SAXSdb — 5xfc

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

Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1

Homo sapiens

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 92–250	Fragment：UNP residues 92-250 Non-standard monomer：Yes (specific site not provided by mmCIF)	MBE 4-nitrophenyl beta-D-mannopyranoside × 1	X-RAY DIFFRACTION X-ray crystallization conditions：BATCH MODE；pH 7；293 K；HEPES-NaOH, PEG4000	Resolution 1.40 Å R-free 0.207
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 92–250	Fragment：UNP residues 92-250 Non-standard monomer：Yes (specific site not provided by mmCIF)	MBE 4-nitrophenyl beta-D-mannopyranoside × 1	X-RAY DIFFRACTION X-ray crystallization conditions：BATCH MODE；pH 7；293 K；HEPES-NaOH, PEG4000	Resolution 1.40 Å R-free 0.207

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 5XFC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5GGF Crystal structure of human protein O-mannose beta-1,2-N-acetylglucosaminyltransferase form II Deposited 2016-06-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 92–660（569 aa） Fragment：UNP residues 92-660	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；1.4-1.6M Na malonate	Resolution 2.49 Å R-free 0.253
5GGF Crystal structure of human protein O-mannose beta-1,2-N-acetylglucosaminyltransferase form II Deposited 2016-06-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 92–660（569 aa） Fragment：UNP residues 92-660	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；1.4-1.6M Na malonate	Resolution 2.49 Å R-free 0.253
5GGF Crystal structure of human protein O-mannose beta-1,2-N-acetylglucosaminyltransferase form II Deposited 2016-06-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 92–660（569 aa） Fragment：UNP residues 92-660	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；1.4-1.6M Na malonate	Resolution 2.49 Å R-free 0.253
5GGG Crystal structure of human protein O-mannose beta-1,2-N-acetylglucosaminyltransferase form I Deposited 2016-06-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 92–660（569 aa） Fragment：UNP residues 92-660	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；Na malonate	Resolution 3.00 Å R-free 0.241
5GGI Crystal structure of human protein O-mannose beta-1,2-N-acetylglucosaminyltransferase in complex with Mn, UDP and Mannosyl-peptide Deposited 2016-06-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 92–660（569 aa） Fragment：UNP residues 92-660	Not recorded	UDP URIDINE-5'-DIPHOSPHATE × 1 MN MANGANESE (II) ION × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；NaKPO4	Resolution 2.60 Å R-free 0.238
5GGI Crystal structure of human protein O-mannose beta-1,2-N-acetylglucosaminyltransferase in complex with Mn, UDP and Mannosyl-peptide Deposited 2016-06-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 92–660（569 aa） Fragment：UNP residues 92-660	Not recorded	UDP URIDINE-5'-DIPHOSPHATE × 1 MN MANGANESE (II) ION × 1 MAN alpha-D-mannopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；NaKPO4	Resolution 2.60 Å R-free 0.238
5GGJ Crystal structure of N-terminal domain of human protein O-mannose beta-1,2-N-acetylglucosaminyltransferase in complex with Man-alpha-pNP Deposited 2016-06-16	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 92–250（159 aa） Fragment：UNP residues 92-250	Not recorded	PNA 4-nitrophenyl alpha-D-mannopyranoside × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.8；293 K；Tris-HCl, PEG-6000	Resolution 1.42 Å R-free 0.209
5GGJ Crystal structure of N-terminal domain of human protein O-mannose beta-1,2-N-acetylglucosaminyltransferase in complex with Man-alpha-pNP Deposited 2016-06-16	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 92–250（159 aa） Fragment：UNP residues 92-250	Not recorded	PNA 4-nitrophenyl alpha-D-mannopyranoside × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.8；293 K；Tris-HCl, PEG-6000	Resolution 1.42 Å R-free 0.209
5GGK Crystal structure of N-terminal domain of human protein O-mannose beta-1,2-N-acetylglucosaminyltransferase in complex with Man-beta-pNP Deposited 2016-06-16	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 92–250（159 aa） Fragment：UNP residues 92-250	Not recorded	MBE 4-nitrophenyl beta-D-mannopyranoside × 1 GOL GLYCEROL × 2 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；Tris-HCl, PEG-10000	Resolution 1.30 Å R-free 0.175
