9gne

CryoEM structure of mammalian AAP in complex with acetyl-alanyl-chloromethylketone

Method: ELECTRON MICROSCOPY D_max: 135.6 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	9gne
沉积日期 deposition_date	2024-09-02
最后修订 last_revision	2025-10-22
结构标题 title	CryoEM structure of mammalian AAP in complex with acetyl-alanyl-chloromethylketone
关键词 keywords	covalent inhibitor, serine-protease, flexible active site, oligopeptidase, self-assembly, HYDROLASE; HYDROLASE
实验方法 method	ELECTRON MICROSCOPY

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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	45.55 Å
回转半径 Rg (电子) rg_electron	44.94 Å
零角强度 I(0) i0	2017340000.00
分子量 molecular_weight	253000.0 kDa
排除体积 excluded_volume	247780 Å³
包络体积 envelope_volume	505450 Å³
水化壳体积 shell_volume	91425 Å³
包络直径 envelope_diameter	134.9 Å
壳层 Rg shell_rg	52.95 Å
包络 Rg envelope_rg	42.74 Å
形状 Rg shape_rg	44.95 Å
总 Rg total_rg	45.18 Å
总原子数 total_atoms	19244
残基数 n_residues	2736
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	135.6 Å
Rg (实空间) rg_real	45.23 Å
Rg 误差 (实空间) rg_real_error	1.00 Å
I(0) (实空间) i0_real	2.0170e+09
I(0) 误差 (实空间) i0_real_error	3.3250e+07
Rg (倒空间) rg_reciprocal	45.54 Å
I(0) (倒空间) i0_reciprocal	2018000000.0000
解质量估计 total_estimate	0.8885
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	65.8 Å
偏度 Skewness skewness	0.016
峰度 Kurtosis kurtosis	-0.684
角度范围 angular_range	— – 0.1750 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	180400000.0000
实空间数据点数 n_real_points	36
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.964; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.677

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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 (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	19244

MERQVLLSEPEEAAALYRGLSRQPALSAACLGPEVTTQYGGRYRTVHTEWTQRDLERMENIRFCRQYLVFHDGDSVVFAGPAGNSVETRGELLSRESPSGTMKAVLRKAGGTGTAEEKQFLEVWEKNRKLKSFNLSALEKHGPVYEDDCFGCLSWSHSETHLLYVADKKRPKAESFFQTKALDVTGSDDEMARTKKPDQAIKGDQFLFYEDWGENMVSKSTPVLCVLDIESGNISVLEGVPESVSPGQAFWAPGDTGVVFVGWWHEPFRLGIRFCTNRRSALYYVDLTGGKCELLSDESVAVTSPRLSPDQCRIVYLRFPSLVPHQQCGQLCLYDWYTRVTSVVVDIVPRQLGEDFSGIYCSLLPLGCWSADSQRVVFDSPQRSRQDLFAVDTQMGSVTSLTAGGSGGSWKLLTIDRDLMVVQFSTPSVPPSLKVGFLPPAGKEQAVSWVSLEEAEPFPDISWSIRVLQPPPQQEHVQYAGLDFEAILLQPSNSPEKTQVPMVVMPHGGPHSSFVTAWMLFPAMLCKMGFAVLLVNYRGSTGFGQDSILSLPGNVGHQDVKDVQFAVEQVLQEEHFDAGRVALMGGSHGGFLSCHLIGQYPETYSACVVRNPVINIASMMGSTDIPDWCMVEAGFSYSSDCLPDLSVWAAMLDKSPIKYAPQVKTPLLLMLGQEDRRVPFKQGMEYYRVLKARNVPVRLLLYPKSTHALSEVEVESDSFMNAVLWLCTHLGS

Entity 2 non-polymer

描述 description	~{N}-[(2~{S},3~{S})-3-oxidanylbutan-2-yl]ethanamide
分子量 formula_weight	131.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

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7. 引用文献 (1)

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分辨率 resolution	3.20 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	412960

fit	/app/data/saxs_computation/gn/9gne/9gne.fit
pddf	/app/data/pr_computation/gn/9gne/9gne.pr.out
profile	/app/data/saxs_computation/gn/9gne/9gne.dat