SAXSdb — 5f87

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

O-glucosyltransferase rumi

Drosophila melanogaster

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 21–407	Fragment：UNP residues 21-407	UDP URIDINE-5'-DIPHOSPHATE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES pH7.4, 1.2M sodium citrate tribasic, 6% glycerol	Resolution 3.20 Å R-free 0.203
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 21–407	Fragment：UNP residues 21-407	UDP URIDINE-5'-DIPHOSPHATE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES pH7.4, 1.2M sodium citrate tribasic, 6% glycerol	Resolution 3.20 Å R-free 0.203
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 21–407	Fragment：UNP residues 21-407	UDP URIDINE-5'-DIPHOSPHATE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES pH7.4, 1.2M sodium citrate tribasic, 6% glycerol	Resolution 3.20 Å R-free 0.203
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 21–407	Fragment：UNP residues 21-407	UDP URIDINE-5'-DIPHOSPHATE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES pH7.4, 1.2M sodium citrate tribasic, 6% glycerol	Resolution 3.20 Å R-free 0.203
5	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain E； UniProt 21–407	Fragment：UNP residues 21-407	UDP URIDINE-5'-DIPHOSPHATE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES pH7.4, 1.2M sodium citrate tribasic, 6% glycerol	Resolution 3.20 Å R-free 0.203
6	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain F； UniProt 21–407	Fragment：UNP residues 21-407	UDP URIDINE-5'-DIPHOSPHATE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES pH7.4, 1.2M sodium citrate tribasic, 6% glycerol	Resolution 3.20 Å R-free 0.203

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 5F87	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5F84 Crystal structure of Drosophila Poglut1 (Rumi) complexed with its glycoprotein product (glucosylated EGF repeat) and UDP Deposited 2015-12-09	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 21–407（387 aa） Fragment：UNP residues 21-407	Not recorded	UDP URIDINE-5'-DIPHOSPHATE × 1 SO4 SULFATE ION × 5 BGC beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.62M ammonium sulfate	Resolution 2.50 Å R-free 0.239
5F85 Crystal structure of Drosophila Poglut1 (Rumi) complexed with its substrate protein (EGF repeat) and UDP Deposited 2015-12-09	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 21–407（387 aa） Fragment：UNP residues 21-407	Not recorded	UDP URIDINE-5'-DIPHOSPHATE × 1 GOL GLYCEROL × 1 SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.62M ammonium sulfate	Resolution 2.15 Å R-free 0.243
5F86 Crystal structure of Drosophila Poglut1 (Rumi) complexed with its substrate protein (EGF repeat) Deposited 2015-12-09	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 21–407（387 aa） Fragment：UNP residues 21-407	Not recorded	GOL GLYCEROL × 1 SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.62M ammonium sulfate	Resolution 1.90 Å R-free 0.221

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

View Construct and Data Evidence

UniProt name	RUMI_DROME
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 9–395； UniProt 21–407 Author chain B； PDBConstruct 9–395； UniProt 21–407 Author chain C； PDBConstruct 9–395； UniProt 21–407 Author chain D； PDBConstruct 9–395； UniProt 21–407 Author chain E； PDBConstruct 9–395； UniProt 21–407 Author chain F； PDBConstruct 9–395； UniProt 21–407

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	5f87
Deposition date deposition_date	2015-12-09
Structure title title	Crystal structure of Drosophila Poglut1 (Rumi) complexed with UDP
Keywords keywords	glycosyltransferase, protein O-glucosyltransferase, Notch regulation, EGF repeat, 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	61.78 Å
Radius of gyration Rg (electron density) rg_electron	62.09 Å
Forward intensity I(0) i0	944759000.00
Molecular weight molecular_weight	259630.0 kDa
Excluded volume excluded_volume	324870 Å³
Envelope volume envelope_volume	481520 Å³
Hydration-shell volume shell_volume	66428 Å³
Envelope diameter envelope_diameter	198.1 Å
Shell Rg shell_rg	61.44 Å
Envelope Rg envelope_rg	60.11 Å
Shape Rg shape_rg	62.09 Å
Total Rg total_rg	62.09 Å
Total atoms total_atoms	18330
Residues n_residues	2190
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	183.9 Å
Rg (real space) rg_real	62.09 Å
Rg uncertainty (real space) rg_real_error	1.90 Å
I(0) (real space) i0_real	9.4480e+08
I(0) uncertainty (real space) i0_real_error	2.1560e+07
Rg (reciprocal space) rg_reciprocal	61.43 Å
I(0) (reciprocal space) i0_reciprocal	943600000.0000
Solution quality estimate total_estimate	0.5888
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	44.1 Å
Skewness Skewness skewness	0.212
Kurtosis Kurtosis kurtosis	-0.919
Angular range angular_range	— – 0.1250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	27790000.0000
Real-space data points n_real_points	26
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.935; Stabil: 1.000; Sysdev: 0.004; Positv: 1.000; Valcen: 0.833; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	O-glucosyltransferase rumi
Molecular weight formula_weight	46820.2 kDa
EC 编号 ec_number	2.4.1.-
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	18330

AAQPAEALEDDGLCSADQKSCAQSEPDQINEDEFSFKIRRQIEKANADYKPCSSDPQDSDCSCHANVLKRDLAPYKSTGVTRQMIESSARYGTKYKIYGHRLYRDANCMFPARCEGIEHFLLPLVATLPDMDLIINTRDYPQLNAAWGNAAGGPVFSFSKTKEYRDIMYPAWTFWAGGPATKLHPRGIGRWDQMREKLEKRAAAIPWSQKRSLGFFRGSRTSDERDSLILLSRRNPELVEAQYTKNQGWKSPKDTLDAPAADEVSFEDHCKYKYLFNFRGVAASFRLKHLFLCKSLVFHVGDEWQEFFYDQLKPWVHYVPLKSYPSQQEYEHILSFFKKNDALAQEIAQRGYDFIWEHLRMKDIKCYWRKLLKRYVKLLQYEVKPEDQLIYIGPKARALVPR

来源 Source

来源生物 organism	Drosophila melanogaster
通用名 common_name	Fruit fly
NCBI Class编号 ncbi_taxonomy_id	7227
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 non-polymer

Description description	URIDINE-5'-DIPHOSPHATE
Molecular weight formula_weight	404.2 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	6

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8. Citations (1)

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Unit-cell length a length_a	241.908 Å
Unit-cell length b length_b	241.908 Å
Unit-cell length c length_c	47.315 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	18

Space group space_group	P 31
Space-group number int_tables_number	144
Crystal system crystal_system	—

Resolution resolution	3.200 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1702
R_work r_work	0.1684
R_free r_free	0.2026

fit	/app/data/saxs_computation/f8/5f87/5f87.fit
pddf	/app/data/pr_computation/f8/5f87/5f87.pr.out
profile	/app/data/saxs_computation/f8/5f87/5f87.dat

Crystal structure of Drosophila Poglut1 (Rumi) complexed with UDP

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

O-glucosyltransferase rumi

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