SAXSdb — 9mfy

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9mfy
沉积日期 deposition_date	2024-12-10
结构标题 title	Motor domain-Pac1 complex with ADP AAA1 and Apo AAA3 from yeast full-length dynein-1 and Pac1 in 0.1 mM ATP condition
关键词 keywords	dynein, 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	52.71 Å
回转半径 Rg (电子) rg_electron	52.43 Å
零角强度 I(0) i0	1558550000.00
分子量 molecular_weight	339350.0 kDa
排除体积 excluded_volume	428350 Å³
包络体积 envelope_volume	615130 Å³
水化壳体积 shell_volume	95924 Å³
包络直径 envelope_diameter	178.2 Å
壳层 Rg shell_rg	58.30 Å
包络 Rg envelope_rg	50.67 Å
形状 Rg shape_rg	52.44 Å
总 Rg total_rg	52.60 Å
总原子数 total_atoms	23892
残基数 n_residues	2939
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	171.3 Å
Rg (实空间) rg_real	52.61 Å
Rg 误差 (实空间) rg_real_error	1.41 Å
I(0) (实空间) i0_real	1.5590e+09
I(0) 误差 (实空间) i0_real_error	3.3600e+07
Rg (倒空间) rg_reciprocal	52.78 Å
I(0) (倒空间) i0_reciprocal	1559000000.0000
解质量估计 total_estimate	0.8731
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	68.5 Å
偏度 Skewness skewness	0.229
峰度 Kurtosis kurtosis	-0.421
角度范围 angular_range	— – 0.1500 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	134300000.0000
实空间数据点数 n_real_points	31
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.916; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.613

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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	Nuclear distribution protein PAC1
分子量 formula_weight	56973.6 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
原子数 atom_count	23892

MTNWQQQLPLTDTQKNELDKSVLRYLNWNYKQTVRHEHAQDYESVRHAIVTLSGFLLQESVDRQEFISNNDTSNESMVDIDELLLPKKWNSIVRLQKKIIELEQNTETLVSQIKDLNTQVSELAQFKPTTSNGTSAHNVLKWIPRNLPSCLINVESSVTSVKLHPNLPIVFVATDHGKLYAFDLFNYTIPLASLQSHTKAITSMDVLFTNYTNSSKKNYLVIVTASKDLQIHVFKWVSEECKFQQIRSLLGHEHIVSAVKIWQKNNDVHIASCSRDQTVKIWDFHNGWSLKTFQPHSQWVRSIDVLGDYIISGSHDTTLRLTHWPSGNGLSVGTGHEFPIEKVKFIHFIEDSPEIRFRTPSTDRYKNWGMQYCVSASRDRTIKIWEIPLPTLMAHRAPIPNPTDSNFRCVLTLKGHLSWVRDISIRGQYLFSCADDKSVRCWDLNTGQCLHVWEKLHTGFVNCLDLDVDFDSNVTPRQMMVTGGLDCKSNVFMR

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;brewer's yeast ;
NCBI 分类编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Saccharomyces cerevisiae

Entity 2 polymer

描述 description	Dynein heavy chain, cytoplasmic
分子量 formula_weight	471918.8 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

