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9r5u

The structure of CaPGI in complex with fragments

Method: X-RAY DIFFRACTION D_max: 83.5 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9r5u
deposition_date	2025-05-09
last_revision	2026-05-20
title	The structure of CaPGI in complex with fragments
keywords	Candida, fragment, PGI, 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	29.04 Å
rg_electron	28.07 Å
i0	451004000.00
molecular_weight	114600.0 kDa
excluded_volume	111330 Å³
envelope_volume	175040 Å³
shell_volume	48316 Å³
envelope_diameter	89.7 Å
shell_rg	38.02 Å
envelope_rg	28.22 Å
shape_rg	28.05 Å
total_rg	28.76 Å
total_atoms	8706
n_residues	1100
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	83.5 Å
rg_real	28.82 Å
rg_real_error	0.30 Å
i0_real	4.5100e+08
i0_real_error	6.0810e+06
rg_reciprocal	28.92 Å
i0_reciprocal	451000000.0000
total_estimate	0.9062
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	37.9 Å
skewness	0.043
kurtosis	-0.545
angular_range	— – 0.2750 Å⁻¹
current_alpha	0.0000
highest_alpha	93310000.0000
n_real_points	56
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.962; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.966; Smooth: 0.923

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Glucose-6-phosphate isomerase
formula_weight	61670.4 kDa
ec_number	5.3.1.9
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	9463

GPLGSMASFKLATDLPEWKKLEETYKSVGEKFSVRDAFAKDPKRFEEFSWIYKNYDDSKILFDFSKNLVNKEILDQLVTLAKEAGVEKLRDAMFAGDHINTTEDRAVYHVALRNRALRKMPVDGKDTAQEVDDVLKHMKEFSDSIRDGSWTGYTGKSITDVVNIGIGGSDLGPVMVTEALKAYSKPGLNVHFISNIDGTHTAETLKNLNPETTLFLIASKTFTTAETITNATSAKNWFLATAKDSKHIAKHFAALSTNEKEVVAFGIDAKNMFGFESWVGGRYSVWSAIGLSVAIYIGFENFNDFLKGAEAMDQHFLTTPLENNIPVIGGLLSVWYNNFFGAQTHLVVPFDQYLHRFPAYLQQLSMESNGKSVTRANVFTNYQTGTILFGEPATNAQHSFFQLVHQGTKLIPADFILAAQSHNPIEKNLHQRMLASNFFAQSEALMVGKDEAKVKAEGATGGLVPHKEFSGNRPTTSILAQKITPATLGSLIAYYEHLTFTEGAIWNINSFDQWGVELGKVLAKVIGKELDDKKAVATHDASTNGLINQFKEWEE

Source

organism	Candida albicans
ncbi_taxonomy_id	5476
host_organism	Escherichia coli

Entity 2 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	6

Entity 3 non-polymer

description	[(2~{R},3~{R},4~{R},5~{S})-3,4,5-tris(oxidanyl)piperidin-2-yl]methyl dihydrogen phosphate
formula_weight	243.2 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	N-propan-2-ylurea
formula_weight	102.1 kDa
src_method	syn
entity_count	5

Entity 5 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	737

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6. Citations (1)

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length_a	87.310 Å
length_b	101.440 Å
length_c	139.130 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	1.700 Å
resolution_low	59.760 Å
r_factor	0.1860
r_work	0.1842
r_free	0.2206

fit	/app/data/saxs_computation/r5/9r5u/9r5u.fit
pddf	/app/data/pr_computation/r5/9r5u/9r5u.pr.out
profile	/app/data/saxs_computation/r5/9r5u/9r5u.dat