SAXSdb — 3n3h

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

Lectin

Erythrina corallodendron

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 27–268	Fragment：mECorL Mutation：Y106G	MN MANGANESE (II) ION × 1 CA CALCIUM ION × 1 CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；20% PEG 3350, 0.25M diammonium hydrogen citrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 2.00 Å R-free 0.202

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 3N3H	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AX0 ERYTHRINA CORALLODENDRON LECTIN IN COMPLEX WITH N-ACTYLGALACTOSAMINE Deposited 1997-10-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 27–265（239 aa）	Not recorded	A2G 2-acetamido-2-deoxy-alpha-D-galactopyranose × 2 MN MANGANESE (II) ION × 2 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.	Resolution 1.90 Å R-free 0.200
1AX1 ERYTHRINA CORALLODENDRON LECTIN IN COMPLEX WITH LACTOSE Deposited 1997-10-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 27–265（239 aa）	Not recorded	MN MANGANESE (II) ION × 2 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.	Resolution 1.95 Å R-free 0.200
1AX2 ERYTHRINA CORALLODENDRON LECTIN IN COMPLEX WITH N-ACETYLLACTOSAMINE Deposited 1997-10-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 27–265（239 aa）	Not recorded	MN MANGANESE (II) ION × 2 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.	Resolution 1.95 Å R-free 0.177
1AXY ERYTHRINA CORALLODENDRON LECTIN Deposited 1997-10-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 27–265（239 aa）	Not recorded	MN MANGANESE (II) ION × 2 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.	Resolution 1.95 Å R-free 0.200
1AXZ ERYTHRINA CORALLODENDRON LECTIN IN COMPLEX WITH D-GALACTOSE Deposited 1997-10-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 27–265（239 aa）	Not recorded	GLA alpha-D-galactopyranose × 2 GAL beta-D-galactopyranose × 2 MN MANGANESE (II) ION × 2 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.	Resolution 1.95 Å R-free 0.206
1FYU Crystal structure of erythrina corallodendron lectin in hexagonal crystal form Deposited 2000-10-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 27–281（255 aa） Chain B 27–281（255 aa）	Not recorded	MN MANGANESE (II) ION × 2 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；PEG 8000, sodium chloride, Hepes buffer, sodium azides, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.60 Å R-free 0.202
1LTE STRUCTURE OF A LEGUME LECTIN WITH AN ORDERED N-LINKED CARBOHYDRATE IN COMPLEX WITH LACTOSE Deposited 1991-06-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 27–265（239 aa）	Not recorded	MN MANGANESE (II) ION × 2 CA CALCIUM ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å
1SFY Crystal structure of recombinant Erythrina corallodandron Lectin Deposited 2004-02-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 27–265（239 aa） Fragment：residues 1-239	Not recorded	MN MANGANESE (II) ION × 2 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；300 K；25% Ammonium Sulphate 100mM MES, 0.025% Sodium Azide, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 2.55 Å R-free 0.208
1SFY Crystal structure of recombinant Erythrina corallodandron Lectin Deposited 2004-02-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 27–265（239 aa） Fragment：residues 1-239	Not recorded	MN MANGANESE (II) ION × 2 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；300 K；25% Ammonium Sulphate 100mM MES, 0.025% Sodium Azide, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 2.55 Å R-free 0.208
1SFY Crystal structure of recombinant Erythrina corallodandron Lectin Deposited 2004-02-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 27–265（239 aa） Fragment：residues 1-239 Chain D 27–265（239 aa） Fragment：residues 1-239	Not recorded	MN MANGANESE (II) ION × 2 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；300 K；25% Ammonium Sulphate 100mM MES, 0.025% Sodium Azide, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 2.55 Å R-free 0.208
1SFY Crystal structure of recombinant Erythrina corallodandron Lectin Deposited 2004-02-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 27–265（239 aa） Fragment：residues 1-239 Chain F 27–265（239 aa） Fragment：residues 1-239	Not recorded	MN MANGANESE (II) ION × 2 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；300 K；25% Ammonium Sulphate 100mM MES, 0.025% Sodium Azide, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 2.55 Å R-free 0.208
3N35 Erythrina corallodendron lectin mutant (Y106G) with N-Acetylgalactosamine Deposited 2010-05-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 27–268（242 aa） Fragment：mECorL	Mutation：Y106G	MN MANGANESE (II) ION × 1 CA CALCIUM ION × 1 A2G 2-acetamido-2-deoxy-alpha-D-galactopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；20% PEG 3350, 0.25M diammonium hydrogen citrate , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 2.00 Å R-free 0.189
3N36 Erythrina corallodendron lectin mutant (Y106G) in complex with Galactose Deposited 2010-05-19	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 27–268（242 aa） Fragment：mECorL	Mutation：Y106G	MN MANGANESE (II) ION × 1 CA CALCIUM ION × 1 GLA alpha-D-galactopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；20% PEG 3350, 0.25M diammonium hydrogen citrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 2.30 Å R-free 0.208