5GGK Crystal structure of N-terminal domain of human protein O-mannose beta-1,2-N-acetylglucosaminyltransferase in complex with Man-beta-pNP Deposited 2016-06-16	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 92–250（159 aa） Fragment：UNP residues 92-250	Not recorded	MBE 4-nitrophenyl beta-D-mannopyranoside × 1 GOL GLYCEROL × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；Tris-HCl, PEG-10000	Resolution 1.30 Å R-free 0.175
5GGL Crystal structure of N-terminal domain of human protein O-mannose beta-1,2-N-acetylglucosaminyltransferase in complex with GlcNAc-alpha-pNP Deposited 2016-06-16	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 92–250（159 aa） Fragment：UNP residues 92-250	Not recorded	6ZC 4-nitrophenyl 2-acetamido-2-deoxy-alpha-D-glucopyranoside × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.8；293 K；Tris-HCl, PEG-8000	Resolution 1.27 Å R-free 0.161
5GGL Crystal structure of N-terminal domain of human protein O-mannose beta-1,2-N-acetylglucosaminyltransferase in complex with GlcNAc-alpha-pNP Deposited 2016-06-16	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 92–250（159 aa） Fragment：UNP residues 92-250	Not recorded	6ZC 4-nitrophenyl 2-acetamido-2-deoxy-alpha-D-glucopyranoside × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.8；293 K；Tris-HCl, PEG-8000	Resolution 1.27 Å R-free 0.161
5GGN Crystal structure of N-terminal domain of human protein O-mannose beta-1,2-N-acetylglucosaminyltransferase in complex with GlcNAc-beta-pNP Deposited 2016-06-16	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 92–250（159 aa） Fragment：UNP residues 92-250	Not recorded	LEC 4-nitrophenyl 2-acetamido-2-deoxy-beta-D-glucopyranoside × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.8；293 K；Tris-HCl, PEG-6000	Resolution 1.21 Å R-free 0.166
5GGN Crystal structure of N-terminal domain of human protein O-mannose beta-1,2-N-acetylglucosaminyltransferase in complex with GlcNAc-beta-pNP Deposited 2016-06-16	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 92–250（159 aa） Fragment：UNP residues 92-250	Not recorded	LEC 4-nitrophenyl 2-acetamido-2-deoxy-beta-D-glucopyranoside × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.8；293 K；Tris-HCl, PEG-6000	Resolution 1.21 Å R-free 0.166
5GGO Crystal structure of N-terminal domain of human protein O-mannose beta-1,2-N-acetylglucosaminyltransferase in complex with GalNac-beta1,3-GlcNAc-beta-pNP Deposited 2016-06-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 92–250（159 aa） Fragment：UNP residues 97-250	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.8；293 K；Tris-HCl, PEG-6000	Resolution 1.50 Å R-free 0.208
5GGO Crystal structure of N-terminal domain of human protein O-mannose beta-1,2-N-acetylglucosaminyltransferase in complex with GalNac-beta1,3-GlcNAc-beta-pNP Deposited 2016-06-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain B 92–250（159 aa） Fragment：UNP residues 97-250	Not recorded	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.8；293 K；Tris-HCl, PEG-6000	Resolution 1.50 Å R-free 0.208
5GGP Crystal structure of N-terminal domain of human protein O-mannose beta-1,2-N-acetylglucosaminyltransferase in complex with GlcNAc-beta1,2-Man-peptide Deposited 2016-06-16	Different mutation/modification 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 92–250（159 aa） Fragment：UNP residues 92-250	Not recorded	NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；MES-NaOH, LiCl2, Na acetate, PEG-6000	Resolution 1.60 Å R-free 0.246
5GGP Crystal structure of N-terminal domain of human protein O-mannose beta-1,2-N-acetylglucosaminyltransferase in complex with GlcNAc-beta1,2-Man-peptide Deposited 2016-06-16	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 92–250（159 aa） Fragment：UNP residues 92-250	Not recorded	NA SODIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；MES-NaOH, LiCl2, Na acetate, PEG-6000	Resolution 1.60 Å R-free 0.246

