9gou

Cryo-EM structure of acylaminoacyl-peptidase in complex with dichlorvos

Method: ELECTRON MICROSCOPY D_max: 138.2 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

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9gou
沉积日期 deposition_date	2024-09-06
最后修订 last_revision	2025-10-22
结构标题 title	Cryo-EM structure of acylaminoacyl-peptidase in complex with dichlorvos
关键词 keywords	;serine-protease, covalent inhibitor, dichlorvos, dimethoxy-phosphate, acyl-peptide-hydrolase, oxidized protein hydrolase, APEH, AARE, AAP, OPH, HYDROLASE ;; HYDROLASE
实验方法 method	ELECTRON MICROSCOPY

▼

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

回转半径 Rg (Guinier) rg_guinier	46.08 Å
回转半径 Rg (电子) rg_electron	45.45 Å
零角强度 I(0) i0	2383860000.00
分子量 molecular_weight	273410.0 kDa
排除体积 excluded_volume	266680 Å³
包络体积 envelope_volume	528350 Å³
水化壳体积 shell_volume	94227 Å³
包络直径 envelope_diameter	137.2 Å
壳层 Rg shell_rg	53.56 Å
包络 Rg envelope_rg	43.30 Å
形状 Rg shape_rg	45.44 Å
总 Rg total_rg	45.69 Å
总原子数 total_atoms	20746
残基数 n_residues	2788
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

▼

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

最大尺寸 Dmax dmax	138.2 Å
Rg (实空间) rg_real	45.75 Å
Rg 误差 (实空间) rg_real_error	0.86 Å
I(0) (实空间) i0_real	2.3840e+09
I(0) 误差 (实空间) i0_real_error	4.3680e+07
Rg (倒空间) rg_reciprocal	46.07 Å
I(0) (倒空间) i0_reciprocal	2385000000.0000
解质量估计 total_estimate	0.8957
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	65.0 Å
偏度 Skewness skewness	0.015
峰度 Kurtosis kurtosis	-0.682
角度范围 angular_range	— – 0.1700 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	208900000.0000
实空间数据点数 n_real_points	35
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.961; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.779

▶

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

▶

5. 实体与聚合体信息 (2)

Entity 1 polymer

描述 description	Acylamino-acid-releasing enzyme
分子量 formula_weight	81324.4 kDa
EC 编号 ec_number	3.4.19.1
来源方法 src_method	nat
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	20746

MERQVLLSEPEEAAALYRGLSRQPALSAACLGPEVTTQYGGRYRTVHTEWTQRDLERMENIRFCRQYLVFHDGDSVVFAGPAGNSVETRGELLSRESPSGTMKAVLRKAGGTGTAEEKQFLEVWEKNRKLKSFNLSALEKHGPVYEDDCFGCLSWSHSETHLLYVADKKRPKAESFFQTKALDVTGSDDEMARTKKPDQAIKGDQFLFYEDWGENMVSKSTPVLCVLDIESGNISVLEGVPESVSPGQAFWAPGDTGVVFVGWWHEPFRLGIRFCTNRRSALYYVDLTGGKCELLSDESVAVTSPRLSPDQCRIVYLRFPSLVPHQQCGQLCLYDWYTRVTSVVVDIVPRQLGEDFSGIYCSLLPLGCWSADSQRVVFDSPQRSRQDLFAVDTQMGSVTSLTAGGSGGSWKLLTIDRDLMVVQFSTPSVPPSLKVGFLPPAGKEQAVSWVSLEEAEPFPDISWSIRVLQPPPQQEHVQYAGLDFEAILLQPSNSPEKTQVPMVVMPHGGPHSSFVTAWMLFPAMLCKMGFAVLLVNYRGSTGFGQDSILSLPGNVGHQDVKDVQFAVEQVLQEEHFDAGRVALMGGSHGGFLSCHLIGQYPETYSACVVRNPVINIASMMGSTDIPDWCMVEAGFSYSSDCLPDLSVWAAMLDKSPIKYAPQVKTPLLLMLGQEDRRVPFKQGMEYYRVLKARNVPVRLLLYPKSTHALSEVEVESDSFMNAVLWLCTHLGS

Entity 2 non-polymer

描述 description	dimethyl hydrogen phosphite
分子量 formula_weight	110.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

▶

7. 引用文献 (1)

▶

分辨率 resolution	2.65 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	199800

fit	/app/data/saxs_computation/go/9gou/9gou.fit
pddf	/app/data/pr_computation/go/9gou/9gou.pr.out
profile	/app/data/saxs_computation/go/9gou/9gou.dat