SAXSdb — 4wlz

▼

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

Xyloside xylosyltransferase 1

Mus musculus

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 87–392	Not recorded	MN MANGANESE (II) ION × 1 UDP URIDINE-5'-DIPHOSPHATE × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；20 mM HEPES, 1.5 M Li2SO4	Resolution 3.03 Å R-free 0.288
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 87–392	Not recorded	MN MANGANESE (II) ION × 1 UDP URIDINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；20 mM HEPES, 1.5 M Li2SO4	Resolution 3.03 Å R-free 0.288
3	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 87–392 Chain B； UniProt 87–392	Not recorded	MN MANGANESE (II) ION × 2 UDP URIDINE-5'-DIPHOSPHATE × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；20 mM HEPES, 1.5 M Li2SO4	Resolution 3.03 Å R-free 0.288

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 4WLZ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4WLG crystal structure of mouse Xyloside xylosyltransferase 1, apo form Deposited 2014-10-07	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 87–392（306 aa） Fragment：unp residues 87-392	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；20 mM HEPES, 1.5 M Li2SO4	Resolution 3.00 Å R-free 0.276
4WLG crystal structure of mouse Xyloside xylosyltransferase 1, apo form Deposited 2014-10-07	Different construct Different ligand/ion Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 87–392（306 aa） Fragment：unp residues 87-392	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；20 mM HEPES, 1.5 M Li2SO4	Resolution 3.00 Å R-free 0.276
4WLG crystal structure of mouse Xyloside xylosyltransferase 1, apo form Deposited 2014-10-07	Different construct Different ligand/ion Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 87–392（306 aa） Fragment：unp residues 87-392 Chain B 87–392（306 aa） Fragment：unp residues 87-392	Not recorded	SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；20 mM HEPES, 1.5 M Li2SO4	Resolution 3.00 Å R-free 0.276
4WLM Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese Deposited 2014-10-07	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 87–392（306 aa） Fragment：unp residues 87-392	Not recorded	SO4 SULFATE ION × 2 MN MANGANESE (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；20 mM HEPES, 1.5 M Li2SO4	Resolution 3.00 Å R-free 0.287
4WLM Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese Deposited 2014-10-07	Different construct Different ligand/ion Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 87–392（306 aa） Fragment：unp residues 87-392	Not recorded	SO4 SULFATE ION × 3 MN MANGANESE (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；20 mM HEPES, 1.5 M Li2SO4	Resolution 3.00 Å R-free 0.287
4WLM Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese Deposited 2014-10-07	Different construct Different ligand/ion Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 87–392（306 aa） Fragment：unp residues 87-392 Chain B 87–392（306 aa） Fragment：unp residues 87-392	Not recorded	SO4 SULFATE ION × 5 MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；20 mM HEPES, 1.5 M Li2SO4	Resolution 3.00 Å R-free 0.287
4WM0 Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with acceptor ligand Deposited 2014-10-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 87–392（306 aa） Fragment：unp residues 87-392	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2 M Li2SO4, 0.1 M Bis-Tris, and 21% PEG3350	Resolution 2.37 Å R-free 0.233
4WMA Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese,acceptor ligand and UDP-Glucose Deposited 2014-10-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 87–392（306 aa） Fragment：unp residues 87-392	Not recorded	MN MANGANESE (II) ION × 1 UPG URIDINE-5'-DIPHOSPHATE-GLUCOSE × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2 M Li2SO4, 0.1 M Bis-Tris, and 21% PEG3350	Resolution 1.62 Å R-free 0.243
4WMB crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese, acceptor ligand and UDP Deposited 2014-10-08	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 87–392（306 aa） Fragment：unp residues 87-392	Not recorded	MN MANGANESE (II) ION × 1 UDP URIDINE-5'-DIPHOSPHATE × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2 M Li2SO4, 0.1 M Bis-Tris, pH 6.5, and 21% PEG3350	Resolution 2.05 Å R-free 0.235
4WMI Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese, product ligand and UDP (Product complex I) Deposited 2014-10-09	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 87–392（306 aa） Fragment：unp residues 87-392	Not recorded	MN MANGANESE (II) ION × 1 UDP URIDINE-5'-DIPHOSPHATE × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M Li2SO4, 0.1 M Bis-Tris, pH 6.5, and 21% PEG3350	Resolution 1.87 Å R-free 0.226
4WMK Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese, product ligand and UDP (Product complex II) Deposited 2014-10-09	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 87–392（306 aa） Fragment：unp residues 87-392	Not recorded	MN MANGANESE (II) ION × 1 UDP URIDINE-5'-DIPHOSPHATE × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M Li2SO4, 0.1 M Bis-Tris, and 21% PEG3350	Resolution 2.08 Å R-free 0.246
4WN2 Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese, product ligand and UDP (Product complex III) Deposited 2014-10-10	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 87–392（306 aa） Fragment：unp residues 87-392	Not recorded	MN MANGANESE (II) ION × 1 UDP URIDINE-5'-DIPHOSPHATE × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2 M Li2SO4, 0.1 M Bis-Tris, and 21% PEG3350	Resolution 1.95 Å R-free 0.239
4WNH Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese,acceptor ligand and UDP-Xylose Deposited 2014-10-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 87–392（306 aa） Fragment：unp residues 87-392	Not recorded	MN MANGANESE (II) ION × 1 UDX URIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2 M Li2SO4, 0.1 M Bis-Tris, pH 6.5, and 21% PEG3350	Resolution 1.95 Å R-free 0.224

