SAXSdb — 9zpu

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ribokinase

Brucella suis 1330

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 9–312 Chain B； UniProt 9–312 Chain C； UniProt 9–312 Chain D； UniProt 9–312 Chain E； UniProt 9–312 Chain F； UniProt 9–312	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6 SO4 SULFATE ION × 43 CL CHLORIDE ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；Salt RX B6: 2.0M Ammonium citrate tribasic, 0.1M Bis-Tris Propane pH 7.0. BrsuA.01141.a.B2.PW39414 at 19.5 mg/mL. 2 mM ADP ane Ribose-5-phosphate were added prior to crystallization but only ADP was bound. plate clover plate BK 6, pg 3 position D1, Puck: PSL-0516, Cryo: 2.5M LiSO4	Resolution 2.85 Å R-free 0.259

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9ZPU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
11BL Crystal Structure of a Ribokinase from Brucella suis in complex ADP (P21 form) Deposited 2026-02-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 9–312（304 aa） Chain C 9–312（304 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；Grid Salt screen B1: 2.4 M AmSO4 + 0.3 M Tri-Sodium Citrate pH 4.0. BrsuA.01141.a.B2.PW39414 at 19.5 mg/mL. 2 mM ATP and MgCl2 were added prior to crystallization but only ADP was bound. Clover_Plate B6, BK 6, pg 3, Puck: PSL-1507, Cryo: 2.5M LiSO4	Resolution 2.90 Å R-free 0.286
11BL Crystal Structure of a Ribokinase from Brucella suis in complex ADP (P21 form) Deposited 2026-02-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 9–312（304 aa） Chain D 9–312（304 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 PO4 PHOSPHATE ION × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；Grid Salt screen B1: 2.4 M AmSO4 + 0.3 M Tri-Sodium Citrate pH 4.0. BrsuA.01141.a.B2.PW39414 at 19.5 mg/mL. 2 mM ATP and MgCl2 were added prior to crystallization but only ADP was bound. Clover_Plate B6, BK 6, pg 3, Puck: PSL-1507, Cryo: 2.5M LiSO4	Resolution 2.90 Å R-free 0.286
13JB Crystal Structure of a Ribokinase from Brucella suis in complex ATP (P21 form) Deposited 2026-05-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 9–312（304 aa） Chain B 9–312（304 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 SO4 SULFATE ION × 13	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；Grid Salt screen B1: 2.4 M AmSO4 + 0.3 M Tri-Sodium Citrate pH 4.0. BrsuA.01141.a.B2.PW39414 at 19.5 mg/mL. 2 mM ATP and MgCl2 were added prior to crystallization. CloverPlate A3/apo B6, pg 3, Puck: PSL-0713, Cryo: 2.5M LiSO4	Resolution 2.60 Å R-free 0.233

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A0H3GDY9_BRUSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 9–312； UniProt 9–312 Author chain B； PDBConstruct 9–312； UniProt 9–312 Author chain C； PDBConstruct 9–312； UniProt 9–312 Author chain D； PDBConstruct 9–312； UniProt 9–312 Author chain E； PDBConstruct 9–312； UniProt 9–312 Author chain F； PDBConstruct 9–312； UniProt 9–312

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9zpu
Deposition date deposition_date	2025-12-17
最后修订 last_revision	2025-12-31
Structure title title	Crystal Structure of a Ribokinase from Brucella suis in complex with ADP
Keywords keywords	SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, ribokinase, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	44.20 Å
Radius of gyration Rg (electron density) rg_electron	44.25 Å
Forward intensity I(0) i0	612462000.00
Molecular weight molecular_weight	191620.0 kDa
Excluded volume excluded_volume	235460 Å³
Envelope volume envelope_volume	331700 Å³
Hydration-shell volume shell_volume	64904 Å³
Envelope diameter envelope_diameter	159.1 Å
Shell Rg shell_rg	46.99 Å
Envelope Rg envelope_rg	43.16 Å
Shape Rg shape_rg	44.26 Å
Total Rg total_rg	44.37 Å
Total atoms total_atoms	13385
Residues n_residues	1830
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	150.1 Å
Rg (real space) rg_real	44.35 Å
Rg uncertainty (real space) rg_real_error	1.21 Å
I(0) (real space) i0_real	6.1250e+08
I(0) uncertainty (real space) i0_real_error	9.9300e+06
Rg (reciprocal space) rg_reciprocal	44.20 Å
I(0) (reciprocal space) i0_reciprocal	612400000.0000
Solution quality estimate total_estimate	0.8381
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	58.4 Å
Skewness Skewness skewness	0.486
Kurtosis Kurtosis kurtosis	0.026
Angular range angular_range	— – 0.1800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	103100000.0000
Real-space data points n_real_points	37
GNOM version gnom_version	4.1.3
Quality Criteria 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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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Ribokinase
Molecular weight formula_weight	32129.5 kDa
EC 编号 ec_number	2.7.1.15
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	13412

MAHHHHHHKIFVFGSVNVDVSARMAALPRPGQTVNASGYGIGLGGKGANQAVAVAKLGGAIRFVGAVGHDAFGELALKQMREFGLDTGSVRVIDDVDTGMAIIQVEETGQNTIAVCAGANARWSSADIDAYGADIAKARITLLQREVPHEANLAVAKAVRAAGGTVLLDPAPVGDASQMADLIALSDIISPNETEAAEITGIEPTDLASAEAAGRKLLERGPKIVILKLGSRGALLVTADEVKHFTPFKVKVVDTVAAGDSFNGGFAVAFSQARPLHDCVRYGSAAGAIAVTRVGAGAAAPTAREVEELIGR

来源 Source

来源生物 organism	Brucella suis 1330
NCBI Class编号 ncbi_taxonomy_id	204722
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	43

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	27

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8. Citations (1)

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Unit-cell length a length_a	225.093 Å
Unit-cell length b length_b	138.228 Å
Unit-cell length c length_c	80.872 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.04 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.850 Å
Low-resolution limit resolution_low	45.050 Å
R factor r_factor	0.1977
R_work r_work	0.1945
R_free 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

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

Ribokinase

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction