SAXSdb — 8hmc

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8hmc
沉积日期 deposition_date	2022-12-03
结构标题 title	base module state 1 of Tetrahymena IFT-A
关键词 keywords	intraflagellar transport complex, PROTEIN TRANSPORT; PROTEIN TRANSPORT
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	54.80 Å
回转半径 Rg (电子) rg_electron	54.92 Å
零角强度 I(0) i0	1354080000.00
分子量 molecular_weight	310040.0 kDa
排除体积 excluded_volume	389140 Å³
包络体积 envelope_volume	598230 Å³
水化壳体积 shell_volume	91921 Å³
包络直径 envelope_diameter	186.7 Å
壳层 Rg shell_rg	56.49 Å
包络 Rg envelope_rg	53.73 Å
形状 Rg shape_rg	54.91 Å
总 Rg total_rg	55.00 Å
总原子数 total_atoms	21797
残基数 n_residues	2693
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	185.8 Å
Rg (实空间) rg_real	54.91 Å
Rg 误差 (实空间) rg_real_error	2.13 Å
I(0) (实空间) i0_real	1.3540e+09
I(0) 误差 (实空间) i0_real_error	2.8280e+07
Rg (倒空间) rg_reciprocal	54.69 Å
I(0) (倒空间) i0_reciprocal	1354000000.0000
解质量估计 total_estimate	0.8653
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	57.6 Å
偏度 Skewness skewness	0.367
峰度 Kurtosis kurtosis	-0.483
角度范围 angular_range	— – 0.1450 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	148300000.0000
实空间数据点数 n_real_points	30
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.870; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.635

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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	Intraflagellar transport protein 122 homolog
分子量 formula_weight	143939.4 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	21797

MKCSELWTEIIPKNDPNSNITNQVWSCSFNNDGSILLACVGDAILVYDSFTGNLVNKAIRGGQKEQINCIKFSKDGKRFATASNDKTVWVWSFDVNKNPKLAPEVKYSHTDKVLCLAFNPLTHQIFSGGAQDYALWTPDQQSIEKSKFKDKIITCAWSWDGLYLGFGTMGGIIGIRNRALEQLAEIQRSFPIWCMDWTPITPDYQNSVLVVGVWEQSIAHYNIQGQQLGSDKKLTYDPIDINFSTQGEFLLVSGTNNKCTLYTREGGFLIDVATKNDWVWNNKLKPVIKEAGSVAVQDQLHVALTTNDGEISMFKIQQLTVHALEGDKYAYRDNLTDIVVQSMSSNQRIRLKCKELVKNISIYKDKLAAHLTERILIYGTSSEDSQMKYKLHKRIVKKVEAHILEIVSNHLIACVKNKVQLYQLSGDLEKEWVFDSRVNCIKIIGGMPNKEGAYVGLKNGQIFKIFVDNSFPIPILNHNISIKNIDASQKRKRLAVVDKNSNLTVYDLSNKEQVFQEMNIVSCAFNNNFDDLLAFSSTDTTFIRCSNHPPLSQKISGQVVGFKANKLFVLNDNVMSTIDVSMTQTMIKYLERKEFQSAYEISLLGVTDQDFLYLGNEALIATQFAIARKCYTRIKKLDFIYLLEKAEKDFKKNTFVEGFYQGEIYALQTKFYEAENALTKSNLASQAKEMWIILKEFDKAMRITDTGASPINRGQNKEINSDASRKDLLIQRAEWEVKQGNWKKGGELYIQAEVYKKAIEVYVTNNFSEGIVEVCRNADAETQRKEIEQCAAYFKKAKLHQYTKEAYLKLQDNKALLQLNIDLEKWDEAMTLAKAHPEFMEIVKLPYANWLAKQDRYEESLKAYRKIGKHDMATKMLYNLSQNAVFEKRFSDAALFTWMIATEHLGLIRNMKAPTPEDIENLMKFYQYRDDAEIYFAYSKVQSFVDEPFLPLSGHAYMLNIFNAARFAINKLGNRQLYGVQHSYLYYSLGKVSKQLEGYKTARICYEKLASYKIPTEWSEEIELSTLLIRSKPYSDQESLLPICNRCYNQNPALTEGNRCSSCMHQFQNCFISFENLPLVEFKLDPKITHKRFIELINSDKSKTQPNKKKKKANDGWQESHQGDQQVLTFNNSPQKGGNDNESSPFLDKLNEVFEIQQTTQEYIPVTLDENIVSSLSIDEVYWVDYTKYCYTAEIKYYKSMLTDIPLKNCQECGTFYILDEYEFEISKTQKCPFCRSVDERAGPQKDVFDF