9 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PMGT1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–164； UniProt 92–250 Author chain B； PDBConstruct 6–164； UniProt 92–250

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	5xfc
Deposition date deposition_date	2017-04-10
Structure title title	Serial femtosecond X-ray structure of a stem domain of human O-mannose beta-1,2-N-acetylglucosaminyltransferase solved by Se-SAD using XFEL (refined against 13,000 patterns)
Keywords keywords	glycosyltransferase, carbohydrate-binding domain, SUGAR BINDING PROTEIN; SUGAR BINDING PROTEIN
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	22.64 Å
Radius of gyration Rg (electron density) rg_electron	21.71 Å
Forward intensity I(0) i0	20695100.00
Molecular weight molecular_weight	34064.0 kDa
Excluded volume excluded_volume	42414 Å³
Envelope volume envelope_volume	50535 Å³
Hydration-shell volume shell_volume	20188 Å³
Envelope diameter envelope_diameter	73.3 Å
Shell Rg shell_rg	27.56 Å
Envelope Rg envelope_rg	21.83 Å
Shape Rg shape_rg	21.69 Å
Total Rg total_rg	22.56 Å
Total atoms total_atoms	2380
Residues n_residues	300
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	73.0 Å
Rg (real space) rg_real	22.68 Å
Rg uncertainty (real space) rg_real_error	0.50 Å
I(0) (real space) i0_real	2.0700e+07
I(0) uncertainty (real space) i0_real_error	3.0070e+05
Rg (reciprocal space) rg_reciprocal	22.67 Å
I(0) (reciprocal space) i0_reciprocal	20700000.0000
Solution quality estimate total_estimate	0.8962
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.2 Å
Skewness Skewness skewness	0.386
Kurtosis Kurtosis kurtosis	-0.427
Angular range angular_range	— – 0.3500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5050000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.899; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.973; Smooth: 0.975

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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	Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1
Molecular weight formula_weight	17763.7 kDa
EC 编号 ec_number	2.4.1.-
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	2559

GPLGSGSGPRRVLDVEVYSSRSKVYVAVDGTTVLEDEAREQGRGIHVIVLNQATGHVMAKRVFDTYSPHEDEAMVLFLNMVAPGRVLICTVKDEGSFHLKDTAKALLRSLGSQAGPALGWRDTWAFVGRKGGPVFGEKHSKSPALSSWGDPVLLKTDVPLSSAE

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	4-nitrophenyl beta-D-mannopyranoside
Molecular weight formula_weight	301.2 kDa
Source method src_method	man
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	171

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8. Citations (1)

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Unit-cell length a length_a	71.210 Å
Unit-cell length b length_b	91.050 Å
Unit-cell length c length_c	53.750 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 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.400 Å
Low-resolution limit resolution_low	23.143 Å
R factor r_factor	0.1717
R_work r_work	0.1704
R_free r_free	0.2067

fit	/app/data/saxs_computation/xf/5xfc/5xfc.fit
pddf	/app/data/pr_computation/xf/5xfc/5xfc.pr.out
profile	/app/data/saxs_computation/xf/5xfc/5xfc.dat

Serial femtosecond X-ray structure of a stem domain of human O-mannose beta-1,2-N-acetylglucosaminyltransferase solved by Se-SAD using XFEL (refined against 13,000 patterns)

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

Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 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