9 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	XXLT1_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–306； UniProt 87–392 Author chain B； PDBConstruct 1–306； UniProt 87–392

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	4wlz
Deposition date deposition_date	2014-10-08
Structure title title	Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese and UDP
Keywords keywords	glycosyltransferase, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	28.43 Å
Radius of gyration Rg (electron density) rg_electron	27.78 Å
Forward intensity I(0) i0	73517800.00
Molecular weight molecular_weight	68218.0 kDa
Excluded volume excluded_volume	85593 Å³
Envelope volume envelope_volume	104460 Å³
Hydration-shell volume shell_volume	31722 Å³
Envelope diameter envelope_diameter	98.8 Å
Shell Rg shell_rg	34.77 Å
Envelope Rg envelope_rg	27.88 Å
Shape Rg shape_rg	27.75 Å
Total Rg total_rg	28.57 Å
Total atoms total_atoms	4804
Residues n_residues	576
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

▼

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

Maximum dimension Dmax dmax	95.6 Å
Rg (real space) rg_real	28.51 Å
Rg uncertainty (real space) rg_real_error	0.90 Å
I(0) (real space) i0_real	7.3520e+07
I(0) uncertainty (real space) i0_real_error	1.2320e+06
Rg (reciprocal space) rg_reciprocal	28.49 Å
I(0) (reciprocal space) i0_reciprocal	73520000.0000
Solution quality estimate total_estimate	0.8726
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.0 Å
Skewness Skewness skewness	0.416
Kurtosis Kurtosis kurtosis	-0.337
Angular range angular_range	— – 0.2800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	18680000.0000
Real-space data points n_real_points	57
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.828; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.942; Smooth: 0.921

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Xyloside xylosyltransferase 1
Molecular weight formula_weight	35295.5 kDa
EC 编号 ec_number	2.4.2.-
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	4804

SLEGGVVVPVDYHLLMMFTKAEHNAPLQAKARVALSSLLRLAKFEAHEVLNLHFVSEEASREVAKALLRELLPPAAGFKCKVIFHDVAVLTDKLFPVVEAMQKYFSAGSGTYYSDSIFFLSVAMHQIMPKEIPRIIQLDLDLKYKTNIRELFEEFDNFLPGAVIGIAREMQPVYRHTFWQFRHENPKTRVGDPPPEGLPGFNSGVMLLNLEAMRQSPLYSHLLEPSWVQQLADKYHFRGHLGDQDFFTMIGMEHPELFHVLDCTWNRQLCTWWRDHGYSDVFQAYFRCEGHVKIYHGNCNTPIPED

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	Mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	URIDINE-5'-DIPHOSPHATE
Molecular weight formula_weight	404.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

▶

8. Citations (1)

▶

Unit-cell length a length_a	89.662 Å
Unit-cell length b length_b	89.662 Å
Unit-cell length c length_c	154.987 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	12

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	3.030 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2331
R_work r_work	0.2303
R_free r_free	0.2882

fit	/app/data/saxs_computation/wl/4wlz/4wlz.fit
pddf	/app/data/pr_computation/wl/4wlz/4wlz.pr.out
profile	/app/data/saxs_computation/wl/4wlz/4wlz.dat

Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese and UDP

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

Xyloside xylosyltransferase 1

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