8rvg

Structure of the binding domain of BoNT/A mutant Y1117V in complex with the GD1a ganglioside receptor

Method: X-RAY DIFFRACTION D_max: 118.3 Å Quality: GOOD

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8rvg
沉积日期 deposition_date	2024-02-01
结构标题 title	Structure of the binding domain of BoNT/A mutant Y1117V in complex with the GD1a ganglioside receptor
关键词 keywords	botulinum neurotoxin, receptor binding, ganglioside, TOXIN; TOXIN
实验方法 method	X-RAY DIFFRACTION

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2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	34.82 Å
回转半径 Rg (电子) rg_electron	34.50 Å
零角强度 I(0) i0	146904000.00
分子量 molecular_weight	98181.0 kDa
排除体积 excluded_volume	123240 Å³
包络体积 envelope_volume	156010 Å³
水化壳体积 shell_volume	39618 Å³
包络直径 envelope_diameter	127.2 Å
壳层 Rg shell_rg	38.99 Å
包络 Rg envelope_rg	34.09 Å
形状 Rg shape_rg	34.46 Å
总 Rg total_rg	34.95 Å
总原子数 total_atoms	6922
残基数 n_residues	832
球谐函数阶数 n_harmonics	20
q 范围 q_range	— – 0.5000 Å⁻¹
数据点数 n_points	101
壳层类型 shell_type	directional
溶剂电子密度 solvent_density	0.3340 e/Å³
壳层衬度 contrast_shell	0.0300 e/Å³
CRYSOL 版本 crysol_version	4.1.3

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3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	118.3 Å
Rg (实空间) rg_real	35.05 Å
Rg 误差 (实空间) rg_real_error	1.11 Å
I(0) (实空间) i0_real	1.4690e+08
I(0) 误差 (实空间) i0_real_error	2.5580e+06
Rg (倒空间) rg_reciprocal	34.91 Å
I(0) (倒空间) i0_reciprocal	146900000.0000
解质量估计 total_estimate	0.8496
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	34.2 Å
偏度 Skewness skewness	0.531
峰度 Kurtosis kurtosis	-0.223
角度范围 angular_range	— – 0.2250 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	56480000.0000
实空间数据点数 n_real_points	46
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.796; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.889; Smooth: 0.762

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4. 晶体学与实验 4. Crystallography & Experiment

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5. 实体与聚合体信息 (3)

Entity 1 polymer

描述 description	Botulinum neurotoxin A heavy chain
分子量 formula_weight	51649.4 kDa
突变 mutation	Y1117V
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	7268

MGSSHHHHHHSSGLVPRGSHMDTSILNLRYESNHLIDLSRYASKINIGSKVNFDPIDKNQIQLFNLESSKIEVILKNAIVYNSMYENFSTSFWIRIPKYFNSISLNNEYTIINCMENNSGWKVSLNYGEIIWTLQDTQEIKQRVVFKYSQMINISDYINRWIFVTITNNRLNNSKIYINGRLIDQKPISNLGNIHASNNIMFKLDGCRDTHRYIWIKYFNLFDKELNEKEIKDLYDNQSNSGILKDFWGDYLQYDKPYYMLNLVDPNKYVDVNNVGIRGYMYLKGPRGSVMTTNIYLNSSLYRGTKFIIKKYASGNKDNIVRNNDRVYINVVVKNKEYRLATNASQAGVEKILSALEIPDVGNLSQVVVMKSKNDQGITNKCKMNLQDNNGNDIGFIGFHQFNNIAKLVASNWYNRQIERSSRTLGCSWEFIPVDDGWGERPLQ

来源 Source

来源生物 organism	Clostridium botulinum
NCBI 分类编号 ncbi_taxonomy_id	1491
宿主生物 host_organism	Escherichia coli BL21

Entity 2 branched

描述 description	;N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-beta-D-galactopyranose ;
分子量 formula_weight	836.7 kDa
来源方法 src_method	man
拷贝数 entity_count	2

Entity 3 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	313

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7. 引用文献 (1)

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晶胞边长 a length_a	73.531 Å
晶胞边长 b length_b	104.421 Å
晶胞边长 c length_c	112.889 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	1.900 Å
最低分辨率 resolution_low	55.010 Å
R 因子 r_factor	0.2196
R_work r_work	0.2175
R_free r_free	0.2597

fit	/app/data/saxs_computation/rv/8rvg/8rvg.fit
pddf	/app/data/pr_computation/rv/8rvg/8rvg.pr.out
profile	/app/data/saxs_computation/rv/8rvg/8rvg.dat

Structure of the binding domain of BoNT/A mutant Y1117V in complex with the GD1a ganglioside receptor

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

1. 结构基本信息 1. Structure Basics

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

4. 晶体学与实验 4. Crystallography & Experiment

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

衍射实验 Diffraction