SAXSdb — 8of8

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8of8
沉积日期 deposition_date	2023-03-14
结构标题 title	Cryo-EM structure of actomyosin-5a-S1 with the full-length lever (nucleotide free)
关键词 keywords	;myosin, cytoskeletal motor, myosin-va, myo5a, myosin-5a, S1, rigor, nucleotide free, apo, lever, 6IQ, actomyosin, actomyosin-5a, actin, actomyosin-va, actin bound, MOTOR PROTEIN ;; MOTOR 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	95.41 Å
回转半径 Rg (电子) rg_electron	100.30 Å
零角强度 I(0) i0	1204250000.00
分子量 molecular_weight	224690.0 kDa
排除体积 excluded_volume	251710 Å³
包络体积 envelope_volume	693490 Å³
水化壳体积 shell_volume	67034 Å³
包络直径 envelope_diameter	343.7 Å
壳层 Rg shell_rg	67.03 Å
包络 Rg envelope_rg	96.86 Å
形状 Rg shape_rg	100.30 Å
总 Rg total_rg	99.92 Å
总原子数 total_atoms	15859
残基数 n_residues	2865
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	260.1 Å
Rg (实空间) rg_real	88.84 Å
Rg 误差 (实空间) rg_real_error	1.75 Å
I(0) (实空间) i0_real	1.1540e+09
I(0) 误差 (实空间) i0_real_error	2.2430e+07
Rg (倒空间) rg_reciprocal	83.48 Å
I(0) (倒空间) i0_reciprocal	1161000000.0000
解质量估计 total_estimate	0.7845
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	48.8 Å
偏度 Skewness skewness	0.493
峰度 Kurtosis kurtosis	-0.881
角度范围 angular_range	— – 0.0800 Å⁻¹
当前正则化参数 α current_alpha	0.1748
最高正则化参数 α highest_alpha	33130000.0000
实空间数据点数 n_real_points	17
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.005; Oscil: 0.539; Stabil: 0.921; Sysdev: 1.000; Positv: 1.000; Valcen: 0.634; Smooth: 0.274

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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 (3)

Entity 1 polymer

描述 description	Calmodulin-1
分子量 formula_weight	16721.3 kDa
来源方法 src_method	man
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F
原子数 atom_count	15859

ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI 分类编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 polymer

描述 description	Actin, alpha skeletal muscle
分子量 formula_weight	41875.6 kDa
来源方法 src_method	nat
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	J,K,L

DEDETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQEYDEAGPSIVHRKCF

Entity 3 polymer

描述 description	Unconventional myosin-Va
分子量 formula_weight	106596.2 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	M

MAASELYTKFARVWIPDPEEVWKSAELLKDYKPGDKVLLLHLEEGKDLEYRLDPKTGELPHLRNPDILVGENDLTALSYLHEPAVLHNLRVRFIDSKLIYTYCGIVLVAINPYEQLPIYGEDIINAYSGQNMGDMDPHIFAVAEEAYKQMARDERNQSIIVSGESGAGKTVSAKYAMRYFATVSGSASEANVEEKVLASNPIMESIGNAKTTRNDNSSRFGKYIEIGFDKRYRIIGANMRTYLLEKSRVVFQAEEERNYHIFYQLCASAKLPEFKMLRLGNADSFHYTKQGGSPMIEGVDDAKEMAHTRQACTLLGISESYQMGIFRILAGILHLGNVGFASRDSDSCTIPPKHEPLTIFCDLMGVDYEEMCHWLCHRKLATATETYIKPISKLQATNARDALAKHIYAKLFNWIVDHVNQALHSAVKQHSFIGVLDIYGFETFEINSFEQFCINYANEKLQQQFNMHVFKLEQEEYMKEQIPWTLIDFYDNQPCINLIESKLGILDLLDEECKMPKGTDDTWAQKLYNTHLNKCALFEKPRMSNKAFIIKHFADKVEYQCEGFLEKNKDTVFEEQIKVLKSSKFKMLPELFQDDEKAISPTSATSSGRTPLTRVPVKPTKGRPGQTAKEHKKTVGHQFRNSLHLLMETLNATTPHYVRCIKPNDFKFPFTFDEKRAVQQLRACGVLETIRISAAGFPSRWTYQEFFSRYRVLMKQKDVLGDRKQTCKNVLEKLILDKDKYQFGKTKIFFRAGQVAYLEKLRADKLRAACIRIQKTIRGWLLRKRYLCMQRAAITVQRYVRGYQARCYAKFLRRTKAATTIQKYWRMYVVRRRYKIRRAATIVIQSYLRGYLTRNRYRKILREYKAVIIQKRVRGWLARTHYKRTMKAIVYLQCCFRRMMAKRELKKDYKDDDDK

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI 分类编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Spodoptera frugiperda

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7. 引用文献 (1)

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分辨率 resolution	7.50 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	22337

fit	/app/data/saxs_computation/of/8of8/8of8.fit
pddf	/app/data/pr_computation/of/8of8/8of8.pr.out
profile	/app/data/saxs_computation/of/8of8/8of8.dat

Cryo-EM structure of actomyosin-5a-S1 with the full-length lever (nucleotide free)

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

冷冻电镜 EM 3D

5. 实体与聚合体信息 (3)

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

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)