SAXSdb — 8q72

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8q72
沉积日期 deposition_date	2023-08-15
结构标题 title	E. coli plasmid-borne JetABCD(E248A) core in a cleavage-competent state
关键词 keywords	;SMC complexes, DNA loop extrusion, nuclease, bacterial immunity, defense system, topoisomerase, plamid restriction, MksBEFG, Wadjet, EptABCD, horizontal gene transfer, DNA binding protein, DNA kinking ;; DNA BINDING 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	73.60 Å
回转半径 Rg (电子) rg_electron	73.40 Å
零角强度 I(0) i0	6059610000.00
分子量 molecular_weight	612980.0 kDa
排除体积 excluded_volume	749200 Å³
包络体积 envelope_volume	1331900 Å³
水化壳体积 shell_volume	157040 Å³
包络直径 envelope_diameter	308.6 Å
壳层 Rg shell_rg	72.16 Å
包络 Rg envelope_rg	70.23 Å
形状 Rg shape_rg	73.36 Å
总 Rg total_rg	73.54 Å
总原子数 total_atoms	84390
残基数 n_residues	5106
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	254.9 Å
Rg (实空间) rg_real	73.44 Å
Rg 误差 (实空间) rg_real_error	1.92 Å
I(0) (实空间) i0_real	6.0550e+09
I(0) 误差 (实空间) i0_real_error	1.2620e+08
Rg (倒空间) rg_reciprocal	73.62 Å
I(0) (倒空间) i0_reciprocal	6060000000.0000
解质量估计 total_estimate	0.8602
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	85.0 Å
偏度 Skewness skewness	0.284
峰度 Kurtosis kurtosis	-0.287
角度范围 angular_range	— – 0.1050 Å⁻¹
当前正则化参数 α current_alpha	0.0232
最高正则化参数 α highest_alpha	302700000.0000
实空间数据点数 n_real_points	22
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.840; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.963; Smooth: 0.695

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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 (6)

Entity 1 polymer

描述 description	JetC
分子量 formula_weight	124562.9 kDa
突变 mutation	;"G" as been added to the C-terminus. ;
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	A,B,F,G
原子数 atom_count	84390

MNQVSGLAGKESFILTRIELFNWGGFHGLHQAAIHQDGTAVIGPTGSGKTTLVDALMTLLCANPRYNLASTGGHESDRDLISYVRGVSGPGDGGEGQSHIARPGKTVTGIAATLEREGKQVRLGALLWFDSTSSSVTDMKRLWLFSDNPGQTLEHWLNVYHEGGTRLLRQMEKEAIGLWTYPNKKQYLARLRDFFEVGENAFTLLNRAAGLKQLNSIDEIFRELVLDDHSAFDRAAEVANSFDGLTEIHQELETARKQQQSLQPVALSWEKYQKQERQLADWLTLESLLPLWFAQQASHLWREKINLLNARLAEAQTSEEQLQSQLDLQKKVVSDCMQRYLQVGGANIDELNERIKDWQKTLGSREALARQYQQLTRNLGLPSDLSQPQLEANQHEAEARCEQIAVDIKLKQEEAYQKGALSHHITEELRERENERAEIARRPDSNLPAHYQAFRSELAKALNVDESELPFVAELIQVKPEEAQWRGAIERAVGSNRLRILVAPESAQEALRWVNQRNNRLHVRLLEVKLPHSPARFFDDGFTRKLLWKDHPWREAVKALLAESDRHCVDSPEQLHDTPHAMTVQGLMSGKQRFYDKHDQKRLDEDWLTGFDNRDRLNFLAKEIATLQEQVKTANAAFEFAKGEVGLLQNQAASFQKIEQIDFDSIDVPGAKSQLDALRERLENLTRPDSDASVAKAKLDEAQTIESELDKQLRAANKVTNVLDTELTLARAAERKAQQTAQQGMKEEERELCASHFPVVTLEQLPDIRDLERQHERGIQHEIERVKAELHRLNIELTKRMSEAKRVDTGALVEAGADLDDIPVYLQRLQELTEEALPEKLNRFLDYLNRSSDDGVTQLLSHIEHEVLVIEERLNELNETMFRVDFQPDRYLRLDTKKVVHESLRTLEKAQRQLNAARFVDDNGESHYKALQVLVAQLRDACERNRTLGAKALLDPRFRLEFAVSVMDRQSGNVIESRTGSQGGSGGEKEIIASYVLTASLSYALCPAGSRYPLFGTIILDEAFSRSSHAVAGRIIAALREFGLHAVFITPNKEMRLLRDHTRSAIVVHRRGQNSNMASLSWEELERHYQRRGNAG

