SAXSdb — 8eey

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8eey
沉积日期 deposition_date	2022-09-07
结构标题 title	Cas7-11 in complex with DR-mismatched target RNA, Csx29 and Csx30
关键词 keywords	CRISPR, endonuclease, endopeptidase, 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	51.58 Å
回转半径 Rg (电子) rg_electron	52.40 Å
零角强度 I(0) i0	1431890000.00
分子量 molecular_weight	297820.0 kDa
排除体积 excluded_volume	365560 Å³
包络体积 envelope_volume	512710 Å³
水化壳体积 shell_volume	85488 Å³
包络直径 envelope_diameter	221.6 Å
壳层 Rg shell_rg	51.67 Å
包络 Rg envelope_rg	52.71 Å
形状 Rg shape_rg	52.46 Å
总 Rg total_rg	52.19 Å
总原子数 total_atoms	20886
残基数 n_residues	2459
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	201.9 Å
Rg (实空间) rg_real	52.03 Å
Rg 误差 (实空间) rg_real_error	2.99 Å
I(0) (实空间) i0_real	1.4320e+09
I(0) 误差 (实空间) i0_real_error	3.1990e+07
Rg (倒空间) rg_reciprocal	51.21 Å
I(0) (倒空间) i0_reciprocal	1430000000.0000
解质量估计 total_estimate	0.7512
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	52.1 Å
偏度 Skewness skewness	0.695
峰度 Kurtosis kurtosis	0.204
角度范围 angular_range	— – 0.1550 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	190400000.0000
实空间数据点数 n_real_points	32
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.455; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.552; Smooth: 0.846

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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	Csx30
分子量 formula_weight	62688.2 kDa
突变 mutation	;427-MKKDKKA-433 replaced with 427-GGS-429. A gap exists because low-resolution density in EM map permitted modeling of only a single residue of the insertion, G at position 427. ;
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	E
原子数 atom_count	20886

MNTTTYNTTTDALLEWGKVYFQKEDFSEFLDNLEAYISDAGDSLKDELESGVEKLVLGIKSAEAVIFGEAVIGTTPENEAWYDAEESFLTLDCAVWLSQALDRVVRRQDASLADSLIARLDEAINRVAEKLYADNLSPLRFSSLNEIRRSALEATDEKYHYLFPWHGAACDVDENILLILTEEYHLIGADKAGANLSEELRGDLPFIFAELERDEVLRAYVEKENALSLALENTMREHWAFGLLEAARDEGYNHPYPADVGMRIHQVARAVFSQTNLSPAERLAVAIAGACFTPEISEDRRLEILLDCEERVCEIEAPTGDDTSVRVIKDLKALADHRVRHEIPAESLVSLWFEQIEAAGTDFDTKTPMDELVLRMLSDNVITLSVDRKAASQTETDDVKPQKGKIIPFPVPDIANDEVEYQKAVGGGSANDSKVKFPGLLEIQGCRDGDKAILLEDTDDAAANHRKLFSILKAGKLNSAFFIQSDDGEWVESESKPTMEDNRIILHDSHHSSFVWILDTGSMQLRQSVKCVKDALNKKTGSAKKLKPKTMIVWVTIPQEG

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	Cas7-11
分子量 formula_weight	183845.0 kDa
突变 mutation	D429A,D654A
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

