SAXSdb — 3be8

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

Neuroligin-4, X-linked

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 44–619 Chain B； UniProt 44–619	Fragment：extracellular cholinesterase-like domain	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 FLC CITRATE ANION × 2 PO4 PHOSPHATE ION × 2 CL CHLORIDE ION × 6 NA SODIUM ION × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.2；277 K；10% PEG-3000, 0.1M sodium phosphate-citrate, 0.3M sodium chloride, 0.01M calcium chloride, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.20 Å R-free 0.201

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 3BE8	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2WQZ Crystal structure of synaptic protein neuroligin-4 in complex with neurexin-beta 1: alternative refinement Deposited 2009-08-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 43–619（577 aa） Fragment：ACETYLCHOLINESTERASE-LIKE DOMAIN, RESIDUES 43-619	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；8% PEG 20000, 0.1M MES PH6.5	Resolution 3.90 Å R-free 0.276
2WQZ Crystal structure of synaptic protein neuroligin-4 in complex with neurexin-beta 1: alternative refinement Deposited 2009-08-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 43–619（577 aa） Fragment：ACETYLCHOLINESTERASE-LIKE DOMAIN, RESIDUES 43-619	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；8% PEG 20000, 0.1M MES PH6.5	Resolution 3.90 Å R-free 0.276
2XB6 Revisited crystal structure of Neurexin1beta-Neuroligin4 complex Deposited 2010-04-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 44–619（576 aa） Fragment：CHOLINESTERASE-LIKE DOMAIN, RESIDUES 43-619	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 EDO 1,2-ETHANEDIOL × 16 CL CHLORIDE ION × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.3；100MM MES PH6.3,10% PEG 20000, 2MM CACL2	Resolution 2.60 Å R-free 0.236
2XB6 Revisited crystal structure of Neurexin1beta-Neuroligin4 complex Deposited 2010-04-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 44–619（576 aa） Fragment：CHOLINESTERASE-LIKE DOMAIN, RESIDUES 43-619	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 EDO 1,2-ETHANEDIOL × 14 CL CHLORIDE ION × 3 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.3；100MM MES PH6.3,10% PEG 20000, 2MM CACL2	Resolution 2.60 Å R-free 0.236

2 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NLGNX_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–588； UniProt 44–619 Author chain B； PDBConstruct 13–588； UniProt 44–619

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	3be8
Deposition date deposition_date	2007-11-16
Structure title title	Crystal structure of the synaptic protein neuroligin 4
Keywords keywords	;Neuroligin, cell adhesion protein, synaptic protein, a/b-hydrolase fold, four-helix bundle, Glycoprotein, Membrane, Transmembrane, CELL ADHESION ;; 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	39.10 Å
Radius of gyration Rg (electron density) rg_electron	39.17 Å
Forward intensity I(0) i0	223150000.00
Molecular weight molecular_weight	122290.0 kDa
Excluded volume excluded_volume	152890 Å³
Envelope volume envelope_volume	191770 Å³
Hydration-shell volume shell_volume	42779 Å³
Envelope diameter envelope_diameter	144.7 Å
Shell Rg shell_rg	42.50 Å
Envelope Rg envelope_rg	39.20 Å
Shape Rg shape_rg	39.10 Å
Total Rg total_rg	39.57 Å
Total atoms total_atoms	8615
Residues n_residues	1077
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	133.0 Å
Rg (real space) rg_real	39.59 Å
Rg uncertainty (real space) rg_real_error	1.24 Å
I(0) (real space) i0_real	2.2310e+08
I(0) uncertainty (real space) i0_real_error	3.6290e+06
Rg (reciprocal space) rg_reciprocal	39.29 Å
I(0) (reciprocal space) i0_reciprocal	223100000.0000
Solution quality estimate total_estimate	0.7819
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	33.3 Å
Skewness Skewness skewness	0.515
Kurtosis Kurtosis kurtosis	-0.545
Angular range angular_range	— – 0.2000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	62390000.0000
Real-space data points n_real_points	41
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.594; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.681; Smooth: 0.699

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	Neuroligin-4, X-linked
Molecular weight formula_weight	66230.2 kDa
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	9309

DYKDDDDKLAAAQYPVVNTNYGKIRGLRTPLPNEILGPVEQYLGVPYASPPTGERRFQPPEPPSSWTGIRNTTQFAAVCPQHLDERSLLHDMLPIWFTANLDTLMTYVQDQNEDCLYLNIYVPTEDDIHDQNSKKPVMVYIHGGSYMEGTGNMIDGSILASYGNVIVITINYRLGILGFLSTGDQAAKGNYGLLDQIQALRWIEENVGAFGGDPKRVTIFGSGAGASCVSLLTLSHYSEGLFQKAIIQSGTALSSWAVNYQPAKYTRILADKVGCNMLDTTDMVECLRNKNYKELIQQTITPATYHIAFGPVIDGDVIPDDPQILMEQGEFLNYDIMLGVNQGEGLKFVDGIVDNEDGVTPNDFDFSVSNFVDNLYGYPEGKDTLRETIKFMYTDWADKENPETRRKTLVALFTDHQWVAPAVATADLHAQYGSPTYFYAFYHHCQSEMKPSWADSAHGDEVPYVFGIPMIGPTELFSCNFSKNDVMLSAVVMTYWTNFAKTGDPNQPVPQDTKFIHTKPNRFEEVAWSRYNPKDQLYLHIGLKPRVRDHYRATKVAFWLELVPHLHNLNEIFQYVSTTTKVPPPDMT

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	Homo sapiens

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	4

Entity 3 Entity 3 non-polymer

Description description	CITRATE ANION
Molecular weight formula_weight	189.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 6 Entity 6 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	592

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3be8a1
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	d3be8a2
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	d3be8b1
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	d3be8b2
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 (2 domains)

Domain ID domain_id	3be8A00
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	3be8B00
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	139.730 Å
Unit-cell length b length_b	154.050 Å
Unit-cell length c length_c	81.300 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	2.200 Å
Low-resolution limit resolution_low	29.680 Å
R factor r_factor	0.1686
R_work r_work	0.1669
R_free r_free	0.2008

fit	/app/data/saxs_computation/be/3be8/3be8.fit
pddf	/app/data/pr_computation/be/3be8/3be8.pr.out
profile	/app/data/saxs_computation/be/3be8/3be8.dat

Crystal structure of the synaptic protein neuroligin 4