8rt5

;I-layer structure (TrwF/VirB9CTD, TrwE/VirB10CTD) of the outer membrane core complex from the fully-assembled R388 type IV secretion system determined by cryo-EM. ;

Method: ELECTRON MICROSCOPY D_max: 166.6 Å Quality: REASONABLE

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	8rt5
沉积日期 deposition_date	2024-01-25
结构标题 title	;I-layer structure (TrwF/VirB9CTD, TrwE/VirB10CTD) of the outer membrane core complex from the fully-assembled R388 type IV secretion system determined by cryo-EM. ;
关键词 keywords	;type IV secretion system type 4 secretion system T4SS I-layer core complex outer membrane complex R388 plasmid conjugation bacterial secretion secretion secretion system protein complex VirB10 VirB9 TrwE TrwF, 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	62.20 Å
回转半径 Rg (电子) rg_electron	61.24 Å
零角强度 I(0) i0	913680000.00
分子量 molecular_weight	247630.0 kDa
排除体积 excluded_volume	307310 Å³
包络体积 envelope_volume	568670 Å³
水化壳体积 shell_volume	77114 Å³
包络直径 envelope_diameter	159.2 Å
壳层 Rg shell_rg	70.67 Å
包络 Rg envelope_rg	54.50 Å
形状 Rg shape_rg	61.25 Å
总 Rg total_rg	61.42 Å
总原子数 total_atoms	17456
残基数 n_residues	2129
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	166.6 Å
Rg (实空间) rg_real	61.79 Å
Rg 误差 (实空间) rg_real_error	1.14 Å
I(0) (实空间) i0_real	9.1370e+08
I(0) 误差 (实空间) i0_real_error	1.7030e+07
Rg (倒空间) rg_reciprocal	62.48 Å
I(0) (倒空间) i0_reciprocal	914700000.0000
解质量估计 total_estimate	0.7125
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	113.3 Å
偏度 Skewness skewness	-0.285
峰度 Kurtosis kurtosis	-1.076
角度范围 angular_range	— – 0.1250 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	16810000.0000
实空间数据点数 n_real_points	26
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.519; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.703; Smooth: 0.000

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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	TrwE protein
分子量 formula_weight	42443.8 kDa
来源方法 src_method	man
拷贝数 entity_count	16

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,D,G,J,M,P,S,u,V,Y,b,e,h,k,n,y
原子数 atom_count	17456

MFGRKKGDVIDAGAELERAEQERIEGEYGASELASERRPHTPGARTLLMVLLCVIAVVLVTLSYKAYKVRGVVEDDDAQPQQVVRQVIPGYTPRPIRPEPENVPEPPQPTTSVPAIQPAPVTQPVRPQPTGPREKTPYELARERMLRSGLTAGSGGGEDLPRPQGGDVPAGGLMGGGGGGGELAEKLQPMRLSGSSAGRLGNRDMLITQGTQLDCVLETRLVTTQPGMTTCHLTRDVYSTSGRVVLLDRGSKVVGFYQGGLRQGQARIFVQWSRIETPSGVVINLDSPGTGPLGEAGLGGWIDRHFWERFGGAIMISLIGDLGDWASRQGSRQGDNSIQFSNTANGVESAAAEALRNSINIPPTLYKNQGERVNILVARDLDFSDVYSLESIPTK

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	TrwF protein
分子量 formula_weight	29749.6 kDa
来源方法 src_method	man
拷贝数 entity_count	16

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B,E,H,K,N,Q,T,v,W,Z,c,f,i,l,o,z

MKKLAIVALLASLHAVPALALDVPSSSRYDHRIRYVTYNPADVVQVDTVLGVATHIMLEEGEQYLTHAFGDSEAYAFARKGRHIFIKPQAELANTNLIVVTDRRSYKFRLQMRNDRNGAMYELAFRYPDTQARQTREANARAAVEAAFEQRVGAYYNLKYMMSGDKDIAPVNAWDDGRFTYFKFSANADLPSIYFVDAEGNESLVPRTTVGSSNNIIAVHKVNPKWMIRLGNRALAIFNEAYDPNGVPNDTGTASPAVRRVNKGGN

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

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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	2.69 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	784923

fit	/app/data/saxs_computation/rt/8rt5/8rt5.fit
pddf	/app/data/pr_computation/rt/8rt5/8rt5.pr.out
profile	/app/data/saxs_computation/rt/8rt5/8rt5.dat

;I-layer structure (TrwF/VirB9CTD, TrwE/VirB10CTD) of the outer membrane core complex from the fully-assembled R388 type IV secretion system determined by cryo-EM. ;

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

冷冻电镜 EM 3D

5. 实体与聚合体信息 (2)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)