9hxq

Cryo-EM structure of acylaminoacyl peptidase (AAP) in covalent complex with inhibitor AEBSF

Method: ELECTRON MICROSCOPY D_max: 135.2 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

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9hxq
沉积日期 deposition_date	2025-01-08
最后修订 last_revision	2025-10-22
结构标题 title	Cryo-EM structure of acylaminoacyl peptidase (AAP) in covalent complex with inhibitor AEBSF
关键词 keywords	inhibitor, covalent, serine-protease, acylpeptide hydrolase, APEH, OPH, acylaminoacyl peptidase, sulphonate, 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	46.16 Å
回转半径 Rg (电子) rg_electron	45.36 Å
零角强度 I(0) i0	1190010000.00
分子量 molecular_weight	294120.0 kDa
排除体积 excluded_volume	370810 Å³
包络体积 envelope_volume	528390 Å³
水化壳体积 shell_volume	94269 Å³
包络直径 envelope_diameter	137.1 Å
壳层 Rg shell_rg	53.57 Å
包络 Rg envelope_rg	43.26 Å
形状 Rg shape_rg	45.39 Å
总 Rg total_rg	45.61 Å
总原子数 total_atoms	20740
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

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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	135.2 Å
Rg (实空间) rg_real	45.83 Å
Rg 误差 (实空间) rg_real_error	0.74 Å
I(0) (实空间) i0_real	1.1900e+09
I(0) 误差 (实空间) i0_real_error	1.8760e+07
Rg (倒空间) rg_reciprocal	46.16 Å
I(0) (倒空间) i0_reciprocal	1190000000.0000
解质量估计 total_estimate	0.8750
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	63.6 Å
偏度 Skewness skewness	0.016
峰度 Kurtosis kurtosis	-0.685
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	233200000.0000
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: 0.977; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.452

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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	B,A,C,D
原子数 atom_count	20740

MERQVLLSEPEEAAALYRGLSRQPALSAACLGPEVTTQYGGRYRTVHTEWTQRDLERMENIRFCRQYLVFHDGDSVVFAGPAGNSVETRGELLSRESPSGTMKAVLRKAGGTGTAEEKQFLEVWEKNRKLKSFNLSALEKHGPVYEDDCFGCLSWSHSETHLLYVADKKRPKAESFFQTKALDVTGSDDEMARTKKPDQAIKGDQFLFYEDWGENMVSKSTPVLCVLDIESGNISVLEGVPESVSPGQAFWAPGDTGVVFVGWWHEPFRLGIRFCTNRRSALYYVDLTGGKCELLSDESVAVTSPRLSPDQCRIVYLRFPSLVPHQQCGQLCLYDWYTRVTSVVVDIVPRQLGEDFSGIYCSLLPLGCWSADSQRVVFDSPQRSRQDLFAVDTQMGSVTSLTAGGSGGSWKLLTIDRDLMVVQFSTPSVPPSLKVGFLPPAGKEQAVSWVSLEEAEPFPDISWSIRVLQPPPQQEHVQYAGLDFEAILLQPSNSPEKTQVPMVVMPHGGPHSSFVTAWMLFPAMLCKMGFAVLLVNYRGSTGFGQDSILSLPGNVGHQDVKDVQFAVEQVLQEEHFDAGRVALMGGSHGGFLSCHLIGQYPETYSACVVRNPVINIASMMGSTDIPDWCMVEAGFSYSSDCLPDLSVWAAMLDKSPIKYAPQVKTPLLLMLGQEDRRVPFKQGMEYYRVLKARNVPVRLLLYPKSTHALSEVEVESDSFMNAVLWLCTHLGS

Entity 2 non-polymer

描述 description	4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE
分子量 formula_weight	203.2 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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晶胞边长 a length_a	1.000 Å
晶胞边长 b length_b	1.000 Å
晶胞边长 c length_c	1.000 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	—

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

分辨率 resolution	2.800 Å
最低分辨率 resolution_low	— Å
R 因子 r_factor	—
R_work r_work	—
R_free r_free	—

分辨率 resolution	2.80 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	169418

fit	/app/data/saxs_computation/hx/9hxq/9hxq.fit
pddf	/app/data/pr_computation/hx/9hxq/9hxq.pr.out
profile	/app/data/saxs_computation/hx/9hxq/9hxq.dat

Cryo-EM structure of acylaminoacyl peptidase (AAP) in covalent complex with inhibitor AEBSF

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

冷冻电镜 EM 3D

5. 实体与聚合体信息 (2)

Entity 1 polymer

聚合体 Polymer

Entity 2 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)