MCKNEARLANELIEFVAATVTGIKNSPKENEQAFIDYLHCQYLERFQFFLGLLDGREFDTLFVFLFEELDRTIVTIDIGEEAIYDANLANKKYSTLLIIKSRSVIVDAEPIATQISAIYLPGPVNAGNLASIITHGVSSVFGQLIKSDTKTYSVETIDKTRRKLDDISKQFQQLHTSIETPDLLAMVPSIIKLAVSKGATSHDYANYLPSNDLESMRFLNILQSIANKWFLVLKQTLAIDRDIKNGSFLDEVEFWSNFYEVLKSLIEQTQSQEFQVCLSVLTNAKRFHNLTNLLNEGSLSDKFKLADKYNQFLSSIPIDEVRQASNLEDLQELFPVLASSLKKFRYSGYPVQRFVVLMDKISQEVMDAILSNLSDLFQLEYGSFLGLYEKSAGMIEEWDDIVQDVNLLIREDLRKRAPQELLIQKLTFTSASVKATLDEILSTRKRFFSLAETIKSISPSTYHEEIQRLYHPFEQIHDISVNFRLKLEQAESEFSKNMLDLEKKLQNTLASFMDSDHCPTEKLSYLVKFKPLMELCPRIKVKVLENQQILLLEIKKDIRQLETGLELLPKILHVEALNNIPPISARISYFLNVQSRIDNIVQYLEALFGSNWNDTLEGRSISTSIVQLRKETNPHDVFLHWLGNFPEKATANLLTTPILKLIRNNEDDYELKVNFDFALAAAYSELRSLTYMAFQVPSHIVRIARTYMYLYPRAINLVELIQTFFSLSKSLSYTFYTNIFLKRNVQTVWLLLQQILITPWESLQEESSEMSCSVHSLARLEKSIDGILSDYQILKNSEPQFAKEFSGLKSFDGTADDLHEVEEIISNIQAIFENLFTKGLTNVSDHISTFNNLIISIILEKVRLNLKKMHFPKHVLKLSFNEGRITSSPSLAAMKRSLLKDIEALLNKVVLINFLHDPDHPLSTTLTFNSLVIKLKDDIQNCIEQVQNLHCKINSYVKEWQKMEFLWQITEEAFLEVVDNSTQRCFGILKGLLDSQSKFDLIISRNNFSKNLVLHTEDAQRHIRSKMDSWILYVSKHLLTIYERDARKLHEDMNRDREAVEDMDINFTSLKNITVIIEAVNVNKRHLTERDIQIKLLGSVMRALTKLKVRFPSHFVYIDQLDNDFSSLRQSLSYVEQELQKHRVVIAKSLEEGVENINNLSQSLNESWSVRKPISPTLTPPEALKILEFFNESITKLKKKMHSVAAAAKMLLIPVVLNDQLTHVVEEVKTYDLVWRSIKNLWEDVQRTFETPWCRVDVLLLQSDLANFLRRADELPRAVKQFEMYKSLFSQVNMLTSVNKILVELKDGALKPRHWNMIFRDIGKRQIQKNLLDKLEFSLKDVMVLNLTLNEILLTKIIERAQKEFVIEKSLNRIKKFWKEAQYEVIEHSSGLKLVREWDVLEQACKEDLEELVSMKASNYYKIFEQDCLDLESKLTKLSEIQVNWVEVQFYWLDLYGILGENLDIQNFLPLETSKFKSLTSEYKMITTRAFQLDTTIEVIHIPNFDTTLKLTIDSLKMIKSSLSTFLERQRRQFPRFYFLGNDDLLKIIGSGKHHDQVSKFMKKMFGSIESIIFLEDFITGVRSVEGEVLNLNEKIELKDSIQAQEWLNILDTEIKLSVFTQFRDCLGQLKDGTDIEVVVSKYIFQAILLSAQVMWTELVEKCLQTNQFSKYWKEVDMKIKGLLDKLNKSSDNVKKKIEALLVEYLHFNNVIGQLKNCSTKEEARLLWAKVQKFYQKNDTLDDLNSVFISQSGYLLQYKFEYIGIPERLIYTPLLLIGFATLTDSLHQKYGGCFFGPAGTGKTETVKAFGQNLGRVVVVFNCDDSFDYQVLSRLLVGITQIGAWGCFDEFNRLDEKVLSAVSANIQQIQNGLQVGKSHITLLEEETPLSPHTAVFITLNPGYNGRSELPENLKKSFREFSMKSPQSGTIAEMILQIMGFEDSKSLASKIVHFLELLSSKCSSMNHYHFGLRTLKGVLRNCSPLISEFGEGEKTVVESLKRVILPSLGDTDELVFKDELSKIFDSAGTPLNSKAIVQCLKDAGQRSGFSMSEEFLKKCMQFYYMQKTQQALILVGKAGCGKTATWKTVIDAMAIFDGHANVVYVIDTKVLTKESLYGSMLKATLEWRDGLFTSILRRVNDDITGTFKNSRIWVVFDSDLDPEYVEAMNSVLDDNKILTLPNGERLPIPPNFRILFETDNLDHTTPATITRCGLLWFSTDVCSISSKIDHLLNKSYEALDNKLSMFELDKLKDLISDSFDMASLTNIFTCSNDLVHILGVRTFNKLETAVQLAVHLISSYRQWFQNLDDKSLKDVITLLIKRSLLYALAGDSTGESQRAFIQTINTYFGHDSQELSDYSTIVIANDKLSFSSFCSEIPSVSLEAHEVMRPDIVIPTIDTIKHEKIFYDLLNSKRGIILCGPPGSGKTMIMNNALRNSSLYDVVGINFSKDTTTEHILSALHRHTNYVTTSKGLTLLPKSDIKNLVLFCDEINLPKLDKYGSQNVVLFLRQLMEKQGFWKTPENKWVTIERIHIVGACNPPTDPGRIPMSERFTRHAAILYLGYPSGKSLSQIYEIYYKAIFKLVPEFRSYTEPFARASVHLYNECKARYSTGLQSHYLFSPRELTRLVRGVYTAINTGPRQTLRSLIRLWAYEAWRIFADRLVGVKEKNSFEQLLYETVDKYLPNQDLGNISSTSLLFSGLLSLDFKEVNKTDLVNFIEERFKTFCDEELEVPMVIHESMVDHILRIDRALKQVQGHMMLIGASRTGKTILTRFVAWLNGLKIVQPKIHRHSNLSDFDMILKKAISDCSLKESRTCLIIDESNILETAFLERMNTLLANADIPDLFQGEEYDKLLNNLRNKTRSLGLLLDTEQELYDWFVGEIAKNLHVVFTICDPTNNKSSAMISSPALFNRCIINWMGDWDTKTMSQVANNMVDVIPMEFTDFIVPEVNKELVFTEPIQTIRDAVVNILIHFDRNFYQKMKVGVNPRSPGYFIDGLRALVKLVTAKYQDLQENQRFVNVGLEKLNESVLKVNELNKTLSKKSTELTEKEKEARSTLDKMLMEQNESERKQEATEEIKKILKVQEEDIRKRKEVVMKSIQDIEPTILEAQRGVKNIKKQQLTEIRSMVNPPSGVKIVMEAVCAILGYQFSNWRDIQQFIRKDDFIHNIVHYDTTLHMKPQIRKYMEEEFLSDPNFTYETINRASKACGPLYQWVNAQINFSKVLENVDPLRQEMKRIEFESLKTKANLLAAEEMTQDLEASIEVSKRKYSLLIRDVEAIKTEMSNVQANLDRSISLVKSLTFEKERWLNTTKQFSKTSQELIGNCIISSIYETYFGHLNERERADMLVILKRLLGKFAVKYDVNYRFIDYLVTLDEKMKWLECGLDKNDYFLENMSIVMNSQDAVPFLLDPSSHMITVISNYYGNKTVLLSFLEEGFVKRLENAIRFGSVVIIQDGEFFDPIISRLISREFNHAGNRVTVEIGDHEVDVSGDFKLFIHSCDPSGDIPIFLRSRVRLVHFVTNKESIETRIFDITLTEENAEMQRKREDLIKLNTEYKLKLKNLEKRLLEELNNSQGNMLENDELMVTLNNLKKEAMNIEKKLSESEEFFPQFDNLVEEYSIIGKHSVKIFSMLEKFGQFHWFYGISIGQFLSCFKRVFIKKSRETRAARTRVDEILWLLYQEVYCQFSTALDKKFKMIMAMTMFCLYKFDIESEQYKEAVLTMIGVLSESSDGVPKLTVDTNNDLRYLWDYVTTKSYISALNWFKNEFFVDEWNIADVVANSENNYFTMASERDVDGTFKLIELAKASKESLKIIPLGSIENLNYAQEEISKSKIEGGWILLQNIQMSLSWVKTYLHKHVEETKAAEEHEKFKMFMTCHLTGDKLPAPLLQRTDRFVYEDIPGILDTVKDLWGSQFFTGKISGVWSVYCTFLLSWFHALITARTRLVPHGFSKKYYFNDCDFQFASVYLENVLATNSTNNIPWAQVRDHIATIVYGGKIDEEKDLEVVAKLCAHVFCGSDNLQIVPGVRIPQPLLQQSEEEERARLTAILSNTIEPADSLSSWLQLPRESILNYERLQAKEVASSTEQLLQEM

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;brewer's yeast ;
NCBI 分类编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Spodoptera frugiperda

Entity 3 non-polymer

描述 description	ADENOSINE-5'-DIPHOSPHATE
分子量 formula_weight	427.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	ADENOSINE-5'-TRIPHOSPHATE
分子量 formula_weight	507.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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 (2)

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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	3.300 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	3.30 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	178195

fit	/app/data/saxs_computation/mf/9mfy/9mfy.fit
pddf	/app/data/pr_computation/mf/9mfy/9mfy.pr.out
profile	/app/data/saxs_computation/mf/9mfy/9mfy.dat

Motor domain-Pac1 complex with ADP AAA1 and Apo AAA3 from yeast full-length dynein-1 and Pac1 in 0.1 mM ATP condition

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 (5)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

7. 引用文献 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)