revision	2026-06-10
title	Crystal structure of Phaeodactylibacter sp. Phosphoglucomutase
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	23.97 Å
rg_electron	22.81 Å
i0	59827000.00
molecular_weight	59297.0 kDa
excluded_volume	73752 Å³
envelope_volume	85239 Å³
shell_volume	30059 Å³
envelope_diameter	75.4 Å
shell_rg	30.67 Å
envelope_rg	22.94 Å
shape_rg	22.79 Å
total_rg	23.72 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	73.2 Å
rg_real	23.80 Å
rg_real_error	0.40 Å
i0_real	5.9830e+07
i0_real_error	6.9410e+05
rg_reciprocal	23.84 Å
i0_reciprocal	59830000.0000
total_estimate	0.9049
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	29.7 Å
skewness	0.125
kurtosis	-0.513
angular_range	— – 0.3300 Å⁻¹
current_alpha	0.0000
highest_alpha	12520000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.929; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.988

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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	4667

MALHPQAGKTATPDQLVNIPRLITAYFTGQPDPSVREQRVSFGTSGHRGSSLNRSFNEQHILATTQAICLYRQKEGINGPVFMGIDSHALSEPAQATALEVLAANGVETMIAAGDEYTPTPAVSQAILAYNRGRAGGLADGIVITPSHNPPEDGGFKYNMTNGGPAESNVTAWIEAKANELLENGLREVKRIPFQRAMKASTTHRYDYLGAYVNGLGQVIDMDAIRSSGLEMGVDPLGGAGVHYWGHIADHYRLNLTVVDTEVDPTFRFMSLDWDGKIRMDPSSPYAMQRLIRLKDDYPVAFACDTDHDRHGIVTRSAGLMPPNHYLAVAIDYLFRHRPKWKPETGIGKTLVSSQMIDRVAARLGRKLVEVPVGFKWFVDGLFDGSLGFGGEESAGASFLDREGNAWSTDKDGIIAALLAGEITARTGKDPGEIYREFTREFGEPAYGRIDAPATPAQKDKLKKLSREQVTSSQLAGEKIEAILTEAPGNGASIGGLKAVTANGWFAARPSGTEDIYKIYAESFKGEEHLRQLQKEAQELVDRVIG

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 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	485

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6. Citations (1)

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length_a	117.252 Å
length_b	59.314 Å
length_c	96.835 Å
angle_alpha	90.00 °
angle_beta	116.31 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	1.580 Å
resolution_low	49.370 Å
r_factor	0.1641
r_work	0.1636
r_free	0.1836

fit	/app/data/saxs_computation/v6/9v68/9v68.fit
pddf	/app/data/pr_computation/v6/9v68/9v68.pr.out
profile	/app/data/saxs_computation/v6/9v68/9v68.dat

Crystal structure of Phaeodactylibacter sp. Phosphoglucomutase

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