SAXSdb — 1c3f

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

ENDO-BETA-N-ACETYLGLUCOSAMINIDASE H

Streptomyces plicatus

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 48–312	Mutation：D130N	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；17% PEG8000, 200 MM ZINC ACETATE 100 MM CACODYLATE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.K	Resolution 2.10 Å

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 1C3F	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1C8X Endo-Beta-N-Acetylglucosaminidase H, D130E Mutant Deposited 1999-07-30	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 48–312（265 aa）	Mutation：D130E	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；30% PEG1000, 100 MM CACODYLATE, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293.K	Resolution 2.00 Å
1C8Y Endo-Beta-N-Acetylglucosaminidase H, D130A Mutant Deposited 1999-07-30	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 48–312（265 aa）	Mutation：D130A	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；25% PEG1000, 100 MM ZN(AC)2, 100 MM CACODYLATE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å
1C90 Endo-Beta-N-Acetylglucosaminidase H, E132Q Mutant Deposited 1999-07-30	Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 48–312（265 aa）	Mutation：E132Q	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；19% PEG1000, 100 MM ZN(AC)2 100 MM CACODYLATE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 Å
1C90 Endo-Beta-N-Acetylglucosaminidase H, E132Q Mutant Deposited 1999-07-30	Different mutation/modification Different experimental conditions	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 48–312（265 aa）	Mutation：E132Q	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；19% PEG1000, 100 MM ZN(AC)2 100 MM CACODYLATE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 Å
1C91 Endo-Beta-N-Acetylglucosaminidase H, E132D Deposited 1999-07-30	Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 48–312（265 aa）	Mutation：E132D	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；15% PEG1000, 100 MM ZN(AC)2 100 MM CACODYLATE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 Å
1C92 Endo-Beta-N-Acetylglucosaminidase H, E132A Mutant Deposited 1999-07-30	Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 48–312（265 aa）	Mutation：E132A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；24% PEG1500, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 Å
1C93 Endo-Beta-N-Acetylglucosaminidase H, D130N/E132Q Double Mutant Deposited 1999-07-30	Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 48–312（265 aa）	Mutation：D130N AND E132Q	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；34% PEG1500, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 Å
1EDT CRYSTAL STRUCTURE OF ENDO-BETA-N-ACETYLGLUCOSAMINIDASE H AT 1.9 ANGSTROMS RESOLUTION: ACTIVE SITE GEOMETRY AND SUBSTRATE RECOGNITION Deposited 1995-03-31	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 43–313（271 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å
30ID Recombinant Streptomyces plicatus EndoH Deposited 2026-04-28	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 48–312（265 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.2M Magnesium chloride, 0.1 M TRIS pH 8.5, 25% (w/v) PEG 3350 (Index H1)	Resolution 1.99 Å R-free 0.261
30ID Recombinant Streptomyces plicatus EndoH Deposited 2026-04-28	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 48–312（265 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.2M Magnesium chloride, 0.1 M TRIS pH 8.5, 25% (w/v) PEG 3350 (Index H1)	Resolution 1.99 Å R-free 0.261
30ID Recombinant Streptomyces plicatus EndoH Deposited 2026-04-28	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 48–312（265 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.2M Magnesium chloride, 0.1 M TRIS pH 8.5, 25% (w/v) PEG 3350 (Index H1)	Resolution 1.99 Å R-free 0.261
30ID Recombinant Streptomyces plicatus EndoH Deposited 2026-04-28	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 48–312（265 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.2M Magnesium chloride, 0.1 M TRIS pH 8.5, 25% (w/v) PEG 3350 (Index H1)	Resolution 1.99 Å R-free 0.261
6VE1 Crystal structure of endo-beta-N-acetylglucosaminidase H at high pH Deposited 2019-12-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 47–313（267 aa） Fragment：UNP residues 47-313 Chain D 47–313（267 aa） Fragment：UNP residues 47-313	Not recorded	MG MAGNESIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；pH 9；295 K；PEG20000, magnesium nitrate, TAPS, pH 9.0	Resolution 2.10 Å R-free 0.258
6VE1 Crystal structure of endo-beta-N-acetylglucosaminidase H at high pH Deposited 2019-12-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 47–313（267 aa） Fragment：UNP residues 47-313 Chain C 47–313（267 aa） Fragment：UNP residues 47-313	Not recorded	MG MAGNESIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；pH 9；295 K；PEG20000, magnesium nitrate, TAPS, pH 9.0	Resolution 2.10 Å R-free 0.258

9 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	EBAG_STRPL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–265； UniProt 48–312

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	1c3f
Deposition date deposition_date	1999-07-27
Structure title title	Endo-Beta-N-Acetylglucosaminidase H, D130N Mutant
Keywords keywords	(BETA-ALPHA)8-BARREL, HYDROLASE; HYDROLASE
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	19.29 Å
Radius of gyration Rg (electron density) rg_electron	17.88 Å
Forward intensity I(0) i0	14868600.00
Molecular weight molecular_weight	28496.0 kDa
Excluded volume excluded_volume	35382 Å³
Envelope volume envelope_volume	38906 Å³
Hydration-shell volume shell_volume	18244 Å³
Envelope diameter envelope_diameter	63.5 Å
Shell Rg shell_rg	24.08 Å
Envelope Rg envelope_rg	18.06 Å
Shape Rg shape_rg	17.85 Å
Total Rg total_rg	18.82 Å
Total atoms total_atoms	2016
Residues n_residues	265
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	63.8 Å
Rg (real space) rg_real	19.20 Å
Rg uncertainty (real space) rg_real_error	0.42 Å
I(0) (real space) i0_real	1.4870e+07
I(0) uncertainty (real space) i0_real_error	1.9050e+05
Rg (reciprocal space) rg_reciprocal	19.21 Å
I(0) (reciprocal space) i0_reciprocal	14870000.0000
Solution quality estimate total_estimate	0.6611
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.3 Å
Skewness Skewness skewness	0.198
Kurtosis Kurtosis kurtosis	-0.413
Angular range angular_range	— – 0.4100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3005000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.842; Stabil: 1.000; Sysdev: 0.356; Positv: 1.000; Valcen: 0.998; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1c3fa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.8 — (Trans)glycosidases
Family Family family	c.1.8.5 — Type II chitinase

CATH v4.4 (1 domains)

Domain ID domain_id	1c3fA00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	80 — Glycosidases

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8. Citations (1)

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Unit-cell length a length_a	84.000 Å
Unit-cell length b length_b	84.000 Å
Unit-cell length c length_c	88.200 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 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.2090
R_work r_work	0.2090
R_free r_free	—

Description description	ENDO-BETA-N-ACETYLGLUCOSAMINIDASE H
Molecular weight formula_weight	28524.4 kDa
EC 编号 ec_number	3.2.1.96
Mutation mutation	D130N
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2270

Endo-Beta-N-Acetylglucosaminidase H, D130N Mutant

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

ENDO-BETA-N-ACETYLGLUCOSAMINIDASE H

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Streptomyces plicatus
NCBI Class编号 ncbi_taxonomy_id	1922
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	254

fit	/app/data/saxs_computation/c3/1c3f/1c3f.fit
pddf	/app/data/pr_computation/c3/1c3f/1c3f.pr.out
profile	/app/data/saxs_computation/c3/1c3f/1c3f.dat