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13jb

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

Method: X-RAY DIFFRACTION D_max: 91.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	13jb
deposition_date	2026-05-08
last_revision	2026-05-20
title	Crystal Structure of a Ribokinase from Brucella suis in complex ATP (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	28.43 Å
rg_electron	27.96 Å
i0	74736700.00
molecular_weight	64354.0 kDa
excluded_volume	79231 Å³
envelope_volume	97961 Å³
shell_volume	30068 Å³
envelope_diameter	93.0 Å
shell_rg	34.70 Å
envelope_rg	27.79 Å
shape_rg	27.95 Å
total_rg	28.62 Å
total_atoms	4497
n_residues	610
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	91.4 Å
rg_real	28.55 Å
rg_real_error	0.63 Å
i0_real	7.4740e+07
i0_real_error	1.0420e+06
rg_reciprocal	28.52 Å
i0_reciprocal	74730000.0000
total_estimate	0.8706
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	27.7 Å
skewness	0.403
kurtosis	-0.579
angular_range	— – 0.2800 Å⁻¹
current_alpha	0.0000
highest_alpha	39450000.0000
n_real_points	57
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.836; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.922; Smooth: 0.884

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Ribokinase
formula_weight	32129.5 kDa
ec_number	2.7.1.15
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	4526

MAHHHHHHKIFVFGSVNVDVSARMAALPRPGQTVNASGYGIGLGGKGANQAVAVAKLGGAIRFVGAVGHDAFGELALKQMREFGLDTGSVRVIDDVDTGMAIIQVEETGQNTIAVCAGANARWSSADIDAYGADIAKARITLLQREVPHEANLAVAKAVRAAGGTVLLDPAPVGDASQMADLIALSDIISPNETEAAEITGIEPTDLASAEAAGRKLLERGPKIVILKLGSRGALLVTADEVKHFTPFKVKVVDTVAAGDSFNGGFAVAFSQARPLHDCVRYGSAAGAIAVTRVGAGAAAPTAREVEELIGR

Source

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

Entity 2 non-polymer

description	ADENOSINE-5'-TRIPHOSPHATE
formula_weight	507.2 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	13

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	29

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6. Citations (1)

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length_a	50.457 Å
length_b	78.895 Å
length_c	78.120 Å
angle_alpha	90.00 °
angle_beta	108.17 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.600 Å
resolution_low	74.230 Å
r_factor	0.2046
r_work	0.2030
r_free	0.2326

fit	/app/data/saxs_computation/3j/13jb/13jb.fit
pddf	/app/data/pr_computation/3j/13jb/13jb.pr.out
profile	/app/data/saxs_computation/3j/13jb/13jb.dat

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

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