MTTTMKISIEFLEPFRMTKWQESTRRNKNNKEFVRGQAFARWHRNKKDNTKGRPYITGTLLRSAVIRSAENLLTLSDGKISEKTCCPGKFDTEDKDRLLQLRQRSTLRWTDKNPCPDNAETYCPFCELLGRSGNDGKKAEKKDWRFRIHFGNLSLPGKPDFDGPKAIGSQRVLNRVDFKSGKAHDFFKAYEVDHTRFPRFEGEITIDNKVSAEARKLLCDSLKFTDRLCGALCVIRFDEYTPAADSGKQTENVQAEPNANLAEKTAEQIISILDDNKKTEYTRLLADAIRSLRRSSKLVAGLPKDHDGKDDHYLWDIGKKKKDENSVTIRQILTTSADTKELKNAGKWREFCEKLGEALYLKSKDMSGGLKITRRILGDAEFHGKPDRLEKSRSVSIGSVLKETVVCGELVAKTPFFFGAIDEDAKQTALQVLLTPDNKYRLPRSAVRGILRRDLQTYFDSPCNAELGGRPCMCKTCRIMRGITVMDARSEYNAPPEIRHRTRINPFTGTVAEGALFNMEVAPEGIVFPFQLRYRGSEDGLPDALKTVLKWWAEGQAFMSGAASTGKGRFRMENAKYETLDLSDENQRNDYLKNWGWRDEKGLEELKKRLNSGLPEPGNYRDPKWHEINVSIEMASPFINGDPIRAAVDKRGTAVVTFVKYKAEGEEAKPVCAYKAESFRGVIRSAVARIHMEDGVPLTELTHSDCECLLCQIFGSEYEAGKIRFEDLVFESDPEPVTFDHVAIDRFTGGAADKKKFDDSPLPGSPARPLMLKGSFWIRRDVLEDEEYCKALGKALADVNNGLYPLGGKSAIGYGQVKSLGIKGDDKRISRLMNPAFDETDVAVPEKPKTDAEVRIEAEKVYYPHYFVEPHKKVEREEKPCGHQKFHEGRLTGKIRCKLITKTPLIVPDTSNDDFFRPADKEARKEKDEYHKSYAFFRLHKQIMIPGSELRGMVSSVYETVTNSCFRIFDETKRLSWRMDADHQNVLQDFLPGRVTADGKHIQKFSETARVPFYDKTQKHFDILDEQEIAGEKPVRMWVKRFIKRLSLVDPAKHPQKKQDNKWKRRKEGIATFIEQKNGSYYFNVVTNNGCTSFHLWHKPDNFDQEKLEGIQNGEKLDCWVRDSRYQKAFQEIPENDPDGWECKEGYLHVVGPSKVEFSDKKGDVINNFQGTLPSVPNDWKTIRTNDFKNRKRKNEPVFCCEDDKGNYYTMAKYCETFFFDLKENEEYEIPEKARIKYKELLRVYNNNPQAVPESVFQSRVARENVEKLKSGDLVYFKHNEKYVEDIVPVRISRTVDDRMIGKRMSADLRPCHGDWVEDGDLSALNAYPEKRLLLRHPKGLCPACRLFGTGSYKGRVRFGFASLENDPEWLIPGKNPGDPFHGGPVMLSLLERPRPTWSIPGSDNKFKVPGRKFYVHHHAWKTIKDGNHPTTGKAIEQSPNNRTVEALAGGNSFSFEIAFENLKEWELGLLIHSLQLEKGLAHKLGMAKSMGFGSVEIDVESVRLRKDWKQWRNGNSEIPNWLGKGFAKLKEWFRDELDFIENLKKLLWFPEGDQAPRVCYPMLRKKDDPNGNSGYEELKDGEFKKEDRQKKLTTPWTPWA

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 3 polymer

描述 description	Csx29
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 4 polymer

描述 description	crRNA
分子量 formula_weight	12134.1 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	C

UUGAUGUCACGGAACCUUUGUUGUCUUCGACAUGGGUA

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 polymer

描述 description	DR-mismatched target RNA
分子量 formula_weight	8931.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	D

UACCCAUGUCGAAGACAACAAAGUAUUU

Entity 6 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	2.53 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	65733

fit	/app/data/saxs_computation/ee/8eey/8eey.fit
pddf	/app/data/pr_computation/ee/8eey/8eey.pr.out
profile	/app/data/saxs_computation/ee/8eey/8eey.dat

Cas7-11 in complex with DR-mismatched target RNA, Csx29 and Csx30

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

Entity 6 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)