SAXSdb — 8dk2

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8dk2
沉积日期 deposition_date	2022-07-01
结构标题 title	CryoEM structure of Pseudomonas aeruginosa PA14 JetABC in an unclamped state trapped in ATP dependent dimeric form
关键词 keywords	;Wadjet, Bacterial defense systems, JetA, JetB, JetC, Anti-plasmid defense system, EptA, EptB, EptC, MksB, MksE, MksF, SMC, DNA BINDING PROTEIN-DNA complex ;; DNA BINDING PROTEIN/DNA
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	71.91 Å
回转半径 Rg (电子) rg_electron	74.13 Å
零角强度 I(0) i0	1816320000.00
分子量 molecular_weight	337850.0 kDa
排除体积 excluded_volume	415930 Å³
包络体积 envelope_volume	779270 Å³
水化壳体积 shell_volume	102210 Å³
包络直径 envelope_diameter	294.7 Å
壳层 Rg shell_rg	58.82 Å
包络 Rg envelope_rg	75.14 Å
形状 Rg shape_rg	74.15 Å
总 Rg total_rg	73.68 Å
总原子数 total_atoms	23727
残基数 n_residues	2892
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	217.4 Å
Rg (实空间) rg_real	68.58 Å
Rg 误差 (实空间) rg_real_error	1.40 Å
I(0) (实空间) i0_real	1.7790e+09
I(0) 误差 (实空间) i0_real_error	3.8230e+07
Rg (倒空间) rg_reciprocal	68.59 Å
I(0) (倒空间) i0_reciprocal	1802000000.0000
解质量估计 total_estimate	0.8546
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	69.2 Å
偏度 Skewness skewness	0.646
峰度 Kurtosis kurtosis	-0.095
角度范围 angular_range	— – 0.1100 Å⁻¹
当前正则化参数 α current_alpha	0.0580
最高正则化参数 α highest_alpha	105700000.0000
实空间数据点数 n_real_points	23
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.830; Stabil: 0.985; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.368

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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 (7)

Entity 1 polymer

描述 description	JetA
分子量 formula_weight	59233.5 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	23727

MKSSHHHHHHENLYFQSNAEESAQQRSERYVSARSQHPAWLLLASRRAPLVLGCLRTLFERAHDGIPMEDALQALSEMLAAYASQELYEIDPDATHLQAGRELREWIKRRLVVEREGRIYATDALESAIQFVDSLDSRIMTSTASRLSVVQREIENLETGLNPSPTGRIASLRRRIQDLEHELARVEAGHVDVLDEAQAIEGMREVYNLATSLRADFRRVEDSWREADRALRHSIISEQSHRGEIVDRLLDGQDALLNTPEGRVFESFQQQLRQSAELEVMRERLRTILRHPAVPKALNRPQQRELRWLALRLVRESQAVLQARARSERDVRGFMKTGLAAEHHRVGQLLNDFFNLALSVDWQRQSERRKPACLPPVGVAITGVPAIERLRFKTLDDDDAGELDLSLKPAGLEQIDDDFWDAFDGLDREALIHDTLAVLVEQGRPVSLGELASLLPPAHDLETFALWLAMAREAGIEVLTEERQFVELVDEDEQRWGFNLPYVGLDHEALKDIDWEL

来源 Source

来源生物 organism	Pseudomonas aeruginosa PA14
NCBI 分类编号 ncbi_taxonomy_id	652611
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	JetC
分子量 formula_weight	126683.2 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

