SAXSdb — 9n5i

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9n5i
沉积日期 deposition_date	2025-02-04
结构标题 title	Endogenous Pfs230D13-14 in complex with Pfs48/45 bound to anti-Pfs48/45 Fabs RUPA-71 and RUPA-44
关键词 keywords	Pfs48/45, Pfs230, Malaria, transmission-blocking antibodies, IMMUNE SYSTEM; IMMUNE SYSTEM
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	37.98 Å
回转半径 Rg (电子) rg_electron	37.97 Å
零角强度 I(0) i0	254719000.00
分子量 molecular_weight	130820.0 kDa
排除体积 excluded_volume	164310 Å³
包络体积 envelope_volume	214420 Å³
水化壳体积 shell_volume	49486 Å³
包络直径 envelope_diameter	152.8 Å
壳层 Rg shell_rg	41.34 Å
包络 Rg envelope_rg	37.96 Å
形状 Rg shape_rg	37.93 Å
总 Rg total_rg	38.29 Å
总原子数 total_atoms	9224
残基数 n_residues	1125
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	138.6 Å
Rg (实空间) rg_real	38.28 Å
Rg 误差 (实空间) rg_real_error	1.45 Å
I(0) (实空间) i0_real	2.5470e+08
I(0) 误差 (实空间) i0_real_error	4.5970e+06
Rg (倒空间) rg_reciprocal	38.10 Å
I(0) (倒空间) i0_reciprocal	254700000.0000
解质量估计 total_estimate	0.8314
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	39.6 Å
偏度 Skewness skewness	0.571
峰度 Kurtosis kurtosis	-0.014
角度范围 angular_range	— – 0.2100 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	32580000.0000
实空间数据点数 n_real_points	43
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.668; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.927; Smooth: 0.874

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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 (7)

Entity 1 polymer

描述 description	Gametocyte surface protein P230
分子量 formula_weight	363701.8 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	A
原子数 atom_count	9224

