SAXSdb — 8wmn

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8wmn
沉积日期 deposition_date	2023-10-04
结构标题 title	Structure of CbCas9-PcrIIC1 complex bound to 62-bp DNA substrate (symmetric 20-nt complementary)
关键词 keywords	Cas9 complex, DNA BINDING PROTEIN, DNA BINDING PROTEIN-DNA-RNA complex; DNA BINDING PROTEIN/DNA/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	58.66 Å
回转半径 Rg (电子) rg_electron	59.70 Å
零角强度 I(0) i0	3234820000.00
分子量 molecular_weight	414950.0 kDa
排除体积 excluded_volume	493230 Å³
包络体积 envelope_volume	768150 Å³
水化壳体积 shell_volume	109530 Å³
包络直径 envelope_diameter	213.4 Å
壳层 Rg shell_rg	58.32 Å
包络 Rg envelope_rg	58.94 Å
形状 Rg shape_rg	59.78 Å
总 Rg total_rg	59.43 Å
总原子数 total_atoms	28862
残基数 n_residues	2998
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	201.1 Å
Rg (实空间) rg_real	58.99 Å
Rg 误差 (实空间) rg_real_error	2.67 Å
I(0) (实空间) i0_real	3.2350e+09
I(0) 误差 (实空间) i0_real_error	6.8250e+07
Rg (倒空间) rg_reciprocal	58.35 Å
I(0) (倒空间) i0_reciprocal	3232000000.0000
解质量估计 total_estimate	0.8362
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	59.6 Å
偏度 Skewness skewness	0.500
峰度 Kurtosis kurtosis	-0.284
角度范围 angular_range	— – 0.1350 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	226600000.0000
实空间数据点数 n_real_points	28
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.782; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.961; Smooth: 0.560

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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 (5)

Entity 1 polymer

描述 description	deadCbCas9
分子量 formula_weight	170029.1 kDa
突变 mutation	D9A, H837A
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	28878

MIKNILGLALGTNSIGWALVKQDFENKQGEILGMGSRIIPMSQDILGDFGKGNSVSQTAERTKYRSVRRLRERFLLRRERLHRVLYILNFLPEHYASQIDFEKRLGKFKVETEPKLVWKNTDGQFSFLFQNSFNEMLEDFKAAGQELKIPYDWTIYHLRKKAISQKIEKEELAWILLNFNHKRGYYQLRGEDFEEEKDKTFVRLKVDRIVDSGENVKGKILYDVYFENGWKYDKQVVKTEDWVDRTKEFIVSESILKNGETKRTFKAVDSEKDWIAIKTKTEQEIEHSHKTVGTYIYETLLQNPKQKIKGKLVRTIERKFYKEELRQILEKQKEFHQELQSDDLYNDCIRELYRNNEVHQLTLRKKDFVHLFMEDIIFYQRPLRSQKSSVSNCTLEFRKYKGENGAEHTQYLKAIPKSNPYYQEFRLWQWIFNLNLYTKDNDENVTKVFLNTTQDFENLFEFLNTRKEVDQKALLKHFKLNEKTHRWNFVEDKKYPCNETKTMISSRLDKVENISDDFLTRDIEQKIWHIIYSVNDKVEYEKALKSFARKHHLDESSFFEAFRKFPPFKSEYGSFSEKAIKKLLPLMRLGKYWNYAEIDKYSRERIQKIITGEYDENIKDKVREKSVHLTIENDFQGLQLWLAQYIVYGRHSEASMIGKWNSANDLEVFLKDFKQHSLRNPIVEQVITETLRVVKDIWLKYGNGTKDFFNEIHIELGREMKLPADDRKKLTNQITENENTNLRIKALLAEMMNDHSVENVRPFSPMQQEILKIYEDGVLKSDIEIEDDILKISKTAQPSSSDLKRYKLWLEQKYKSPYTGQIIPLNKLFTPEYEIEAIIPQSRYFDDSFSNKIICESAVNKLKDNYIGLGFIKQFGGTIIELGFGKSVKVFDTEEYEDFVKKHYANNRGKRNKLLMEDIPEKMIERQLNDTRYISKYISGILSNIVRVEDGSDEGVNSKNIVPGNGKITTQLKQDWGLNDVWNDLILPRFERMNQLTNSKDFTAWNENHQKFLPTVPIEFSKGFSKKRIDHRHHALDALVIACATTDHVNLLNNQSAKSDTKRYDLKKKLMKFEKVVYHHTQTGEKIEREIPKQFLKPWEKFTVDAKHNLESIIVSFKQNLRVINKATNYYEKYVEKDGTKNKERVEQAGTNWAIRKPMHKDTVSGKVDLPWVKVPKGKILTATRKSLDSSFDLKSIGSITDTGIQKILKNYLAFKDGNPELAFSPEGIDDLNKNIEKYNDGKPHQPINKVRVFELGSKFQVGQTGNKKGKYVEAAKGTNLFFAVYEDEKGKRSYETIPLNEVIERQKQGLTSVPLENEKGSRLLFDLSPNDLVYVPEIDENIDSNFVFSNLNKEKISRIYKVEKTSGTECYFVRQDIAYLIKQYDAKTKIGELESQNKLQVTMTDDRIRITDTCVKINCDRLGNINFITKEKIKQIFNEFR

来源 Source

来源生物 organism	Chryseobacterium
NCBI 分类编号 ncbi_taxonomy_id	59732
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	DNA (62-MER)
分子量 formula_weight	19112.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	C,N

GAGAATGTCGGGGAGCCGAGACAAAACGACGCGTCGTTTTGTCTCGGCTCCCCGACATTCTC

Entity 3 polymer

描述 description	sgRNA
分子量 formula_weight	40936.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	F,O

GAGAAUGUCGGGGAGCCGAGGUUGUGAAUUGCUUUCAAAAAUUAUUGAGAAAUAAUUUUGAAAAGCAAUUCACAAUAAGGAUUAUUCCGUUGUGAAAACAUUCAAGGCGGGGCAACUCGCCUUUUUU

Entity 4 polymer

描述 description	PcrIIC1
分子量 formula_weight	15992.0 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	G,H

MSLDKIAIDTNILLYAYDNRDLDKQDRAVEILLKKPFVTQLVVFEFIKVLERRFKMDKKEITKLTIKLLKEVIIPLSLHRDIYNYSQFLLQRYNFGLSDILVLSDSILNNCTILLSEDMCNGMIVDKKLKIVNPFL

来源 Source

来源生物 organism	Chryseobacterium
NCBI 分类编号 ncbi_taxonomy_id	59732
宿主生物 host_organism	Escherichia coli

Entity 5 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	2.82 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	372199

fit	/app/data/saxs_computation/wm/8wmn/8wmn.fit
pddf	/app/data/pr_computation/wm/8wmn/8wmn.pr.out
profile	/app/data/saxs_computation/wm/8wmn/8wmn.dat

Structure of CbCas9-PcrIIC1 complex bound to 62-bp DNA substrate (symmetric 20-nt complementary)

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 (5)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

Entity 4 polymer

聚合体 Polymer

来源 Source

Entity 5 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)