8flj

Cas1-Cas2/3 integrase and IHF bound to CRISPR leader, repeat and foreign DNA

Method: ELECTRON MICROSCOPY D_max: 217.2 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	8flj
沉积日期 deposition_date	2022-12-21
结构标题 title	Cas1-Cas2/3 integrase and IHF bound to CRISPR leader, repeat and foreign DNA
关键词 keywords	;DNA integration, maintenance of CRISPR repeat elements, IHF-DNA complex, Enzymes altering nucleic acid conformation, Site specific endodeoxyribonucleases: cleavage is not sequence specific, Nucleotidyltransferases, GO:0008301, RECOMBINATION, DNA BINDING PROTEIN, HYDROLASE-DNA complex ;; RECOMBINATION, DNA BINDING PROTEIN, HYDROLASE/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	62.48 Å
回转半径 Rg (电子) rg_electron	61.37 Å
零角强度 I(0) i0	4303870000.00
分子量 molecular_weight	456400.0 kDa
排除体积 excluded_volume	530970 Å³
包络体积 envelope_volume	914570 Å³
水化壳体积 shell_volume	123870 Å³
包络直径 envelope_diameter	222.3 Å
壳层 Rg shell_rg	62.04 Å
包络 Rg envelope_rg	61.49 Å
形状 Rg shape_rg	61.44 Å
总 Rg total_rg	61.22 Å
总原子数 total_atoms	57091
残基数 n_residues	3899
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	217.2 Å
Rg (实空间) rg_real	62.42 Å
Rg 误差 (实空间) rg_real_error	2.69 Å
I(0) (实空间) i0_real	4.3040e+09
I(0) 误差 (实空间) i0_real_error	9.9100e+07
Rg (倒空间) rg_reciprocal	62.49 Å
I(0) (倒空间) i0_reciprocal	4304000000.0000
解质量估计 total_estimate	0.8683
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	78.2 Å
偏度 Skewness skewness	0.299
峰度 Kurtosis kurtosis	-0.323
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	255800000.0000
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: 0.831; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.801

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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 (8)

Entity 1 polymer

描述 description	CRISPR-associated endonuclease Cas1
分子量 formula_weight	38267.1 kDa
EC 编号 ec_number	3.1.-.-
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,C,D
原子数 atom_count	57091

MWSHPQFEKENLYFQGSMDDISPSELKTILHSKRANLYYLQHCRVLVNGGRVEYVTDEGRHSHYWNIPIANTTSLLLGTGTSITQAAMRELARAGVLVGFCGGGGTPLFSANEVDVEVSWLTPQSEYRPTEYLQRWVGFWFDEEKRLVAARHFQRARLERIRHSWLEDRVLRDAGFAVDATALAVAVEDSARALEQAPNHEHLLTEEARLSKRLFKLAAQATRYGEFVRAKRGSGGDPANRFLDHGNYLAYGLAATATWVLGIPHGLAVLHGKTRRGGLVFDVADLIKDSLILPQAFLSAMRGDEEQDFRQACLDNLSRAQALDFMIDTLKDVAQRSTVSA

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 BL21(DE3)

Entity 2 polymer

描述 description	Integration host factor subunit alpha
分子量 formula_weight	11646.3 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	E,G

GPMGALTKAEIAERLYEELGLNKREAKELVELFFEEIRQALEHNEQVKLSGFGNFDLRDKRQRPGRNPKTGEEIPITARRVVTFRPGQKLKARVEAYAGTKS

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 BL21(DE3)

Entity 3 polymer

描述 description	Integration host factor subunit beta
分子量 formula_weight	10805.4 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	F,H

GPMTKSELIERIVTHQGQLSAKDVELAIKTMLEQMSQALATGDRIEIRGFGSFSLHYRAPRVGRNPKTGESVRLDGKFVPHFKPGKELRDRVNEPE

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 BL21(DE3)

Entity 4 polymer

描述 description	CRISPR leader, sense strand of DNA
分子量 formula_weight	42935.6 kDa
突变 mutation	C30A,T31A,T32A,C34A,G35A,G97A,G98A,T99A,T101A,T102A,T103C,C104G,T105C,T108C,T109G,C110A,C111A,T112A,A117C,T118G
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	I

AAGCTTCCGACCCTTTTTTCGGACGATTTAAAAAACCCTTATAAATCAGCAAGTTACGAGACCTCGAAAAAAGAGGGTTTCTGGCGGGAAAAACTCAAAAAACGCTTCGAAATCAACCGGTTATAGGTTTTCGGAGCTA

