SAXSdb — 9arj

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9arj
沉积日期 deposition_date	2024-02-23
结构标题 title	CryoEM structure of BoNT-NTNH-OrfX2 complex from Clostridium botulinum E1, major class
关键词 keywords	Botulinum neurotoxin, Progenitor toxin complex (PTC), TOXIN; TOXIN
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	59.83 Å
回转半径 Rg (电子) rg_electron	61.35 Å
零角强度 I(0) i0	1591540000.00
分子量 molecular_weight	342180.0 kDa
排除体积 excluded_volume	431630 Å³
包络体积 envelope_volume	655140 Å³
水化壳体积 shell_volume	96223 Å³
包络直径 envelope_diameter	231.4 Å
壳层 Rg shell_rg	54.40 Å
包络 Rg envelope_rg	64.22 Å
形状 Rg shape_rg	61.32 Å
总 Rg total_rg	61.26 Å
总原子数 total_atoms	24188
残基数 n_residues	2982
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	208.9 Å
Rg (实空间) rg_real	61.00 Å
Rg 误差 (实空间) rg_real_error	2.10 Å
I(0) (实空间) i0_real	1.5910e+09
I(0) 误差 (实空间) i0_real_error	3.3000e+07
Rg (倒空间) rg_reciprocal	58.81 Å
I(0) (倒空间) i0_reciprocal	1586000000.0000
解质量估计 total_estimate	0.7320
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	56.2 Å
偏度 Skewness skewness	0.807
峰度 Kurtosis kurtosis	0.031
角度范围 angular_range	— – 0.1300 Å⁻¹
当前正则化参数 α current_alpha	0.0003
最高正则化参数 α highest_alpha	167000000.0000
实空间数据点数 n_real_points	27
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.440; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.959; Smooth: 0.232

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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	Toxin
分子量 formula_weight	84690.4 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	C
原子数 atom_count	24188

MTNLKPYIIYDWKETILKNSKDNYSINESIPKIFSKKICGGRFFNSTLSGNWKSWTLTDEGEGPHPVLKCTIDNGYLEIYSNTSSEKHSLKDIEIKVCMSIKPNSDGTHSLCKNSFYIKTNSLKLSEDRLILSHCLDKLILAWFKDNHKYIELFINRSRIQTRVEGDLSLLGWDIESSVSYKTMNEFIKKDNLYEKKFHQYMEVRRNEYTIDGEFGPWQMTTGADGQNIRFLCPIKSATYKINDDVYIAKPDNFIIIQVDLKYFDSKTTIIDPSGLNNGQQFNLKVKTDSTDEINAVILVGSRITDVNEDLYPGDDVSLEIVFKTWFNANIQKFTQIFSYILLNETSKIPEYQWLKPTQISYGSASVTMPDPSNPNKELSNLDASTFAAMAMVENHKNDRPNHAVDNRFLELSKTPAAFAISMPEFLKHFLVTGLQAMQIDNLDAFEVSSENLVITNKKKINFGKIQDQNRQVDALIEPNNFKLAIQNNQVVVEIVDATWQQVVGVTGHFGYRQAYNLILKNENNVYKPMLEESGDVTISYMVTEEAWKTTQDAIISATVGLVVGTIIGTAFSKLSDKLYKFLKSKFIVKNKKASLKISGKDINEVIEMSDISKPQLLSIKKANAKISTEEVGLISQNGSTSLENLAIFKNKPRPIGERVQILGLKLVSGLITTFGWSIGFVLPDILKDVINANINNNFEVLPGIQQFTQQCIGSIQWPDNSELKIDFAKLQGVYLLGGNLVKIPESN

来源 Source

来源生物 organism	;Clostridium botulinum E1 str. 'BoNT E Beluga' ;
NCBI 分类编号 ncbi_taxonomy_id	536233
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	Botulinum neurotoxin
分子量 formula_weight	143587.9 kDa
突变 mutation	H212A,E213A,H216A
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

