8p1f

X-ray structure of acetylcholine-binding protein (AChBP) in complex with FL001909.

Method: X-RAY DIFFRACTION D_max: 179.4 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	8p1f
沉积日期 deposition_date	2023-05-12
结构标题 title	X-ray structure of acetylcholine-binding protein (AChBP) in complex with FL001909.
关键词 keywords	Fragment based drug design, Acetylcholine-binding protein, choline-binding proteins, CHOLINE-BINDING PROTEIN; CHOLINE-BINDING PROTEIN
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	55.62 Å
回转半径 Rg (电子) rg_electron	54.88 Å
零角强度 I(0) i0	3135650000.00
分子量 molecular_weight	461590.0 kDa
排除体积 excluded_volume	573470 Å³
包络体积 envelope_volume	820730 Å³
水化壳体积 shell_volume	119530 Å³
包络直径 envelope_diameter	189.3 Å
壳层 Rg shell_rg	61.88 Å
包络 Rg envelope_rg	53.48 Å
形状 Rg shape_rg	54.88 Å
总 Rg total_rg	55.08 Å
总原子数 total_atoms	32533
残基数 n_residues	4039
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	179.4 Å
Rg (实空间) rg_real	55.44 Å
Rg 误差 (实空间) rg_real_error	1.43 Å
I(0) (实空间) i0_real	3.1360e+09
I(0) 误差 (实空间) i0_real_error	6.2550e+07
Rg (倒空间) rg_reciprocal	55.76 Å
I(0) (倒空间) i0_reciprocal	3137000000.0000
解质量估计 total_estimate	0.8837
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	57.7 Å
偏度 Skewness skewness	0.172
峰度 Kurtosis kurtosis	-0.598
角度范围 angular_range	— – 0.1400 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	727100000.0000
实空间数据点数 n_real_points	29
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.908; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.779

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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 (4)

Entity 1 polymer

描述 description	Acetylcholine-binding protein
分子量 formula_weight	27060.3 kDa
来源方法 src_method	man
拷贝数 entity_count	20

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T
原子数 atom_count	33433

MRRNIFCLACLWIVQACLSLDRADILYNIRQTSRPDVIPTQRDRPVAVSVSLKFINILEVNEITNEVDVVFWQQTTWSDRTLAWNSSHSPDQVSVPISSLWVPDLAAYNAISKPEVLTPQLARVVSDGEVLYMPSIRQRFSCDVSGVDTESGATCRIKIGSWTHHSREISVDPTTENSDDSEYFSQYSRFEILDVTQKKNSVTYSCCPEAYEDVEVSLNFRKKGRSEILGSHHHHHH

来源 Source

来源生物 organism	Lymnaea stagnalis
通用名 common_name	great pond snail
NCBI 分类编号 ncbi_taxonomy_id	6523
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 non-polymer

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	221.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	13

Entity 3 non-polymer

描述 description	4-azanyl-1-phenyl-piperidine-4-carboxylic acid
分子量 formula_weight	220.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 4 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	703

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7. 引用文献 (1)

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晶胞边长 a length_a	116.710 Å
晶胞边长 b length_b	140.710 Å
晶胞边长 c length_c	147.170 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	109.68 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	40

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	2.100 Å
最低分辨率 resolution_low	49.370 Å
R 因子 r_factor	0.2266
R_work r_work	0.2251
R_free r_free	0.2548

fit	/app/data/saxs_computation/p1/8p1f/8p1f.fit
pddf	/app/data/pr_computation/p1/8p1f/8p1f.pr.out
profile	/app/data/saxs_computation/p1/8p1f/8p1f.dat

X-ray structure of acetylcholine-binding protein (AChBP) in complex with FL001909.

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