Entity 5 polymer

描述 description	CRISPR leader and repeat, anti-sense strand of DNA
分子量 formula_weight	52701.6 kDa
突变 mutation	A54G,T55G,A60T,G61T,G62T,A63C,A64G,A67G,G68C,A69G,A70T,A71T,A73T,C74T,C75T,C137T,G138T,A140T,A141T,G142T
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	J

TGATTTTCTTAGCTGCCTACACGGCAGTGAACTAGCTCCGAAAACCTATAACCGGTTGATTTCGAAGCGTTTTTTGAGTTTTTCCCGCCAGAAACCCTCTTTTTTCGAGGTCTCGTAACTTGCTGATTTATAAGGGTTTTTTAAATCGTCCGAAAAAAGGGTCGGAAGCTT

Entity 6 polymer

描述 description	CRISPR repeat and prespacer, sense strand of DNA
分子量 formula_weight	18241.7 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	K

GTGCAAGTCGTTTTGCTAGAGCTACATGTTCACTGCCGTGTAGGCAGCTAAGAAAATCA

Entity 7 polymer

描述 description	Prespacer, anti-sense strand of DNA
分子量 formula_weight	8263.4 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	L

GCTCTAGCAAAACGACTTGCACAACGA

Entity 8 polymer

描述 description	CRISPR-associated nuclease/helicase Cas3 subtype I-F/YPEST
分子量 formula_weight	121273.7 kDa
EC 编号 ec_number	3.1.-.-,3.6.4.-
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

MNILLVSQCEKRALSETRRILDQFAERRGERTWQTPITQAGLDTLRRLLKKSARRNTAVACHWIRGRDHSELLWIVGDASRFNAQGAVPTNRTCRDILRKEDENDWHSAEDIRLLTVMAALFHDIGKASQAFQAKLRNRGKPMADAYRHEWVSLRLFEAFVGPGSSDEDWLRRLADKRETGDAWLSQLARDDRQSAPPGPFQKSRLPPLAQAVGWLIVSHHRLPNGDHRGSASLARLPAPIQSQWCGARDADAKEKAACWQFPHGLPFASAHWRARTALCAQSMLERPGLLARGPALLHDSYVMHVSRLILMLADHHYSSLPADSRLGDPNFPLHANTDRDSGKLKQRLDEHLLGVALHSRKLAGTLPRLERQLPRLARHKGFTRRVEQPRFRWQDKAYDCAMACREQAMEHGFFGLNLASTGCGKTLANGRILYALADPQRGARFSIALGLRSLTLQTGQAYRERLGLGDDDLAILVGGSAARELFEKQQERLERSGSESAQELLAENSHVHFAGTLEDGPLREWLGRNSAGNRLLQAPILACTIDHLMPASESLRGGHQIAPLLRLMTSDLVLDEVDDFDIDDLPALSRLVHWAGLFGSRVLLSSATLPPALVQGLFEAYRSGREIFQRHRGAPGRATEIRCAWFDEFSSQSSAHGAVTSFSEAHATFVAQRLAKLEQLPPRRQAQLCTVHAAGEARPALCRELAGQMNTWMADLHRCHHTEHQGRRISFGLLRLANIEPLIELAQAILAQGAPEGLHVHLCVYHSRHPLLVRSAIERQLDELLKRSDDDAAALFARPTLAKALQASTERDHLFVVLASPVAEVGRDHDYDWAIVEPSSMRSIIQLAGRIRRHRSGFSGEANLYLLSRNIRSLEGQNPAFQRPGFETPDFPLDSHDLHDLLDPALLARIDASPRIVEPFPLFPRSRLVDLEHRRLRALMLADDPPSSLLGVPLWWQTPASLSGALQTSQPFRAGAKERCYALLPDEDDEERLHFSRYEEGTWSNQDNLLRNLDLTYGPRIQTWGTVNYREELVAMAGREDLDLRQCAMRYGEVRLRENTQGWSYHPYLGFKKYN

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 BL21(DE3)

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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	triclinic

分辨率 resolution	3.480 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	3.48 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	366794

fit	/app/data/saxs_computation/fl/8flj/8flj.fit
pddf	/app/data/pr_computation/fl/8flj/8flj.pr.out
profile	/app/data/saxs_computation/fl/8flj/8flj.dat

Cas1-Cas2/3 integrase and IHF bound to CRISPR leader, repeat and foreign DNA

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 (8)

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 polymer

聚合体 Polymer

Entity 7 polymer

聚合体 Polymer

Entity 8 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)