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

View Construct and Data Evidence

UniProt name	LEC_ERYCO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–242； UniProt 27–268

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	3n3h
Deposition date deposition_date	2010-05-20
Structure title title	Erythrina corallodendron lectin mutant (Y106G) in complex with citrate
Keywords keywords	LEGUME LECTIN, GLYCOSYLATION, ERYTHRINA LECTIN, SUGAR, RECOMBINANT LECTIN, 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	18.75 Å
Radius of gyration Rg (electron density) rg_electron	17.39 Å
Forward intensity I(0) i0	12819800.00
Molecular weight molecular_weight	26751.0 kDa
Excluded volume excluded_volume	33401 Å³
Envelope volume envelope_volume	37959 Å³
Hydration-shell volume shell_volume	18145 Å³
Envelope diameter envelope_diameter	67.4 Å
Shell Rg shell_rg	23.85 Å
Envelope Rg envelope_rg	17.86 Å
Shape Rg shape_rg	17.35 Å
Total Rg total_rg	18.47 Å
Total atoms total_atoms	1888
Residues n_residues	242
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	47.9 Å
Rg (real space) rg_real	17.95 Å
Rg uncertainty (real space) rg_real_error	0.04 Å
I(0) (real space) i0_real	1.2230e+07
I(0) uncertainty (real space) i0_real_error	1.0100e+05
Rg (reciprocal space) rg_reciprocal	18.69 Å
I(0) (reciprocal space) i0_reciprocal	12820000.0000
Solution quality estimate total_estimate	0.6845
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	0
Primary peak position r_peak_primary	— Å
Skewness Skewness skewness	0.106
Kurtosis Kurtosis kurtosis	-0.485
Angular range angular_range	— – 0.4250 Å⁻¹
Current regularization parameter α current_alpha	3.0240
Highest regularization parameter α highest_alpha	2439000.0000
Real-space data points n_real_points	74
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.001; Oscil: 0.994; Stabil: 0.973; Sysdev: 0.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Lectin
Molecular weight formula_weight	26492.4 kDa
Mutation mutation	Y106G
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	2046

VETISFSFSEFEPGNDNLTLQGASLITQSGVLQLTKINQNGMPAWDSTGRTLYAKPVHIWDMTTGTVASFETRFSFSIEQPYTRPLPADGLVFFMGPTKSKPAQGGGYLGIFNNSKQDNSYQTLGVEFDTFSNQWDPPQVPHIGIDVNSIRSIKTQPFQLDNGQVANVVIKYDASSKILHAVLVYPSSGAIYTIAEIVDVKQVLPEWVDVGLSGATGAQRDAAETHDVYSWSFQASLPETND

来源 Source

来源生物 organism	Erythrina corallodendron
通用名 common_name	coral tree
NCBI Class编号 ncbi_taxonomy_id	3843
宿主生物 host_organism	Escherichia coli

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	1

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	CITRIC ACID
Molecular weight formula_weight	192.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	158

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3n3ha_
Class class	b — All beta proteins
Fold Fold fold	b.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
Family Family family	b.29.1.1 — Legume lectins

CATH v4.4 (1 domains)

Domain ID domain_id	3n3hA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

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8. Citations (1)

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Unit-cell length a length_a	102.784 Å
Unit-cell length b length_b	102.784 Å
Unit-cell length c length_c	56.975 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	6

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

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	29.670 Å
R factor r_factor	0.1840
R_work r_work	0.1840
R_free r_free	0.2020

fit	/app/data/saxs_computation/n3/3n3h/3n3h.fit
pddf	/app/data/pr_computation/n3/3n3h/3n3h.pr.out
profile	/app/data/saxs_computation/n3/3n3h/3n3h.dat

Erythrina corallodendron lectin mutant (Y106G) in complex with citrate

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

Lectin

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