SAXSdb — 9yfi

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

UTP--glucose-1-phosphate uridylyltransferase

Bordetella pertussis Tohama I

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 26–302 Chain B； UniProt 26–302	Not recorded	SO4 SULFATE ION × 2 MG MAGNESIUM ION × 1 UPG URIDINE-5'-DIPHOSPHATE-GLUCOSE × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；Berkeley B5: 200mM Lithium Sulfate, 20% PEG 3350. BopeA.00118.a.B2.PW39372 at 25.3 mg/mL. 2mM URIDINE-5'-DIPHOSPHATE-GLUCOSE (UPG) + 2mM MgCl2 added to protein prior to crystallization. plate 19925 B5 drop 2, Puck: PSL-0708, Cryo: 80% crystallant + 20% glycerol	Resolution 1.80 Å R-free 0.199

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 9YFI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9O90 Crystal structure of UTP--glucose-1-phosphate uridylyltransferase from Bordetella pertussis Deposited 2025-04-17	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 26–302（277 aa） Chain B 26–302（277 aa）	Not recorded	GLY GLYCINE × 4 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；Morpheus H5: 20% PEG 550 MME, 10% PEG 20K, 0.1M HEPES/MOPS, pH 7.5, 20mM each of DL-Alanine, Glycine, DL-Lysine, DL-Serine, DL-Glutamic acid. BopeA.00118.a.B2.PW39372 at 25.3 mg/mL. plate 19783 H5 drop 1, Puck: PSL-1103, Cryo: direct.	Resolution 1.93 Å R-free 0.215
9YFB Crystal Structure UTP--glucose-1-phosphate uridylyltransferase from Bordetella pertussis in complex with UTP Deposited 2025-09-25	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 26–302（277 aa） Fragment：26-302	Not recorded	MG MAGNESIUM ION × 4 UTP URIDINE 5'-TRIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；Berkeley B9: 100mM Bis-Tris/HCL pH 6.5, 200mM Magnesium chloride, 25% PEG 3550. BopeA.00118.a.B2.PW39372 at 25.3 mg/mL. 2mM UTP + 2mM MgCl2 added to protein prior to crystallization. plate 19925 B9 drop 1, Puck: PSL-0706, Cryo: 80% crystallant + 20% glycerol	Resolution 1.82 Å R-free 0.232
9YFK Crystal Structure UTP--glucose-1-phosphate uridylyltransferase from Bordetella pertussis in complex with URIDINE-5'-DIPHOSPHATE-GLUCOSE (twinned lattice) Deposited 2025-09-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 26–302（277 aa） Fragment：26-302 Chain B 26–302（277 aa） Fragment：26-302	Not recorded	UPG URIDINE-5'-DIPHOSPHATE-GLUCOSE × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；Berkeley B1: 30% PEG 3350, 400 mM NaCl, 100 mM Tris, pH 8.5. BopeA.00118.a.B2.PW39372 at 25.3 mg/mL. 2mM UTP, 2mM D-glucose-1-phosphate and 2mM MgCl2 added to protein prior to crystallization. The product URIDINE-5'-DIPHOSPHATE-GLUCOSE (UPG) was bound. plate 19925 B1 drop 3, Puck: PSL-0713, Cryo: 80% crystallant + 20% glycerol	Resolution 1.68 Å R-free 0.204
9YGK Crystal Structure UTP--glucose-1-phosphate uridylyltransferase from Bordetella pertussis (sulfate bound) Deposited 2025-09-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 26–302（277 aa） Fragment：26-302 Chain B 26–302（277 aa） Fragment：26-302	Not recorded	SO4 SULFATE ION × 19 CL CHLORIDE ION × 3 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；Index B6: 0.1M HEPES pH 7.0, 1.4M Sodium citrate tribasic dihydrate. BopeA.00118.a.B2.PW39372 at 25.3 mg/mL. plate 19780 B6 drop 1, Puck: PSL-1201, Cryo: 2.5M Lithium Sulfate	Resolution 1.95 Å R-free 0.223

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q7VTV0_BORPE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 9–285； UniProt 26–302 Author chain B； PDBConstruct 9–285； UniProt 26–302

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	9yfi
Deposition date deposition_date	2025-09-26
最后修订 last_revision	2025-10-08
Structure title title	Crystal Structure UTP--glucose-1-phosphate uridylyltransferase from Bordetella pertussis in complex with URIDINE-5'-DIPHOSPHATE-GLUCOSE
Keywords keywords	SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, 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	26.70 Å
Radius of gyration Rg (electron density) rg_electron	25.90 Å
Forward intensity I(0) i0	57984300.00
Molecular weight molecular_weight	59696.0 kDa
Excluded volume excluded_volume	74975 Å³
Envelope volume envelope_volume	88138 Å³
Hydration-shell volume shell_volume	29250 Å³
Envelope diameter envelope_diameter	89.9 Å
Shell Rg shell_rg	32.59 Å
Envelope Rg envelope_rg	25.96 Å
Shape Rg shape_rg	25.94 Å
Total Rg total_rg	26.47 Å
Total atoms total_atoms	4195
Residues n_residues	540
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	87.4 Å
Rg (real space) rg_real	26.82 Å
Rg uncertainty (real space) rg_real_error	0.67 Å
I(0) (real space) i0_real	5.7980e+07
I(0) uncertainty (real space) i0_real_error	8.7630e+05
Rg (reciprocal space) rg_reciprocal	26.79 Å
I(0) (reciprocal space) i0_reciprocal	57980000.0000
Solution quality estimate total_estimate	0.8641
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.1 Å
Skewness Skewness skewness	0.519
Kurtosis Kurtosis kurtosis	-0.181
Angular range angular_range	— – 0.2950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	15130000.0000
Real-space data points n_real_points	60
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.816; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.950; Smooth: 0.831

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	UTP--glucose-1-phosphate uridylyltransferase
Molecular weight formula_weight	30991.6 kDa
EC 编号 ec_number	2.7.7.9
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4472

MAHHHHHHVVRKAVFPVAGMGTRFLPATKAMPKEMLPVVDKPLIQYAVEEAVAAGITDLIFVTGRNKRAIEDHFDAAPELETDLEAKGKHELLALVRDILPAHVNCLYIRQSAPLGLGHAVLTAAPAVGNEPFAVLLADDLIDADTPVLKQLIDVAVARQGSVLGVQEVPREDTRKYGIVASQPVDARTERVTHIVEKPAPEQAPTTLAVVGRYVLEAAIFDHLRATTVGAGNEIQLTDGIAALLRERDVYAHRYDGKRYDCGSKAGMFQATVALGRKYHGLIPE

来源 Source

来源生物 organism	Bordetella pertussis Tohama I
NCBI Class编号 ncbi_taxonomy_id	257313
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	URIDINE-5'-DIPHOSPHATE-GLUCOSE
Molecular weight formula_weight	566.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	260

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8. Citations (1)

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Unit-cell length a length_a	93.234 Å
Unit-cell length b length_b	71.301 Å
Unit-cell length c length_c	95.027 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.86 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	47.510 Å
R factor r_factor	0.1728
R_work r_work	0.1714
R_free r_free	0.1994

fit	/app/data/saxs_computation/yf/9yfi/9yfi.fit
pddf	/app/data/pr_computation/yf/9yfi/9yfi.pr.out
profile	/app/data/saxs_computation/yf/9yfi/9yfi.dat

Crystal Structure UTP--glucose-1-phosphate uridylyltransferase from Bordetella pertussis in complex with URIDINE-5'-DIPHOSPHATE-GLUCOSE

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

UTP--glucose-1-phosphate uridylyltransferase

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