SAXSdb — 9c4k

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9c4k
沉积日期 deposition_date	2024-06-04
结构标题 title	Yersinia entomophaga holotoxin complex in prepore conformation
关键词 keywords	Toxin, pore-forming, insecticidal, chitinases; 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	— Å
回转半径 Rg (电子) rg_electron	106.50 Å
零角强度 I(0) i0	49034500000.00
分子量 molecular_weight	1898100.0 kDa
排除体积 excluded_volume	2374600 Å³
包络体积 envelope_volume	3892100 Å³
水化壳体积 shell_volume	327870 Å³
包络直径 envelope_diameter	408.5 Å
壳层 Rg shell_rg	94.08 Å
包络 Rg envelope_rg	105.40 Å
形状 Rg shape_rg	106.50 Å
总 Rg total_rg	106.20 Å
总原子数 total_atoms	133938
残基数 n_residues	16909
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	316.1 Å
Rg (实空间) rg_real	100.90 Å
Rg 误差 (实空间) rg_real_error	1.37 Å
I(0) (实空间) i0_real	4.7310e+10
I(0) 误差 (实空间) i0_real_error	1.0250e+09
Rg (倒空间) rg_reciprocal	97.70 Å
I(0) (倒空间) i0_reciprocal	47840000000.0000
解质量估计 total_estimate	0.8975
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	105.4 Å
偏度 Skewness skewness	0.635
峰度 Kurtosis kurtosis	0.020
角度范围 angular_range	— – 0.0750 Å⁻¹
当前正则化参数 α current_alpha	0.6626
最高正则化参数 α highest_alpha	3620000000.0000
实空间数据点数 n_real_points	16
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.001; Oscil: 0.839; Stabil: 0.970; Sysdev: 1.000; Positv: 1.000; Valcen: 0.956; Smooth: 0.283

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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	Toxin subunit YenA1
分子量 formula_weight	129912.3 kDa
来源方法 src_method	nat
拷贝数 entity_count	5

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,D,G,J,M
原子数 atom_count	133938

MDKYNNYSNVIKNKSSISPLLAAAAKIEPEITVLSSASKSNRSQYSQSLADTLLGLGYRSIFDIAKVSRQRFIKRHDESLLGNGAVIFDKAVSMANQVLQKYRKNRLEKSNSPLVPQTSSSTDASSESQTNKLPEYNQLFPEPWDNFCRPGAIEALDSPASYLLDLYKFIQSVELDGSNQARKLETRRADIPKLSLDNDALYKEVTALSIVNDVLSGSAREYIDQSGQADKAVNQILGDTHFPFTLPYSLPTQQINKGLGASNIELGTVIQRVDPQFSWNTTQEKYNQVLLAYTQLSSEQIALLSLPDVFTQNFLTQTELSAGYLSASTTEILAEKDLSRHGYIVKAADNIKGPTQLVEHSDASYDVIELTCTNQAKETITVKLRGENIITYQRTKARMVPFDNSSPFSRQLKLTFVAEDNPSLGNLDKGPYFANMDIYAAEWVRENVSSETMVSRPFLTMTYRIAIAKAGASLEELQPEADAFFINNFGLSAEDSSQLVKLVAFGDQTGSKAEEIESLLSCGENLPIVSPNVIFANPIFGSYFNDEPFPAPYHFGGVYINAHQRNAMTIIRAEGGREIQSLSNFRLERLNRFIRLQRWLDLPSHQLDLLLTSVMQADADNSQQEITEPVLKSLGLFRHLNLQYKITPEIFSSWLYQLTPFAVSGEIAFFDRIFNREQLFDQPFILDGGSFTYLDAKGSDAKSVKQLCAGLNISAVTFQFIAPLVQSALGLEAGTLVRSFEVVSSLYRLVSIPQTFGLSTEDGLILMNILTDEMGYLAKQPAFDDKQTQDKDFLSIILKMEALSAWLTKNNLTPASLALLLGVTRLAVVPTNNMVTFFKGIANGLSENVCLTTDDFQRQELEGADWWTLLSTNQVIDDMGLVLDIHPVWGKSDEEMLMEKIQSIGVSNDNNTLSIIVQILIQAKNAQENLLSQTISAEYGVERSVVPLQLRWLGSNVYSVLNQVLNNTPTDISSIVPKLSELTYSLLIYTQLINSLKLNKEFIFLRLTQPNWLGLTQPKLSTQLSLPEIYLITCYQDWVVNANKNEDSIHEYLEFANIKKTEAEKTLVDNSEKCAELLAEILAWDAGEILKAASLLGLNPPQATNVFEIDWIRRLQTLSEKTMISTEYLWQMGDLTENSEFSLKEGVGEAVMAALKAQGDSDNV