MKKIITLKNLFLIILVYIFSEKKDLRCNVIKGNNIKDDEDKRFHLFYYSHNLFKTPETKEKKNKKECFYKNGGIYNLSKEIRMRKDTSVKIKQRTCPFHKEGSSFEMGSKNITCFYPIVGKKERKTLDTIIIKKNVTNDHVVSSDMHSNVQEKNMILIRNIDKENKNDIQNVEEKIQRDTYENKDYESDDTLIEWFDDNTNEENFLLTFLKRCLMKIFSSPKRKKTVVQKKHKSNFFINSSLKYIYMYLTPSDSFNLVRRNRNLDEEDMSPRDNFVIDDEEEEEEEEEEEEEEEEEEEEEEEEEYDDYVYEESGDETEEQLQEEHQEEVGAESSEESFNDEDEDSVEARDGDMIRVDEYYEDQDGDTYDSTIKNEDVDEEVGEEVGEEVGEEVGEEVGEEVGEEVGEEVGEEVGEEEGEEVGEGVGEEVGEEEGEEVGEEEGEYVDEKERQGEIYPFGDEEEKDEGGESFTYEKSEVDKTDLFKFIEGGEGDDVYKVDGSKVLLDDDTISRVSKKHTARDGEYGEYGEAVEDGENVIKIIRSVLQSGALPSVGVDELDKIDLSYETTESGDTAVSEDSYDKYASNNTNKEYVCDFTDQLKPTESGPKVKKCEVKVNEPLIKVKIICPLKGSVEKLYDNIEYVPKKSPYVVLTKEETKLKEKLLSKLIYGLLISPTVNEKENNFKEGVIEFTLPPVVHKATVFYFICDNSKTEDDNKKGNRGIVEVYVEPYGNKINGCAFLDEDEEEEKYGNQIEEDEHNEKIKMKTFFTQNIYKKNNIYPCYMKLYSGDIGGILFPKNIKSTTCFEEMIPYNKEIKWNKENKSLGNLVNNSVVYNKEMNAKYFNVQYVHIPTSYKDTLNLFCSIILKEEESNLISTSYLVYVSINEELNFSLFDFYESFVPIKKTIQVAQKNVNNKEHDYTCDFTDKLDKTVPSTANGKKLFICRKHLKEFDTFTLKCNVNKTQYPNIEIFPKTLKDKKEVLKLDLDIQYQMFSKFFKFNTQNAKYLNLYPYYLIFPFNHIGKKELKNNPTYKNHKDVKYFEQSSVLSPLSSADSLGKLLNFLDTQETVCLTEKIRYLNLSINELGSDNNTFSVTFQVPPYIDIKEPFYFMFGCNNNKGEGNIGIVELLISKQEEKIKGCNFHESKLDYFNENISSDTHECTLHAYENDIIGFNCLETTHPNEVEVEVEDAEIYLQPENCFNNVYKGLNSVDITTILKNAQTYNINNKKTPTFLKIPPYNLLEDVEISCQCTIKQVVKKIKVIITKNDTVLLKREVQSESTLDDKIYKCEHENFINPRVNKTFDENVEYTCNIKIENFFNYIQIFCPAKDLGIYKNIQMYYDIVKPTRVPQFKKFNNEELHKLIPNSEMLHKTKEMLILYNEEKVDLLHFYVFLPIYIKDIYEFNIVCDNSKTMWKNQLGGKVIYHITVSKREQKVKGCSFDNEHAHMFSYNKTNVKNCIIDAKPKDLIGFVCPSGTLKLTNCFKDAIVHTNLTNINGILYLKNNLANFTYKHQFNYMEIPALMDNDISFKCICVDLKKKKYNVKSPLGPKVLRALYKKLNIKFDNYVTGTDQNKYLMTYMDLHLSHKRNYLKELFHDLGKKKPADTDANPESIIESLSINESNESGPFPTGDVDAEHLILEGYDTWESLYDEQLEEVIYNDIESLELKDIEQYVLQVNLKAPKLMMSAQIHNNRHVCDFSKNNLIVPESLKKKEELGGNPVNIHCYALLKPLDTLYVKCPTSKDNYEAAKVNISENDNEYELQVISLIEKRFHNFETLESKKPGNGDVVVHNGVVDTGPVLDNSTFEKYFKNIKIKPDKFFEKVINEYDDTEEEKDLESILPGAIVSPMKVLKKKDPFTSYAAFVVPPIVPKDLHFKVECNNTEYKDENQYISGYNGIIHIDISNSNRKINGCDFSTNNSSILTSSVKLVNGETKNCEININNNEVFGIICDNETNLDPEKCFHEIYSKDNKTVKKFREVIPNIDIFSLHNSNKKKVAYAKVPLDYINKLLFSCSCKTSHTNTIGTMKVTLNKDEKEEEDFKTAQGIKHNNVHLCNFFDNPELTFDNNKIVLCKIDAELFSEVIIQLPIFGTKNVEEGVQNEEYKKFSLKPSLVFDDNNNDIKVIGKEKNEVSISLALKGVYGNRIFTFDKNGKKGEGISFFIPPIKQDTDLKFIINETIDNSNIKQRGLIYIFVRKNVSENSFKLCDFTTGSTSLMELNSQVKEKKCTVKIKKGDIFGLKCPKGFAIFPQACFSNVLLEYYKSDYEDSEHINYYIHKDKKYNLKPKDVIELMDENFRELQNIQQYTGISNITDVLHFKNFNLGNLPLNFKNHYSTAYAKVPDTFNSIINFSCNCYNPEKHVYGTMQVESDNRNFDNIKKNENVIKNFLLPNIEKYALLLDDEERQKKIKQQQEEEQQEQILKDQDDRLSRHDDYNKNHTYILYDSNEHICDYEKNESLISTLPNDTKKIQKSICKINAKALDVVTIKCPHTKNFTPKDYFPNSSLITNDKKIVITFDKKNFVTYIDPTKKTFSLKDIYIQSFYGVSLDHLNQIKKIHEEWDDVHLFYPPHNVLHNVVLNNHIVNLSSALEGVLFMKSKVTGDETATKKNTTLPTDGVSSILIPPYVKEDITFHLFCGKSTTKKPNKKNTSLALIHIHISSNRNIIHGCDFLYLENQTNDAISNNNNNSYSIFTHNKNTENNLICDISLIPKTVIGIKCPNKKLNPQTCFDEVYYVKQEDVPSKTITADKYNTFSKDKIGNILKNAISINNPDEKDNTYTYLILPEKFEEELIDTKKVLACTCDNKYIIHMKIEKSTMDKIKIDEKKTIGKDICKYDVTTKVATCEIIDTIDSSVLKEHHTVHYSITLSRWDKLIIKYPTNEKTHFENFFVNPFNLKDKVLYNYNKPINIEHILPGAITTDIYDTRTKIKQYILRIPPYVHKDIHFSLEFNNSLSLTKQNQNIIYGNVAKIFIHINQGYKEIHGCDFTGKYSHLFTYSKKPLPNDDDICNVTIGNNTFSGFACLSHFELKPNNCFSSVYDYNEANKVKKLFDLSTKVELDHIKQNTSGYTLSYIIFNKESTKLKFSCTCSSNYSNYTIRITFDPNYIIPEPQSRAIIKYVDLQDKNFAKYLRKL

