SAXSdb — 1dli

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

UDP-GLUCOSE DEHYDROGENASE

Streptococcus pyogenes

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 1–402	Not recorded	SO4 SULFATE ION × 6 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 UDX URIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE × 2 GOL GLYCEROL × 6	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；298 K；AMMONIUM SULPHATE, GLYCEROL, TRIS-HCL, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.31 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 1DLI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DLJ THE FIRST STRUCTURE OF UDP-GLUCOSE DEHYDROGENASE (UDPGDH) REVEALS THE CATALYTIC RESIDUES NECESSARY FOR THE TWO-FOLD OXIDATION Deposited 1999-12-09	Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–402（402 aa）	Mutation：C260S	SO4 SULFATE ION × 6 NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 2 UGA URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID × 2 GOL GLYCEROL × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；298 K；AMMONIUM SULPHATE, GLYCEROL, TRIS-HCL, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.80 Å R-free 0.213

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	UDG_STRPY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–402； UniProt 1–402

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	1dli
Deposition date deposition_date	1999-12-09
Structure title title	THE FIRST STRUCTURE OF UDP-GLUCOSE DEHYDROGENASE (UDPGDH) REVEALS THE CATALYTIC RESIDUES NECESSARY FOR THE TWO-FOLD OXIDATION
Keywords keywords	ROSSMANN FOLD, TERNARY COMPLEX, CRYSTALLOGRAPHIC DIMER, OXIDOREDUCTASE; OXIDOREDUCTASE
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	23.54 Å
Radius of gyration Rg (electron density) rg_electron	22.79 Å
Forward intensity I(0) i0	37004600.00
Molecular weight molecular_weight	47249.0 kDa
Excluded volume excluded_volume	59354 Å³
Envelope volume envelope_volume	70293 Å³
Hydration-shell volume shell_volume	25597 Å³
Envelope diameter envelope_diameter	82.3 Å
Shell Rg shell_rg	29.79 Å
Envelope Rg envelope_rg	23.09 Å
Shape Rg shape_rg	22.78 Å
Total Rg total_rg	23.65 Å
Total atoms total_atoms	3314
Residues n_residues	402
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	77.7 Å
Rg (real space) rg_real	23.52 Å
Rg uncertainty (real space) rg_real_error	0.61 Å
I(0) (real space) i0_real	3.7000e+07
I(0) uncertainty (real space) i0_real_error	5.7710e+05
Rg (reciprocal space) rg_reciprocal	23.52 Å
I(0) (reciprocal space) i0_reciprocal	37000000.0000
Solution quality estimate total_estimate	0.8073
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.9 Å
Skewness Skewness skewness	0.356
Kurtosis Kurtosis kurtosis	-0.299
Angular range angular_range	— – 0.3350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7927000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.834; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.000

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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	UDP-GLUCOSE DEHYDROGENASE
Molecular weight formula_weight	45537.1 kDa
EC 编号 ec_number	1.1.1.22
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3607

MKIAVAGSGYVGLSLGVLLSLQNEVTIVDILPSKVDKINNGLSPIQDEYIEYYLKSKQLSIKATLDSKAAYKEAELVIIATPTNYNSRINYFDTQHVETVIKEVLSVNSHATLIIKSTIPIGFITEMRQKFQTDRIIFSPEFLRESKALYDNLYPSRIIVSCEENDSPKVKADAEKFALLLKSAAKKNNVPVLIMGASEAEAVKLFANTYLALRVAYFNELDTYAESRKLNSHMIIQGISYDDRIGMHYNNPSFGYGGYCLPKDTKQLLANYNNIPQTLIEAIVSSNNVRKSYIAKQIINVLKEQESPVKVVGVYRLIMKSNSDNFRESAIKDVIDILKSKDIKIIIYEPMLNKLESEDQSVLVNDLENFKKQANIIVTNRYDNELQDVKNKVYSRDIFGRD

来源 Source

来源生物 organism	Streptococcus pyogenes
NCBI Class编号 ncbi_taxonomy_id	1314
宿主生物 host_organism	Escherichia coli

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	3

Entity 3 Entity 3 non-polymer

Description description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Molecular weight formula_weight	663.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	URIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE
Molecular weight formula_weight	536.3 kDa
Source method src_method	syn
Copy count entity_count	1

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	3

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	280

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1dlia1
Class class	a — All alpha proteins
Fold Fold fold	a.100 — 6-phosphogluconate dehydrogenase C-terminal domain-like
Superfamily Superfamily superfamily	a.100.1 — 6-phosphogluconate dehydrogenase C-terminal domain-like
Family Family family	a.100.1.4 — UDP-glucose/GDP-mannose dehydrogenase dimerisation domain

Domain ID domain_id	d1dlia2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.6 — 6-phosphogluconate dehydrogenase-like, N-terminal domain

Domain ID domain_id	d1dlia3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
Superfamily Superfamily superfamily	c.26.3 — UDP-glucose/GDP-mannose dehydrogenase C-terminal domain
Family Family family	c.26.3.1 — UDP-glucose/GDP-mannose dehydrogenase C-terminal domain

CATH v4.4 (3 domains)

Domain ID domain_id	1dliA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	1dliA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	1dliA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1040 — N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2
Homologous superfamily homologous superfamily	10 — N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2

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8. Citations (1)

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Unit-cell length a length_a	106.601 Å
Unit-cell length b length_b	106.601 Å
Unit-cell length c length_c	81.592 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 4 21 2
Space-group number int_tables_number	90
Crystal system crystal_system	—

Resolution resolution	2.310 Å
Low-resolution limit resolution_low	24.230 Å
R factor r_factor	0.1860
R_work r_work	0.1860
R_free r_free	0.2590

fit	/app/data/saxs_computation/dl/1dli/1dli.fit
pddf	/app/data/pr_computation/dl/1dli/1dli.pr.out
profile	/app/data/saxs_computation/dl/1dli/1dli.dat

THE FIRST STRUCTURE OF UDP-GLUCOSE DEHYDROGENASE (UDPGDH) REVEALS THE CATALYTIC RESIDUES NECESSARY FOR THE TWO-FOLD OXIDATION