Entity 2 polymer

描述 description	Toxin subunit YenA2
分子量 formula_weight	156324.9 kDa
来源方法 src_method	nat
拷贝数 entity_count	5

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B,E,H,K,N

MSNSIEAKLQEDLRDALVDYYLGQIVPNSKDFTNLRSTIKNVDDLYDHLLLDTQVSAKVITSRLSLVTQSVQQYINRIALNLEPGLSINQQEATDWEEFANRYGYWAANQQLRMFPEIYVDPTLRLTKTEFFFQLESALNQGKLTDDVAQKAVLGYLNNFEEVSNLEIIAGYQDGIDIENDKTYFVARTRMQPYRYFWRSLDASQRNANSQELYPTAWSEWKAISVPLENVANGIVRPIMMDNRLYISWFEVAEEKETDSDGNIIVSGRYRTKIRLAHLGFDGVWSSGTTLREEVLADQMEEMIAVVDRMEDEPRLALVAFKEMSESWDVVFSYICDSMLIESSNLPTTTHPPKPGDGDKGLSDLDDYGANLVWFYLHETANGGKAEYKQLILYPVIINRDWPIELDKTHQGDFGTVDDFTLNSNYTGDELSLYLQSSSTYKYDFSKSKNIIYGIWKEDANNNRCWLNYKLLTPEDYEPQINATLVMCDKGDVNIITGFSLPNGGVDAGGKIKVTLRVGKKLRDKFQIKQFSQTQYLQFPEASSADVWYIGKQIRLNTLFAKELIGKASRSLDLVLSWETQNSRLEEAILGGAAELIDLDGANGIYFWELFFHMPFMVSWRFNVEQRYEDANRWVKYLFNPFECEDEPALLLGKPPYWNSRPLVDEPFKGYSLTQPSDPDAIAASDPIHYRKAVFNFLTKNIIDQGDMEYRKLQPSARTLARLSYSTASSLLGRRPDVQLTSFWQPLTLEDASYKTDSEIRAIEMQSQPLTFEPVVHDQTMSAVDNDIFMYPMNNELRGLWDRIENRIYNLRHNLTLDGKEINMDLYDSSISPRGLMKQRYQRVVTARNASKMNFKVPNYRFEPMLNRSKSGVETLIQFGSTLLSLLERKDSLSFDAYQMIQSGDLYRFSIDLQQQDIDINKASLEALQVSKQSAQDRYDHFKELYDENISSTEQKVIELQSQAANSLLMAQGMRTAAAALDVIPNIYGLAVGGSHWGAPLNAAAEIIMIKYQADSSKSESLSVSESYRRRRQEWELQYKQAEWEVNSVEQQINLQNMQIKAANKRLEQVEAQQQQAMALLDYFSERFTNESLYTWLISQLSSLYLQAYDAVLSLCLSAEASLLYELNLGEQSFVGGGGWNDLYQGLMAGETLKLALMRMERVYVEQNSRRQEITKTISLKALLGESWPAELNKLKQKTPINFNLEEQIFVEDYQELYQRRIKSVSVSLPMLVGPYEDVCAQLTQTSSSYSTRADLKTVENMLTKRTFADTPHLVRSIQPNQQISLSTGVNDSGLFMLNFDDERFLPFEGSGVDSSWRLQFTNLKQNLDSLNDVILHVKYTAAIGSSTFSQGVRKILANINNDE