Entity 2 polymer

描述 description	Gametocyte surface protein P45/48
分子量 formula_weight	51545.9 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	D

MMLYISAKKAQVAFILYIVLVLRIISGNNDFCKPSSLNSEISGFIGYKCNFSNEGVHNLKPDMRERRSIFCTIHSYFIYDKIRLIIPKKSSSPEFKILPEKCFQKVYTDYENRVETDISELGLIEYEIEENDTNPNYNERTITISPFSPKDIEFFCFCDNTEKVISSIEGRSAMVHVRVLKYPHNILFTNLTNDLFTYLPKTYNESNFVSNVLEVELNDGELFVLACELINKKCFQEGKEKALYKSNKIIYHKNLTIFKAPFYVTSKDVNTECTCKFKNNNYKIVLKPKYEKKVIHGCNFSSNVSSKHTFTDSLDISLVDDSAHISCNVHLSEPKYNHLVGLNCPGDIIPDCFFQVYQPESEELEPSNIVYLDSQINIGDIEYYEDAEGDDKIKLFGIVGSIPKTTSFTCICKKDKKSAYMTVTIDSAYYGFLAKTFIFLIVAILLYI

Entity 3 polymer

描述 description	RUPA-44 Fab kappa chain
分子量 formula_weight	23483.1 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	E

DIQMTQSPATLSASVGDRVTITCRASQSISSWLAWYQQKPGEAPKLLIYKASSLQSGVPSRFSGSGSGTKFSLTISSLQPDDFATFYCQQYHSYPYTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

来源 Source

来源生物 organism	Homo sapiens
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 4 polymer

描述 description	RUPA-44 Fab heavy chain
分子量 formula_weight	24277.3 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	F

QLQLQESGPGLVKPSETLSLTCTVSGGSISRSPYYWGWIRQPPGKGLEWFGSIYNNGSTYYNPPLKSRLTISVDTSKNQFSLKLSSVTAADTAVYYCARHGGSTGMKVVVIAPPDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

来源 Source

来源生物 organism	Homo sapiens
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 5 polymer

描述 description	RUPA-71 Fab heavy chain
分子量 formula_weight	24711.7 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	H

EEQLVESGGGLVKPGRSLRLSCSASGFTLGDYAVTWFRQASGKEPEWVGVIRTKDEGGTTEYAASVKGRFSILRDDSKSIAHLQMNSLKIEDTAVYYCTRNGLRWYDSSGPRGWAFDIWGPGTLVVVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

来源 Source

来源生物 organism	Homo sapiens
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 6 polymer

描述 description	RUPA-71 Fab kappa chain
分子量 formula_weight	23598.2 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	L

EIVMTQSPATVSVSPGERATLSCRTSQSVSNKLAWYQQKPGQAPRLLIYGASTRATGIPARFSGSGSGTQFTLTISSLQSEDFAVYYCQQYNNWPPWTFGRGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

来源 Source

来源生物 organism	Homo sapiens
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 7 branched

描述 description	alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	367.3 kDa
来源方法 src_method	man
拷贝数 entity_count	1

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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	3.390 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	3.39 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	146814

fit	/app/data/saxs_computation/n5/9n5i/9n5i.fit
pddf	/app/data/pr_computation/n5/9n5i/9n5i.pr.out
profile	/app/data/saxs_computation/n5/9n5i/9n5i.dat

Endogenous Pfs230D13-14 in complex with Pfs48/45 bound to anti-Pfs48/45 Fabs RUPA-71 and RUPA-44

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 (7)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

来源 Source

Entity 4 polymer

聚合体 Polymer

来源 Source

Entity 5 polymer

聚合体 Polymer

来源 Source

Entity 6 polymer

聚合体 Polymer

来源 Source

Entity 7 branched

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)