SAXSdb — 6lpc

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

Syntaxin-binding protein 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 1–594 Chain B； UniProt 1–594	Mutation：K332E, K333E	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；289.15 K；4 M ammonium acetate, 0.1 M sodium acetate trihydrate	Resolution 3.40 Å R-free 0.331

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 6LPC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3C98 Revised structure of the munc18a-syntaxin1 complex Deposited 2008-02-15	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–594（594 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.3；294 K；PEG400, Ammonium Acetate, Sodium Acetate, EDTA, 2-mercaptoethanol, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.60 Å R-free 0.263
3PUJ Crystal structure of the MUNC18-1 and SYNTAXIN4 N-Peptide complex Deposited 2010-12-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–594（594 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；60% Tascimate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.31 Å R-free 0.258
3PUJ Crystal structure of the MUNC18-1 and SYNTAXIN4 N-Peptide complex Deposited 2010-12-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–594（594 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；60% Tascimate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.31 Å R-free 0.258
4JEH Crystal Structure of Munc18a and Syntaxin1 lacking N-peptide complex Deposited 2013-02-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–594（594 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；27% PEG 400, 10 mM EDTA, 10 mM DTT, 224 mM ammonium acetate, and 100 mM sodium acetate , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.50 Å R-free 0.223
4JEH Crystal Structure of Munc18a and Syntaxin1 lacking N-peptide complex Deposited 2013-02-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–594（594 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；27% PEG 400, 10 mM EDTA, 10 mM DTT, 224 mM ammonium acetate, and 100 mM sodium acetate , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.50 Å R-free 0.223
4JEU Crystal Structure of Munc18a and Syntaxin1 with native N-terminus complex Deposited 2013-02-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 3–592（590 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.2；298 K；27% PEG 400, 10 mM EDTA, 10 mM DTT, 224 mM ammonium acetate, and 100 mM sodium acetate , pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.20 Å R-free 0.263
7UDB Cryo-EM structure of a synaptobrevin-Munc18-1-syntaxin-1 complex class 2 Deposited 2022-03-18	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–594（594 aa）	Mutation：D326K	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
7UDC cryo-EM structures of a synaptobrevin-Munc18-1-syntaxin-1 complex class1 Deposited 2022-03-18	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–594（594 aa）	Mutation：D326K	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
7XSJ The structure of the Mint1/Munc18-1/syntaxin-1 complex Deposited 2022-05-14	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–594（594 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；297 K；0.2M Sodium Malonate, pH 7.0, 20% (v/v) PEG 3350	Resolution 3.20 Å R-free 0.270

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

View Construct and Data Evidence

UniProt name	STXB1_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–594； UniProt 1–594 Author chain B； PDBConstruct 1–594； UniProt 1–594

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	6lpc
Deposition date deposition_date	2020-01-09
Structure title title	Crystal Structure of rat Munc18-1 with K332E/K333E mutation
Keywords keywords	Synaptic exocytosis, Membrane fusion, SNAREs-binding, EXOCYTOSIS; EXOCYTOSIS
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	38.41 Å
Radius of gyration Rg (electron density) rg_electron	38.06 Å
Forward intensity I(0) i0	161731000.00
Molecular weight molecular_weight	100920.0 kDa
Excluded volume excluded_volume	125220 Å³
Envelope volume envelope_volume	182540 Å³
Hydration-shell volume shell_volume	41074 Å³
Envelope diameter envelope_diameter	121.0 Å
Shell Rg shell_rg	42.84 Å
Envelope Rg envelope_rg	37.26 Å
Shape Rg shape_rg	38.10 Å
Total Rg total_rg	38.27 Å
Total atoms total_atoms	7114
Residues n_residues	1000
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	121.0 Å
Rg (real space) rg_real	38.53 Å
Rg uncertainty (real space) rg_real_error	1.20 Å
I(0) (real space) i0_real	1.6170e+08
I(0) uncertainty (real space) i0_real_error	3.0100e+06
Rg (reciprocal space) rg_reciprocal	38.46 Å
I(0) (reciprocal space) i0_reciprocal	161700000.0000
Solution quality estimate total_estimate	0.8770
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	35.4 Å
Skewness Skewness skewness	0.273
Kurtosis Kurtosis kurtosis	-0.819
Angular range angular_range	— – 0.2050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	23670000.0000
Real-space data points n_real_points	42
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.911; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.922; Smooth: 0.741

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	6lpcA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2060 — Sec1/Munc18 (SM) protein, domain 1

Domain ID domain_id	6lpcA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	830 — Syntaxin Binding Protein 1; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Sec1/Munc18 (SM) protein, domain 3a

Domain ID domain_id	6lpcB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2060 — Sec1/Munc18 (SM) protein, domain 1

Domain ID domain_id	6lpcB02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	830 — Syntaxin Binding Protein 1; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Sec1/Munc18 (SM) protein, domain 3a

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8. Citations (1)

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Unit-cell length a length_a	80.475 Å
Unit-cell length b length_b	80.475 Å
Unit-cell length c length_c	247.657 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 41
Space-group number int_tables_number	76
Crystal system crystal_system	—

Resolution resolution	3.402 Å
Low-resolution limit resolution_low	49.072 Å
R factor r_factor	0.2834
R_work r_work	0.2809
R_free r_free	0.3306

Description description	Syntaxin-binding protein 1
Molecular weight formula_weight	67665.6 kDa
Mutation mutation	K332E, K333E
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	7114

Crystal Structure of rat Munc18-1 with K332E/K333E mutation

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

Syntaxin-binding protein 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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Rattus norvegicus
通用名 common_name	Rat
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli BL21(DE3)

fit	/app/data/saxs_computation/lp/6lpc/6lpc.fit
pddf	/app/data/pr_computation/lp/6lpc/6lpc.pr.out
profile	/app/data/saxs_computation/lp/6lpc/6lpc.dat