Entity 3 polymer

描述 description	Chitinase 2
分子量 formula_weight	69740.6 kDa
EC 编号 ec_number	3.2.1.14
来源方法 src_method	nat
拷贝数 entity_count	5

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C,F,I,L,O

MVNKYTYTSSKAMSDISDVIGEPLAAWDSQVGGRVFNVIFDGKVYTNTYWVERWQVPGIGSSDGNPHNAWKFVRAATADEINKIGNPTTADVKPTENIPSPILVEDKYTEETYSRPDVNFKEDGSQGNLSYTATRVCAPMYNHYVGDKTKPKLSAYITDWCQYDARLDGGGSKEEERGRGFDLATLMQNPATYDRLIFSFLGICGDIGNKSKKVQEVWDGWNAQAPSLGLPQIGKGHIVPLDPYGDLGTARNVGLPPESADTSIESGTFLPYYQQNRAAGLLGGLRELQKKAHAMGHKLDLAFSIGGWSLSSYFSALAENPDERRVFVASVVDFFVRFPMFSCVDIDWEYPGGGGDEGNISSDKDGENYVLLIKELRSALDSRFGYSNRKEISIACSGVKAKLKKSNIDQLVANGLDNIYLMSYDFFGTIWADYIGHHTNLYSPKDPGEQELFDLSAEAAIDYLHNELGIPMEKIHLGYANYGRSAVGGDLTTRQYTKNGPALGTMENGAPEFFDIVKNYMDAEHSLSMGKNGFVLMTDTNADADFLFSEAKGHFISLDTPRTVKQKGEYAAKNKLGGVFSWSGDQDCGLLANAAREGLGYVADSNQETIDMGPLYNPGKEIYLKSISEIKSK

Entity 4 polymer

描述 description	Toxin subunit YenB
分子量 formula_weight	167148.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	P

MQNSQEMAITTLSLPKGGGAINGMGESVGQAGPDGMVTFSIPLPFSAGRGVAPALSLSYSSGAGNGPFGMGWQCSAMSISRRTQKGVPQYNEDDEFLSPSGEVMAIALNDSGFEDVRTANRLQGIPLPFSYKVTRYQPRLIQDFIKIEYWQPVKQTDGTPFWIIYSPDGQTHILGKNSHSRVANAENPSQIASWLLEETVTPTGEHIYYQYSGENQVNCTDAEIALHPQDSAQRYLARIDYGNISPQASLFVLDEELPNLTQWLFHLVFDYGERDISINKIPTFEGGTTGWLARPDMFSRYDFGIEIRNRRLCHQVLGFHRLEALNDRDVTDEIPVLVNRLTLDYDLNNSVSTLVAVRQVAYETDGSPITQPPLEFDYQRFDTGSIPGWQEMPQLEAFNGYQPYQMIDLYGEGTPGILYQETPGAWWYKSPQRQIGGDSNAVTYGAMKALPKIPRLQEGATLMDINGDGRLDWVITSAGVRGFHSIHSTGEWTHFTPLNTLPTEYFHPKAQLADLVGAGLSDLVLIGPKSVRLYANQQGNWAPAQDVTQAENVSLPVIGIDSRQLVAFADMLGSGQQHLVEITADSVKCWPNMGHGRFGQPLTLEGFSQPQTSFNPDRVFLADIDGSGTNDIIYAHSECLEIYLNESGNRFSKPISLLLPDGVNFDNTCQLQAADIQGLGIASLVMTVPHMSPTHWRCDLALNKPWLLNVMNNNRGAETCLFYRSSAQFWLDEKQLVEAAGQQPECHLPFPMHLHWRSEIFDEITGNRLTQEQEYAHGSWDGQEREFRGFGRLIQRDTDGFAQGTVDIPTHPSRTVSWFATGIPEIDTTLSAEFWRGDDQAFSPFSPRFTRWENDSEAGSDVAFIPSEHDAFWLNRAMKGQLLRSELYGDDGTPEAEIPYSVTEMRHQVRALPTTDATVPSAWCSTIETRSYQYQRVAADPQCSQQVVIKADRYGSPLLSVAINYPRRKKPEKSPYPDDLPETLFDSSYDTQQQQLHLTKQQQNYFHLTNDDNWLLGLPKEQRNDGYQYDQERAPANGFTLETLIASNSLIGSNQPFTYLGQSRVAYQGGVDEQPSLQALVAYGETAILDEKTLQAFVGVLDSKTRDELLFSAGYQLAPRLFRVESEPDVWVARQGYSEFGDYSQFWRPLSQRSTLLTGKTTLKWDKHYCVVIETQDAAQLVTQARYDYRFLTPYSLTDANDNQHYVVLNPFGEVIASRFWGTEAGKDAGYSTPQAKPFVVPATIEAALALSPGIPVAHCAIFEPESWMQKLTQHDVSERMADNGTLWNALLQARFVTEDGYVCALGRRRWMARHGLSVLMLTLLAEIPRTPPHSLTITTDRYDSDDQQQLRQRILFSDGFGRLLQSAQRVEAGESWQRSEDSSLVVNVSGTPALVVTDNRWAVSGRTEYDGKGQGIRVYQPYFLDDWRYLSDDSARTDLFADTHIYDPLGREYQVITAKGYRRERQYTPWFVVNQDENDTAANLAI