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

MKSSHHHHHHENLYFQSNAKQALLWRDSETFILTSIELYNWGGFQGYHRAEIDPSGTAVIGPTGSGKTTLVDALMTLLCANPRYNLASTGGHESDRDLVSYVRGVTGPGDGGVEQSHIARQGKTVTAIAATLERDGAQVRLGAVLWFEGTSSSASDLKKLWLLSESPEQTLEHWLSQHHAGGMRALRQMEKDGMGIWPYPSKKAFLARLRDYFEVGENAFTLLNRAAGLKQLNSIDEIFRELVLDDRSAFERAAEVASSFDDLTDIHRELETARKQQRSLQPVADGWERYRALQEQLQDKQALEGILPVWFAEQGYRLWLAETNRLEKEHKQAELDQAQCRSQLEIQKGVVDQHRQRYLRVGGAGIDQLRGRIADWVRECDKRRLKAEQYQRLAKGLGLADELSAAALEENQQQIAARLEILAQQTTDARQKAFDAGLVQQELNGRLQSLQQERAEVERRPGSNLPGHFHAFRGDLAQELGVDESALPFVAELVQVKPEELAWRGAIERAIGSHRLRILVPQGSSQAALRWVNQRHNRLHVRLLEVKEPSSRPVFFDDGFTRKLTFKEHPYREAVKALLADNDRHCVESTEQLRHTPHAMTAQGLMSGKERFFDKQDQKRLDEDWLTGFDNRDRLAFLAEQIREVNEQLVPAKLALDAAQGDVGQLESQASLLQRIEELQFDDIDRPGAERQLQSLRTQLDTLTRPDSNLAVIKAELDQAEALRESLDQQLQRLIEQCVQLKTQFDQAASATRKAYRGAEKGLSDTQRELAQAHFPILSTDDLGDIDELERKHTRELQGQLKTLGEKLGDQKTELAKRMSDALKADTGALAEVGRELVDVPRYLERLRVLTEEALPEKLKRFLEYLNRSSDDGVTQLLSYIDHEVSMIEERLDDLNSTMQRVDFQPGRYLRLVAKKVIHESLRTLQHAQRQLNSARFIDDEGESHYKALQALVGLLKDACEHSRNQGAKALLDPRFRLEFAVSVIDREGNNLIETRTGSQGGSGGEKEIIASYVLTASLSYALCPDGSSRPLFGTIVLDQAFSRSSHAVAGRIIAALREFGLHAVFITPNKEMRLLRHHTRSAVVVHRRGVESSLVSLSWEALDEHHQQRIRAMHEVAH

来源 Source

来源生物 organism	Pseudomonas aeruginosa PA14
NCBI 分类编号 ncbi_taxonomy_id	652611
宿主生物 host_organism	Escherichia coli

Entity 3 polymer

描述 description	JetB
分子量 formula_weight	27537.0 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	F,G,H,I

MAGIFDRIAGASGADETELTAEPMALDDGMDGEQPAMSANIQVDERRTPQRVREAVQEMLKYGLLEESHKPNLYRSALTNIEVVDRILEPLDLAMGVDEVRGLVFVTVRQGEVAEQDDWSHPLVRRQRLNLEQSLLIAILRQHFIAYEQESGTGASQALVAVDELIPQLQVYLGELGSEAKERNRIITLLDQLKGHGLVSALDAHDRVIIRPIITHLANPENLQALVVWLREQVEGAVTPAAGGEEDEA

来源 Source

来源生物 organism	Pseudomonas aeruginosa PA14
NCBI 分类编号 ncbi_taxonomy_id	652611
宿主生物 host_organism	Escherichia coli

Entity 4 polymer

描述 description	DNA (26-MER)
分子量 formula_weight	7864.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	P

TTTTTTTTTTTTTTTTTTTTTTTTTT

Entity 5 polymer

描述 description	DNA (26-MER)
分子量 formula_weight	8098.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	Q

AAAAAAAAAAAAAAAAAAAAAAAAAA

Entity 6 non-polymer

描述 description	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
分子量 formula_weight	523.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 7 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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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	4.10 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	56600

fit	/app/data/saxs_computation/dk/8dk2/8dk2.fit
pddf	/app/data/pr_computation/dk/8dk2/8dk2.pr.out
profile	/app/data/saxs_computation/dk/8dk2/8dk2.dat

CryoEM structure of Pseudomonas aeruginosa PA14 JetABC in an unclamped state trapped in ATP dependent dimeric form

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 (7)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 polymer

聚合体 Polymer

来源 Source

Entity 4 polymer

聚合体 Polymer

Entity 5 polymer

聚合体 Polymer

Entity 6 non-polymer

Entity 7 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)