MPKINSFNYNDPVNDRTILYIKPGGCQEFYKSFNIMKNIWIIPERNVIGTTPQDFHPPTSLKNGDSSYYDPNYLQSDEEKDRFLKIVTKIFNRINNNLSGGILLEELSKANPYLGNDNTPDNQFHIGDASAVEIKFSNGSQDILLPNVIIMGAEPDLFETNSSNISLRNNYMPSNHGFGSIAIVTFSPEYSFRFNDNSMNEFIQDPALTLMAALIASLHGLYGAKGITTKYTITQKQNPLITNIRGTNIEEFLTFGGTDLNIITSAQSNDIYTNLLADYKKIASKLSKVQVSNPLLNPYKDVFEAKYGLDKDASGIYSVNINKFNDIFKKLYSFTEFDLATKFQVKCRQTYIGQYKYFKLSNLLNDSIYNISEGYNINNLKVNFRGQNANLNPRIITPITGRGLVKKIIRFCKNIVSVKGIRKSICIEINNGELFFVASENSYNDDNINTPKEIDDTVTSNNNYENDLDQVILNFNSESAPGLSDEKLNLTIQNDAYIPKYDSNGTSDIEQHDVNELNVFFYLDAQKVPEGENNVNLTSSIDTALLEQPKIYTFFSSEFINNVNKPVQAALFVSWIQQVLVDFTTEANQKSTVDKIADISIVVPYIGLALNIGNEAQKGNFKDALELLGAGILLEFEPELLIPTILVFTIKSFLGSSDNKNKVIKAINNALKERDEKWKEVYSFIVSNWMTKINTQFNKRKEQMYQALQNQVNAIKTIIESKYNSYTLEEKNELTNKYDIKQIENELNQKVSIAMNNIDRFLTESSISYLMKLINEVKINKLREYDENVKTYLLNYIIQHGSILGESQQELNSMVTDTLNNSIPFKLSSYTDDKILISYFNKFFKRIKSSSVLNMRYKNDKYVDTSGYDSNININGDVYKYPTNKNQFGIYNDKLSEVNISQNDYIIYDNKYKNFSISFWVRIPNYDNKIVNVNNEYTIINCMRDNNSGWKVSLNHNEIIWTLQDNAGINQKLAFNYGNANGISDYINKWIFVTITNDRLGDSKLYINGNLIDQKSILNLGNIHVSDNILFKIVNCSYTRYIGIRYFNIFDKELDETEIQTLYSNEPNTNILKDFWGNYLLYDKEYYLLNVLKPNNFIDRRKDSTLSINNIRSTILLANRLYSGIKVKIQRVNNSSTNDNLVRKNDQVYINFVASKTHLFPLYADTATTNKEKTIKISSSGNRFNQVVVMNSVGNNCTMNFKNNNGNNIGLLGFKADTVVASTWYYTHMRDHTNSNGCFWNFISEEHGWQEK

来源 Source

来源生物 organism	;Clostridium botulinum E1 str. 'BoNT E Beluga' ;
NCBI 分类编号 ncbi_taxonomy_id	536233
宿主生物 host_organism	Escherichia coli

Entity 3 polymer

描述 description	Peptidase M27
分子量 formula_weight	136967.4 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

MKINGNLNIDSPVDNKNVAIVRSRKSDVFFKAFQVAPNIWIVPERYYGESLKINEDQKFDGGIYDSNFLSTNNEKDDFLQATIKLLQRINNNVVGAKLLSLISTAIPFPYENNTEDYRQTNYLSSKNNEHYYTANLVIFGPGSNIIKNNVIYYKKEYAESGMGTMLEIWFQPFLTHKYDEFYVDPALELIKCLIKSLYYLYGIKPNDNLNIPYRLRNEFNSLEYSELDMIDFLISGGIDYKLLNTNPYWFIDKYFIDTSKNFEKYKNDYEIKIKNNNYIANSIKLYLEQKFKINVKDIWELNLSYFSKEFQIMMPERYNNALNHYYRKEYYVIDYFKNYNINGFKNGQIKTKLPLSKYNKEIINKPELIVNLINQNNTVLMKSNIYGDGLKGTVDNFYSNYIIPYNLNYEHSINYSYLDNVNIEEIEKIPPINDEDIYPYRKNADTFIPVYNITKAKEINTTTPLPVNYLQAQMIDSNDINLSSDFLKVISSKGSLVYSFLNNTMDYLEFIKYDKPIDTDKKYYKWLKAIFRNYSLDITETQEISNQFGDTKIIPWIGRALNILNTNNSFVEEFKNLGPISLINKKENITIPKIKIDEIPSSMLNFSFKDLSENLFNIYCKNNFYLKKIYYNFLDQWWTQYYSQYFDLICMASKSVLAQEKLIKKLIQKQLRYLMENSNISSTNLILINLTTTNTLRDISNQSQIAINNIDKFFNNAAMCVFENNIYPKFTSFMEQCIKNINKSTKEFILKCTNINETEKSHLIMQNSFSNLDFDFLDIQNMKNLFNSYTELLIKEQTSPYELSLYAFQEQDNNVIGDTSGKNTLVEYPKDIGLVYGINNNAIHLTGANQNIKFTNDYFENGLTNNFSIYFWLRNLKQNTIKSKLIGSKEDNCGWEIYFENDGLVFNIIDSNGNEKNIYLSNISNNSWHYIVISINRLKDQLLIFIDNILVANEDIKEILNIYSSDIISLLSDNNNVYIEGLSVLNKTINSNEILTDYFSDLNNSYIRNFDEEILQYNRTYELFNYVFPEIAINKIEQNNNIYLSINNENNLNFKPLKFKLLNTNPNKQYVQKWDEVIFSVLDGTEKYLDISTTNNRIQLVDNKNNAQIFIINNDIFISNCLTLTYNNVNIYLSIKNQDYNWVICDLNHDIPKKSYLWILKNI

来源 Source

来源生物 organism	;Clostridium botulinum E1 str. 'BoNT E Beluga' ;
NCBI 分类编号 ncbi_taxonomy_id	536233
宿主生物 host_organism	Escherichia coli

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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	3.40 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	384801

fit	/app/data/saxs_computation/ar/9arj/9arj.fit
pddf	/app/data/pr_computation/ar/9arj/9arj.pr.out
profile	/app/data/saxs_computation/ar/9arj/9arj.dat

CryoEM structure of BoNT-NTNH-OrfX2 complex from Clostridium botulinum E1, major class

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 (3)

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

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)