SAXSdb — 8gs2

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8gs2
沉积日期 deposition_date	2022-09-04
结构标题 title	Structure of the Cas7-11-Csx29-guide RNA-target RNA (non-matching PFS) complex
关键词 keywords	CRISPR, RNase, RNA BINDING PROTEIN-RNA COMPLEX; RNA BINDING PROTEIN/RNA
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	45.55 Å
回转半径 Rg (电子) rg_electron	45.86 Å
零角强度 I(0) i0	976916000.00
分子量 molecular_weight	241790.0 kDa
排除体积 excluded_volume	295570 Å³
包络体积 envelope_volume	405560 Å³
水化壳体积 shell_volume	74883 Å³
包络直径 envelope_diameter	170.7 Å
壳层 Rg shell_rg	48.78 Å
包络 Rg envelope_rg	45.78 Å
形状 Rg shape_rg	45.88 Å
总 Rg total_rg	45.90 Å
总原子数 total_atoms	16935
残基数 n_residues	1977
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	158.3 Å
Rg (实空间) rg_real	45.81 Å
Rg 误差 (实空间) rg_real_error	1.67 Å
I(0) (实空间) i0_real	9.7690e+08
I(0) 误差 (实空间) i0_real_error	1.8970e+07
Rg (倒空间) rg_reciprocal	45.56 Å
I(0) (倒空间) i0_reciprocal	976600000.0000
解质量估计 total_estimate	0.8439
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	153.8 Å
偏度 Skewness skewness	0.496
峰度 Kurtosis kurtosis	-0.270
角度范围 angular_range	— – 0.1750 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	171500000.0000
实空间数据点数 n_real_points	36
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.771; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.889; Smooth: 0.764

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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	crRNA
分子量 formula_weight	30532.9 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	R
原子数 atom_count	16935

GGUUGGAAAGCCGGUUUUCUUUGAUGUCACGGAACCUUUGUUGUCUUCGACAUGGGUAAUGGUUGGAAAGCCGGUUUUCUUUGAUGUCACGGAAC

来源 Source

来源生物 organism	Desulfonema ishimotonii
NCBI 分类编号 ncbi_taxonomy_id	45657
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	target RNA with non-matching PFS
分子量 formula_weight	10662.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	D

GGAUUACCCAUGUCGAAGACAACAAAGCAAGGC

Entity 3 polymer

描述 description	CRISPR-associated RAMP family protein
分子量 formula_weight	185603.8 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A

MTTTMKISIEFLEPFRMTKWQESTRRNKNNKEFVRGQAFARWHRNKKDNTKGRPYITGTLLRSAVIRSAENLLTLSDGKISEKTCCPGKFDTEDKDRLLQLRQRSTLRWTDKNPCPDNAETYCPFCELLGRSGNDGKKAEKKDWRFRIHFGNLSLPGKPDFDGPKAIGSQRVLNRVDFKSGKAHDFFKAYEVDHTRFPRFEGEITIDNKVSAEARKLLCDSLKFTDRLCGALCVIRFDEYTPAADSGKQTENVQAEPNANLAEKTAEQIISILDDNKKTEYTRLLADAIRSLRRSSKLVAGLPKDHDGKDDHYLWDIGKKKKDENSVTIRQILTTSADTKELKNAGKWREFCEKLGEALYLKSKDMSGGLKITRRILGDAEFHGKPDRLEKSRSVSIGSVLKETVVCGELVAKTPFFFGAIDEDAKQTDLQVLLTPDNKYRLPRSAVRGILRRDLQTYFDSPCNAELGGRPCMCKTCRIMRGITVMDARSEYNAPPEIRHRTRINPFTGTVAEGALFNMEVAPEGIVFPFQLRYRGSEDGLPDALKTVLKWWAEGQAFMSGAASTGKGRFRMENAKYETLDLSDENQRNDYLKNWGWRDEKGLEELKKRLNSGLPEPGNYRDPKWHEINVSIEMASPFINGDPIRAAVDKRGTDVVTFVKYKAEGEEAKPVCAYKAESFRGVIRSAVARIHMEDGVPLTELTHSDCECLLCQIFGSEYEAGKIRFEDLVFESDPEPVTFDHVAIDRFTGGAADKKKFDDSPLPGSPARPLMLKGSFWIRRDVLEDEEYCKALGKALADVNNGLYPLGGKSAIGYGQVKSLGIKGDDKRISRLMNPAFDETDVAVPEKPKTDAEVRIEAEKVYYPHYFVEPHKKVEREEKPCGHQKFHEGRLTGKIRCKLITKTPLIVPDTSNDDFFRPADKEARKEKDEYHKSYAFFRLHKQIMIPGSELRGMVSSVYETVTNSCFRIFDETKRLSWRMDADHQNVLQDFLPGRVTADGKHIQKFSETARVPFYDKTQKHFDILDEQEIAGEKPVRMWVKRFIKRLSLVDPAKHPQKKQDNKWKRRKEGIATFIEQKNGSYYFNVVTNNGCTSFHLWHKPDNFDQEKLEGIQNGEKLDCWVRDSRYQKAFQEIPENDPDGWECKEGYLHVVGPSKVEFSDKKGDVINNFQGTLPSVPNDWKTIRTNDFKNRKRKNEPVFCCEDDKGNYYTMAKYCETFFFDLKENEEYEIPEKARIKYKELLRVYNNNPQAVPESVFQSRVARENVEKLKSGDLVYFKHNEKYVEDIVPVRISRTVDDRMIGKRMSADLRPCHGDWVEDGDLSALNAYPEKRLLLRHPKGLCPACRLFGTGSYKGRVRFGFASLENDPEWLIPGKNPGDPFHGGPVMLSLLERPRPTWSIPGSDNKFKVPGRKFYVHHHAWKTIKDGNHPTTGKAIEQSPNNRTVEALAGGNSFSFEIAFENLKEWELGLLIHSLQLEKGLAHKLGMAKSMGFGSVEIDVESVRLRKDWKQWRNGNSEIPNWLGKGFAKLKEWFRDELDFIENLKKLLWFPEGDQAPRVCYPMLRKKDDPNGNSGYEELKDGEFKKEDRQKKLTTPWTPWASSGLVPRGSHHHHHH

