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9zpu

Crystal Structure of a Ribokinase from Brucella suis in complex with ADP

Method: X-RAY DIFFRACTION D_max: 150.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zpu
deposition_date	2025-12-17
last_revision	2025-12-31
title	Crystal Structure of a Ribokinase from Brucella suis in complex with ADP
keywords	SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, ribokinase, TRANSFERASE; TRANSFERASE
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	44.20 Å
rg_electron	44.25 Å
i0	612462000.00
molecular_weight	191620.0 kDa
excluded_volume	235460 Å³
envelope_volume	331700 Å³
shell_volume	64904 Å³
envelope_diameter	159.1 Å
shell_rg	46.99 Å
envelope_rg	43.16 Å
shape_rg	44.26 Å
total_rg	44.37 Å
total_atoms	13385
n_residues	1830
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	150.1 Å
rg_real	44.35 Å
rg_real_error	1.21 Å
i0_real	6.1250e+08
i0_real_error	9.9300e+06
rg_reciprocal	44.20 Å
i0_reciprocal	612400000.0000
total_estimate	0.8381
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	58.4 Å
skewness	0.486
kurtosis	0.026
angular_range	— – 0.1800 Å⁻¹
current_alpha	0.0000
highest_alpha	103100000.0000
n_real_points	37
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.775; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.577

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Ribokinase
formula_weight	32129.5 kDa
ec_number	2.7.1.15
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F
atom_count	13412

MAHHHHHHKIFVFGSVNVDVSARMAALPRPGQTVNASGYGIGLGGKGANQAVAVAKLGGAIRFVGAVGHDAFGELALKQMREFGLDTGSVRVIDDVDTGMAIIQVEETGQNTIAVCAGANARWSSADIDAYGADIAKARITLLQREVPHEANLAVAKAVRAAGGTVLLDPAPVGDASQMADLIALSDIISPNETEAAEITGIEPTDLASAEAAGRKLLERGPKIVILKLGSRGALLVTADEVKHFTPFKVKVVDTVAAGDSFNGGFAVAFSQARPLHDCVRYGSAAGAIAVTRVGAGAAAPTAREVEELIGR

Source

organism	Brucella suis 1330
ncbi_taxonomy_id	204722
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	ADENOSINE-5'-DIPHOSPHATE
formula_weight	427.2 kDa
src_method	syn
entity_count	6

Entity 3 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	43

Entity 4 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	7

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	27

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6. Citations (1)

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length_a	225.093 Å
length_b	138.228 Å
length_c	80.872 Å
angle_alpha	90.00 °
angle_beta	107.04 °
angle_gamma	90.00 °
z_pdb	24

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.850 Å
resolution_low	45.050 Å
r_factor	0.1977
r_work	0.1945
r_free	0.2586

fit	/app/data/saxs_computation/zp/9zpu/9zpu.fit
pddf	/app/data/pr_computation/zp/9zpu/9zpu.pr.out
profile	/app/data/saxs_computation/zp/9zpu/9zpu.dat