SAXSdb — 3bix

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

Neuroligin-1

Rattus norvegicus

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 46–164 Chain A； UniProt 185–297 Chain A； UniProt 306–638 Chain C； UniProt 46–164 Chain C； UniProt 185–297 Chain C； UniProt 306–638	Fragment：extracellular esterase domain	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 NI NICKEL (II) ION × 1 EDO 1,2-ETHANEDIOL × 7	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.7；293 K；1.2 M tri-Sodium citrate, 0.1 M Tris, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.80 Å R-free 0.205
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 46–164 Chain B； UniProt 185–297 Chain B； UniProt 306–638 Chain D； UniProt 46–164 Chain D； UniProt 185–297 Chain D； UniProt 306–638	Fragment：extracellular esterase domain	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 NI NICKEL (II) ION × 1 EDO 1,2-ETHANEDIOL × 7	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.7；293 K；1.2 M tri-Sodium citrate, 0.1 M Tris, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.80 Å R-free 0.205

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 3BIX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3BIW Crystal structure of the Neuroligin-1/Neurexin-1beta synaptic adhesion complex Deposited 2007-12-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 46–164（119 aa） Fragment：extracellular esterase domain of Neuroligin-1 Chain A 185–297（113 aa） Fragment：extracellular esterase domain of Neuroligin-1 Chain A 306–638（333 aa） Fragment：extracellular esterase domain of Neuroligin-1 Chain D 46–164（119 aa） Fragment：extracellular esterase domain of Neuroligin-1 Chain D 185–297（113 aa） Fragment：extracellular esterase domain of Neuroligin-1 Chain D 306–638（333 aa） Fragment：extracellular esterase domain of Neuroligin-1	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；8% PEG6000, 0.1 M MgCl2, 0.1 M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.50 Å R-free 0.276
3BIW Crystal structure of the Neuroligin-1/Neurexin-1beta synaptic adhesion complex Deposited 2007-12-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 46–164（119 aa） Fragment：extracellular esterase domain of Neuroligin-1 Chain B 185–297（113 aa） Fragment：extracellular esterase domain of Neuroligin-1 Chain B 306–638（333 aa） Fragment：extracellular esterase domain of Neuroligin-1 Chain C 46–164（119 aa） Fragment：extracellular esterase domain of Neuroligin-1 Chain C 185–297（113 aa） Fragment：extracellular esterase domain of Neuroligin-1 Chain C 306–638（333 aa） Fragment：extracellular esterase domain of Neuroligin-1	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；8% PEG6000, 0.1 M MgCl2, 0.1 M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.50 Å R-free 0.276
3VKF Crystal Structure of Neurexin 1beta/Neuroligin 1 complex Deposited 2011-11-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 45–638（594 aa） Fragment：Acetylcholinesterase-like domain (UNP RESIDUES 45-638) Chain B 45–638（594 aa） Fragment：Acetylcholinesterase-like domain (UNP RESIDUES 45-638)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M sodium chloride, 0.005M calcium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.30 Å R-free 0.287
3VKF Crystal Structure of Neurexin 1beta/Neuroligin 1 complex Deposited 2011-11-15	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 A 45–638（594 aa） Fragment：Acetylcholinesterase-like domain (UNP RESIDUES 45-638)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M sodium chloride, 0.005M calcium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.30 Å R-free 0.287
3VKF Crystal Structure of Neurexin 1beta/Neuroligin 1 complex Deposited 2011-11-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 45–638（594 aa） Fragment：Acetylcholinesterase-like domain (UNP RESIDUES 45-638)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M sodium chloride, 0.005M calcium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.30 Å R-free 0.287

2 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NLGN1_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–122； UniProt 46–164 Author chain A； PDBConstruct 123–235； UniProt 185–297 Author chain A； PDBConstruct 236–568； UniProt 306–638 Author chain B； PDBConstruct 4–122； UniProt 46–164 Author chain B； PDBConstruct 123–235； UniProt 185–297 Author chain B； PDBConstruct 236–568； UniProt 306–638 Author chain C； PDBConstruct 4–122； UniProt 46–164 Author chain C； PDBConstruct 123–235； UniProt 185–297 Author chain C； PDBConstruct 236–568； UniProt 306–638 Author chain D； PDBConstruct 4–122； UniProt 46–164 Author chain D； PDBConstruct 123–235； UniProt 185–297 Author chain D； PDBConstruct 236–568； UniProt 306–638

