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9zw5

Ubiquitous Bacterial Kinase - UbK1 from Porphyromonas gingivalis

Method: X-RAY DIFFRACTION D_max: 75.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zw5
deposition_date	2026-01-01
title	Ubiquitous Bacterial Kinase - UbK1 from Porphyromonas gingivalis
keywords	Ubiquitous bacterial Kinase, Porohyromonas gingivalis, protein phosphorylation, PorX, CYTOSOLIC PROTEIN; CYTOSOLIC PROTEIN
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	22.60 Å
rg_electron	21.67 Å
i0	18568700.00
molecular_weight	32063.0 kDa
excluded_volume	39758 Å³
envelope_volume	48475 Å³
shell_volume	19502 Å³
envelope_diameter	75.6 Å
shell_rg	27.25 Å
envelope_rg	21.68 Å
shape_rg	21.65 Å
total_rg	22.46 Å
total_atoms	2248
n_residues	282
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	75.8 Å
rg_real	22.65 Å
rg_real_error	0.52 Å
i0_real	1.8570e+07
i0_real_error	2.3600e+05
rg_reciprocal	22.64 Å
i0_reciprocal	18570000.0000
total_estimate	0.8775
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	23.0 Å
skewness	0.402
kurtosis	-0.368
angular_range	— – 0.3500 Å⁻¹
current_alpha	0.0000
highest_alpha	4709000.0000
n_real_points	67
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.820; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.963; Smooth: 0.981

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	tRNA threonylcarbamoyladenosine biosynthesis protein TsaE
formula_weight	15907.8 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	2279

GSHMNTITIDSTSDLGRAARDFIALMGDNTVFAFYAPMGTGKTTFIKAVCEELGVSDVINSPTFSIINEYRSDQTGELIYHFDCYRLNKIENALNLGVEDYFDSGSLCFIEWPELLEPILPNDTVHVRIEELEDGKRRLTF

Source

organism	Porphyromonas gingivalis ATCC 33277
ncbi_taxonomy_id	431947
host_organism	Escherichia coli BL21

Entity 2 non-polymer

description	MANGANESE (II) ION
formula_weight	54.9 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	PHOSPHATE ION
formula_weight	95.0 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	18

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6. Citations (1)

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length_a	46.856 Å
length_b	47.788 Å
length_c	96.997 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 2 21
int_tables_number	18
crystal_system	—

resolution	2.600 Å
resolution_low	42.230 Å
r_factor	0.1925
r_work	0.1892
r_free	0.2544

fit	/app/data/saxs_computation/zw/9zw5/9zw5.fit
pddf	/app/data/pr_computation/zw/9zw5/9zw5.pr.out
profile	/app/data/saxs_computation/zw/9zw5/9zw5.dat

Ubiquitous Bacterial Kinase - UbK1 from Porphyromonas gingivalis

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