来源 Source

来源生物 organism	Desulfonema ishimotonii
NCBI 分类编号 ncbi_taxonomy_id	45657
宿主生物 host_organism	Escherichia coli

Entity 4 polymer

描述 description	CHAT domain-containing protein
分子量 formula_weight	88311.9 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B

MSNPIRDIQDRLKTAKFDNKDDMMNLASSLYKYEKQLMDSSEATLCQQGLSNRPNSFSQLSQFRDSDIQSKAGGQTGKFWQNEYEACKNFQTHKERRETLEQIIRFLQNGAEEKDADDLLLKTLARAYFHRGLLYRPKGFSVPARKVEAMKKAIAYCEIILDKNEEESEALRIWLYAAMELRRCGEEYPENFAEKLFYLANDGFISELYDIRLFLEYTEREEDNNFLDMILQENQDRERLFELCLYKARACFHLNQLNDVRIYGESAIDNAPGAFADPFWDELVEFIRMLRNKKSELWKEIAIKAWDKCREKEMKVGNNIYLSWYWARQRELYDLAFMAQDGIEKKTRIADSLKSRTTLRIQELNELRKDAHRKQNRRLEDKLDRIIEQENEARDGAYLRRNPPCFTGGKREEIPFARLPQNWIAVHFYLNELESHEGGKGGHALIYDPQKAEKDQWQDKSFDYKELHRKFLEWQENYILNEEGSADFLVTLCREIEKAMPFLFKSEVIPEDRPVLWIPHGFLHRLPLHAAMKSGNNSNIEIFWERHASRYLPAWHLFDPAPYSREESSTLLKNFEEYDFQNLENGEIEVYAPSSPKKVKEAIRENPAILLLLCHGEADMTNPFRSCLKLKNKDMTIFDLLTVEDVRLSGSRILLGACESDMVPPLEFSVDEHLSVSGAFLSHKAGEIVAGLWTVDSEKVDECYSYLVEEKDFLRNLQEWQMAETENFRSENDSSLFYKIAPFRIIGFPAE

来源 Source

来源生物 organism	Desulfonema ishimotonii
NCBI 分类编号 ncbi_taxonomy_id	45657
宿主生物 host_organism	Escherichia coli

Entity 5 non-polymer

描述 description	CYTIDINE-5'-MONOPHOSPHATE
分子量 formula_weight	323.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 6 non-polymer

描述 description	ADENOSINE MONOPHOSPHATE
分子量 formula_weight	347.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 7 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 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	2.84 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	71543

fit	/app/data/saxs_computation/gs/8gs2/8gs2.fit
pddf	/app/data/pr_computation/gs/8gs2/8gs2.pr.out
profile	/app/data/saxs_computation/gs/8gs2/8gs2.dat

Structure of the Cas7-11-Csx29-guide RNA-target RNA (non-matching PFS) complex

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

Entity 3 polymer

聚合体 Polymer

来源 Source

Entity 4 polymer

聚合体 Polymer

来源 Source

Entity 5 non-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)