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	3bix
Deposition date deposition_date	2007-12-01
Structure title title	Crystal structure of the extracellular esterase domain of Neuroligin-1
Keywords keywords	;esterase domain, alpha-beta hydrolase, Cell adhesion, Cell junction, Glycoprotein, Membrane, Postsynaptic cell membrane, Synapse, Transmembrane ;; CELL ADHESION
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	44.19 Å
Radius of gyration Rg (electron density) rg_electron	44.00 Å
Forward intensity I(0) i0	889607000.00
Molecular weight molecular_weight	250550.0 kDa
Excluded volume excluded_volume	314320 Å³
Envelope volume envelope_volume	396710 Å³
Hydration-shell volume shell_volume	74077 Å³
Envelope diameter envelope_diameter	149.4 Å
Shell Rg shell_rg	49.77 Å
Envelope Rg envelope_rg	43.42 Å
Shape Rg shape_rg	43.97 Å
Total Rg total_rg	44.34 Å
Total atoms total_atoms	17710
Residues n_residues	2220
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	146.8 Å
Rg (real space) rg_real	44.07 Å
Rg uncertainty (real space) rg_real_error	1.12 Å
I(0) (real space) i0_real	8.8960e+08
I(0) uncertainty (real space) i0_real_error	1.5130e+07
Rg (reciprocal space) rg_reciprocal	44.19 Å
I(0) (reciprocal space) i0_reciprocal	889700000.0000
Solution quality estimate total_estimate	0.8152
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	61.2 Å
Skewness Skewness skewness	0.194
Kurtosis Kurtosis kurtosis	-0.497
Angular range angular_range	— – 0.1800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	391600000.0000
Real-space data points n_real_points	37
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.864; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; 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	Neuroligin-1
Molecular weight formula_weight	64229.0 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	19833

ADPQKLDDVDPLVTTNFGKIRGIKKELNNEILGPVIQFLGVPYAAPPTGEHRFQPPEPPSPWSDIRNATQFAPVCPQNIIDGRLPEVMLPVWFTNNLDVVSSYVQDQSEDCLYLNIYVPTEDDIRDSGGPKPVMVYIHGGSYMEGTGNLYDGSVLASYGNVIVITVNYRLGVLGFLSTGDQAAKGNYGLLDLIQALRWTSENIGFFGGDPLRITVFGSGAGGSCVNLLTLSHYSEKGLFQRAIAQSGTALSSWAVSFQPAKYARILATKVGCNVSDTVELVECLQKKPYKELVDQDVQPARYHIAFGPVIDGDVIPDDPQILMEQGEFLNYDIMLGVNQGEGLKFVENIVDSDDGVSASDFDFAVSNFVDNLYGYPEGKDVLRETIKFMYTDWADRHNPETRRKTLLALFTDHQWVAPAVATADLHSNFGSPTYFYAFYHHCQTDQVPAWADAAHGDEVPYVLGIPMIGPTELFPCNFSKNDVMLSAVVMTYWTNFAKTGDPNQPVPQDTKFIHTKPNRFEEVAWTRYSQKDQLYLHIGLKPRVKEHYRANKVNLWLELVPHLHNLNDHHHHHH

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Trichoplusia ni

Entity 2 Entity 2 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	14

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1965

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d3bixa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
Family Family family	c.69.1.0 — automated matches

Domain ID domain_id	d3bixa2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3bixb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
Family Family family	c.69.1.0 — automated matches

Domain ID domain_id	d3bixb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3bixc1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
Family Family family	c.69.1.0 — automated matches

Domain ID domain_id	d3bixc2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3bixd1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
Family Family family	c.69.1.0 — automated matches

Domain ID domain_id	d3bixd2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id	3bixA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	3bixB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	3bixC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	3bixD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

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8. Citations (1)

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Unit-cell length a length_a	173.744 Å
Unit-cell length b length_b	173.744 Å
Unit-cell length c length_c	108.045 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 32
Space-group number int_tables_number	145
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	45.880 Å
R factor r_factor	—
R_work r_work	0.1850
R_free r_free	0.2050

fit	/app/data/saxs_computation/bi/3bix/3bix.fit
pddf	/app/data/pr_computation/bi/3bix/3bix.pr.out
profile	/app/data/saxs_computation/bi/3bix/3bix.dat

Crystal structure of the extracellular esterase domain of Neuroligin-1

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

Neuroligin-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