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	JetB
分子量 formula_weight	28020.4 kDa
突变 mutation	;"G" as been added to the C-terminus ;
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	C,D,H,I

MAGFFDKLINRSVTANAGCEPEPSDEEVTDESVEDSLASSETRTLQKIREATQELLKYGLLEEASKPNLYRIVLSHPEEVTRILEPLDLDIGIDEIRGLLYVKVRLDETPAQDEWAHPLVRRQRLNLEQSLLVAILRQHFVAWEQESGTGASQAQIAIDDLLPQLQIYLGDPGSESKERTRLLTLLDQLKGHGLVTSPDAHERIVIRPIIAHLADPINLQALLAWLREQIAQQTSPNDAPEKDSSEEDVG

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 3 polymer

描述 description	JetA
分子量 formula_weight	57818.9 kDa
突变 mutation	;"GPAA" has been added to the N-terminus and "G" to the C-terminus ;
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	E,J

GPAAMEENTRQRTENYISAKNQHPAWILLATRRAPLVLSCLKTLFEKSHDGIPLEEAIQSLSSILIEHVSQEQYDINQDNPFLQASRELREWIKRRLIVERDGRIFATDALEVAITFVESLDNRFMTSTASRLSTVQREIENLETRLNPNPANRVATLRRRISELERELQEAEAGHIEVLETHQAVEHIRDVYNLASSLRADFRRVEDSWREADRALRQSIIGEQYHRGDIVERLLNDQDALLNTPEGRVFDSFQQQLRQSSELKAMSERLRVILSHPSASDALNRLQRHDLRWLVKRLVDESQTVLQARARSERDVRGFMKTGLAAEHHRVGHLLNEFLNLALKLDWQRQMIRKQEVPLPAVGVAVTGIPAIERLRFKEVDDEAEQTLDLSNHAADLTQIGDDFWDAFNGLDREVLIQQTLQLLAKENRPVGLAELAELLPPAHDLETFAVWIGMAREAGIEVIDSQREFAELSDGEGRRWRFNLPTTGLESQALMDIDWEG

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 4 polymer

描述 description	JetD(E248A)
分子量 formula_weight	43938.5 kDa
突变 mutation	;"E248A" mutation has been introduced, "GSLEVLFQ" has been added to the C-terminus. ;
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	M,N

MYSPDELREKLARQWDSAKLRAERLLSPGNWPLCLPIGKPSTKIFAEQTQRVLQHVQRWRQVAVGHVEWEAVSFRASDTPVLMPLRWILNSPSEWINAAADPVVSREFRLLEGIIEQVNPIFHPLLVKHRSLWRHKDPQGVISAATLACRLEPGCAKGLPLRLLSGQGVDTKFIENNISLLTRLLDVRFSGEASEQGLTTFLDAFDESSHWVLVVPLSPGLLPFKKCRVTTAELAETTLPASQVLVVANEQCLHHLPALSDTIAILGCGLDVQWLSSSVLDEKRVAYWGDMDSWGLLMLARARRCRPTLDALLMNRELFEQYASHSAVPEPVIAKEAVPDGLLNEEADFYRYLTRLPRGRLEQEFLPVGIAEEALLRWGKESGSLEVLFQ

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 5 polymer

描述 description	Circular plasmid DNA (1840-MER)
分子量 formula_weight	12303.0 kDa
突变 mutation	The DNA was modelled as polyAT track.
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	P,Q,R,S

ATATATATATATATATATATATATATATATATATATATAT

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 6 non-polymer

描述 description	ADENOSINE-5'-DIPHOSPHATE
分子量 formula_weight	427.2 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	4.17 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	235956

fit	/app/data/saxs_computation/q7/8q72/8q72.fit
pddf	/app/data/pr_computation/q7/8q72/8q72.pr.out
profile	/app/data/saxs_computation/q7/8q72/8q72.dat

E. coli plasmid-borne JetABCD(E248A) core in a cleavage-competent state

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 (6)

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

来源 Source

Entity 5 polymer

聚合体 Polymer

来源 Source

Entity 6 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)