9ots

Cryo-EM structure of the T9SS PORkN ring complex of P. Gingivalis

Method: ELECTRON MICROSCOPY D_max: 168.0 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	9ots
沉积日期 deposition_date	2025-05-27
结构标题 title	Cryo-EM structure of the T9SS PORkN ring complex of P. Gingivalis
关键词 keywords	T9SS, Type IX SECRETION SYSTEM, PORKN RING COMPLEX, PORPHYROMONAS GINGIVALIS, PROTEIN TRANSPORT, MEMBRANE PROTEIN; MEMBRANE PROTEIN
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	48.33 Å
回转半径 Rg (电子) rg_electron	48.42 Å
零角强度 I(0) i0	888063000.00
分子量 molecular_weight	243980.0 kDa
排除体积 excluded_volume	303860 Å³
包络体积 envelope_volume	479050 Å³
水化壳体积 shell_volume	82772 Å³
包络直径 envelope_diameter	185.8 Å
壳层 Rg shell_rg	51.41 Å
包络 Rg envelope_rg	48.55 Å
形状 Rg shape_rg	48.42 Å
总 Rg total_rg	48.55 Å
总原子数 total_atoms	17238
残基数 n_residues	2109
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	168.0 Å
Rg (实空间) rg_real	48.57 Å
Rg 误差 (实空间) rg_real_error	1.50 Å
I(0) (实空间) i0_real	8.8810e+08
I(0) 误差 (实空间) i0_real_error	1.7850e+07
Rg (倒空间) rg_reciprocal	48.33 Å
I(0) (倒空间) i0_reciprocal	887800000.0000
解质量估计 total_estimate	0.8504
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	50.9 Å
偏度 Skewness skewness	0.492
峰度 Kurtosis kurtosis	-0.202
角度范围 angular_range	— – 0.1650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	280100000.0000
实空间数据点数 n_real_points	34
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.774; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.738

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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	Por secretion system protein porK/gldK
分子量 formula_weight	55979.6 kDa
来源方法 src_method	nat
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C
原子数 atom_count	17238

MCRKNRFFALAGFFLFGVFTISSCGSSKRAVGGELTGAKLSSWNEPSPFGMIQVPRGSIVLGNKEADSLWGIPAESRPISVDAFWMDRTEITNAQYRQFVYYVRDSIIRERLADPAYGGNEEYKITENKFGEPVTPHLDWSKPIPSEKRATEEEIAAINSVYYTNPVTHDRKLNPDQMVYRYEVYDYRSAALREHQLKAAKRNLNTDIKVDPNAVVMISKDTAFVDESGNIISETITRPLSSEYDFLNTYIVPIYPDETCWVNDFPNARTEIYTRMYFNHPGYDDYPVVGISWEQAQAFCAWRSEFFRKGIRLPEGQIMDDFRLPTEAEWEYAARMGDSNNKYPWSTEDLRTGRGCFLGNFKPGEGDYTADGHLIPSRVSSFSPNDFGLYDMAGNVAEWTSTAFSESGLKQMSDINPELEYKAALTDPYILKQKVVRGGSWKDVARFIRSATRSHEYQNVGRSYIGFRCVRTSIAFSSGKAPKSSRRSIKK

Entity 2 polymer

描述 description	Por secretion system protein porN/gldN
分子量 formula_weight	41519.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	D,E,F

MKVFKAVIGAILAATVSIPSVAQENTNNRSPQVGRAPRNTEVEQMTTLSNRAQEFNRRLTQKTDNAPWRRVVYRRVDLMEESNAVLYYPPRPIGDRKNLFSTIFGLINSNSLDVYEYLDGFEAFTDQYKIKFQEFLDRFGIYYQPSTNKNAELFKVADSDIPSAEVKAYYVKEEWYFTPTNSDVDIKIQAICPIMTGQDEFGEVRNQPLFWIPYENIRPYIARERVMLSSLNNTRNSTIDDFFRLNLYKGDIVKTENLHNRALAEYCPTPDSMKMESKRIDKELQGFRDGLFVTQDTTWMKQVETKKSKGKKLEKARGKNITSRTRGQGEGAAETEAVEPKKQKASKNKAATRSVRRRK

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7. 引用文献 (1)

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分辨率 resolution	3.200 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	3.20 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	2500000

fit	/app/data/saxs_computation/ot/9ots/9ots.fit
pddf	/app/data/pr_computation/ot/9ots/9ots.pr.out
profile	/app/data/saxs_computation/ot/9ots/9ots.dat

Cryo-EM structure of the T9SS PORkN ring complex of P. Gingivalis

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

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 polymer

聚合体 Polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)