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11bl

Crystal Structure of a Ribokinase from Brucella suis in complex ADP (P21 form)

Method: X-RAY DIFFRACTION D_max: 119.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	11bl
deposition_date	2026-02-16
last_revision	2026-02-25
title	Crystal Structure of a Ribokinase from Brucella suis in complex ADP (P21 form)
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	38.24 Å
rg_electron	37.85 Å
i0	219372000.00
molecular_weight	116390.0 kDa
excluded_volume	144150 Å³
envelope_volume	201060 Å³
shell_volume	43671 Å³
envelope_diameter	120.1 Å
shell_rg	45.11 Å
envelope_rg	36.41 Å
shape_rg	37.86 Å
total_rg	38.25 Å
total_atoms	8182
n_residues	1186
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	119.5 Å
rg_real	38.08 Å
rg_real_error	1.10 Å
i0_real	2.1940e+08
i0_real_error	4.3780e+06
rg_reciprocal	38.18 Å
i0_reciprocal	219400000.0000
total_estimate	0.8840
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	58.3 Å
skewness	0.032
kurtosis	-0.754
angular_range	— – 0.2050 Å⁻¹
current_alpha	0.0000
highest_alpha	113200000.0000
n_real_points	42
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.859; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.916

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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	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	8193

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	4

Entity 3 non-polymer

description	PHOSPHATE ION
formula_weight	95.0 kDa
src_method	syn
entity_count	3

Entity 4 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	3

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	11

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6. Citations (1)

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length_a	78.363 Å
length_b	81.851 Å
length_c	100.634 Å
angle_alpha	90.00 °
angle_beta	106.31 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.900 Å
resolution_low	47.090 Å
r_factor	0.2470
r_work	0.2449
r_free	0.2860

fit	/app/data/saxs_computation/1b/11bl/11bl.fit
pddf	/app/data/pr_computation/1b/11bl/11bl.pr.out
profile	/app/data/saxs_computation/1b/11bl/11bl.dat