Entity 5 polymer

描述 description	Toxin subunit YenC2
分子量 formula_weight	107563.9 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	Q

MDIQLFSKTPSVTVFDNRGLSVRDIAYRRHPDTPKVTEECITYHQFDFRGFLAQSLDPRLNHKEVTNFSYLTDLNGNIIYTQSVDAGNTLVLNDTEGRSVIAMTNISRGENGKDDLSLAVTRTFQYENAPLPGRPLSVTEQVNGENARITEHFVYAGNTPQEKNLNLAGQCVSYYDAAGLIQTDSVSLTGKPLSVSRKLLKNLDDTNILADWQGNDTSAWNSLLATEIYTTVTRTDAAGAVLTTIDAVGNQQRVAFDIAGQLSASWLTLKGGQEQVIIKVLTYSAAGQKLREEGGNGVVTTYTYEAETQRLIGIKTERPNGHAAGAKVLQDLRYEYDPVGNVLSITNDAEETRFWRNQKVVPENAYRYDSLYQLVSASGREVAGAGQQGSDLPSPLVPLPSDSSVYTNYTRTYTYDSAGNLMRIRHSAPATNNNYTLNITVSERSNRGVMSSLTENPADVDALFTASGSQKCLQQGQSLIWTPRGELRTVLLVARGETADDSESYRYDGSSQRILKISSQQTNHSARVQRALYLPGLEWRTMTGGVAEAENLQVICIGEAGRAQVRVLHWESGKPDGIINDQIRWSYDNLTCSSGLEVDGDGLVISMEEYYPYGGTAVWAARSHIETAYKTVRYSGKERDATGLYYYGFRYYQPWAGRWLSADPAGTVDGLNLYRMVRNNPLRLTDPDGMAPLDWLDLDTTNASRDIVKAIYQLNQIDGPHRGVRDTYQRMTESTGMILQETLNNEAVLKGIKQKDKEKKSRGMKFTNSKLKTYAAHAGVLNTLQPDPVYKDGFLNLPGSLGNKNTFPGVELIEDKVKPSLSQYHPDKLGKSQRWKPESSLGYYRVADTEAFITGIRSQYKSSGTDLHAVVEGRIRDHLLANNNVLPKMAGIAGLHAEVQALNYIISNPDIEGGNAERLNGSYIFTQRLVGDVNQDFPACYNCSGIISGLENVMTGRVNNDVRLKRRKSF

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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	triclinic

分辨率 resolution	4.60 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	60315

fit	/app/data/saxs_computation/c4/9c4k/9c4k.fit
pddf	/app/data/pr_computation/c4/9c4k/9c4k.pr.out
profile	/app/data/saxs_computation/c4/9c4k/9c4k.dat

Yersinia entomophaga holotoxin complex in prepore conformation

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

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

Entity 4 polymer

聚合体 Polymer

Entity 5 polymer

聚合体 Polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)