Entity 2 polymer

描述 description	WD40 repeat protein
分子量 formula_weight	138077.0 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	B

MFVFLSKKIGMPNNAKIEAVCWNKEQGWIAAGGEKGILKVLKIEDQRQKDGSNPTTTGQLLVNNTLEYHTSNVYLVTWNDRYRKLTSVEENGIIVVWAYFRELQLWKEEMINDRKKSVVRDLKWSPDGQKVCIAYEDGAVIVGSVEGSPLWRKEFPHKLALIEWSPDSKMMIFGTPEGEVRVYDSQGMEMQRLKIHCLQKLIDPSKSFSPDLPLAAIDWFPQAKMYTDDTPPGLCIAYQCGRVQLMKNEKDDEPVLIDTMMKIFTVKWNPSGSMFAISGTQDENGELKGVVQFYSNAGHHLKTLRVPGSDRVTGVSWEGSGLRIAMAVNQAIFFANIKPDHKWAYMSDGTLAFAYQKIDRVEYTIIFWDTINNKKNLKFVKNLCCLRASGDLCCIVTELIGYDLWQIDLCNSIGSPIDSKQINIYPNAVTMTKTHIIVCSQDHVYAWQYKNQVERLTTFEQQTGLRRVGREQAWFIDKENDSNNQYDKDTYDVEPQSEDVICTVAANENFLLVARISGTINVYTFPHISLENKLHIQTRPSQMSLNKDATRLAIIDHNGNLNILKITPQGDELLPFEKKECWFVKYSDDIPESFVFMERSRMYIVNDQTPEEPIITEGYICQYKDFQVKIVYLDDIMKSPDGVLRKEELTLEIEANILKDIKDQLYKKSMQEMFIVIKQHDNDCLWRVYAKKALEDNDFDSAENAFVQCKDYASLKFLQRVRELDDRERQRAEIQCYFNKVEEAEEIYNKIERRDLSIQMRMKLGDWAQVVDQIREGTGQDVELQKARLELGNYYAENFQWDKAAKQYALAKYNPGLIEAYTRIQDYEGLEKLIAEIPERNELLQDMGDRFQQAGLCDAAVKCYEKFGDIKQAIDCCVLLNHWNLAVELAEQYNFVQIEGLLVQYANQLLEKRRKLEAAELYRKAKRNTEAAKILSQIADDLTERDANPLNIKKMYVMAALEVDLYKKRMLDATMTGQATSTAKTLNSLITSTINTSSADKILNNPWRGAEAWHFFILAQRQLYNGQFKYALKSALRLGEYELEIDQKKIYSLIAIAAYYNKSFRECSRAFVKLQNLENITEDEKERYEAIAVSIFTKHPPLDSPCEYTPCVGKNCSQQVSEYDIHCRACGSNFSPCVASGRPIFQKEFYQCKNCRHKMIESEVSRLKLYNCALCHSPIDFKRFTESNNNNNNNI

Entity 3 polymer

描述 description	Tetratricopeptide repeat protein
分子量 formula_weight	154216.1 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	C

MQNQQQKMQTILIAQSQVYYYIREGFWSTMQRFCQEQYKAFGDPFFIFWKAYGLYQEGLPNEAINELTSIQHKKEIQYATIVALITYHLSTNIVDRETVQNLKFEESTQRRLSSDKAICLAAFFYAFNKEHAKARDLIDEIHSDNFNIRIASAWCYLLEGGKFLEKSVQLFEELYNEQHEINKNLESLMGRSKANEMIKKFDISLNTINEINVLYPDFKGGLIEKAKLLMTVDDWEQLVDYCNKILYDDDKNIMALMLLTFYTFAREGDIETGCERLQKLIQAVEFSESRNMQLMFKISQVFSRISGRNTQILKFTMKLVNQCKQLSPLNAQYFCELAQQLLMVNQFERAEQYFQEASAIDVDNKECLMGLILSKIMQGQTEDAESQIDFINQTTNNGERTSEIAYLEALVSTKQENVDPRVTIKLLEESLKLHIAQANRLYPSFDFYIVLNPDFLMSLSQAYFFQVGMKEMLAGKQPQNGVASKGTKLLDFIIKKIPGLIPAYLLQAKGKMSMGNTQEALKSVTKVIEQDPKNEEAYILSAMIASSSKNFSLAQNQLQQALSNNFMIRDNPLFMLVKGEVEYAQGSYQACLETMKAAYEIPEVKDKANQSKVVSAMSVLQFSDKDRCSIFLLYAKALQQNNNSKEAKKIMTQAISQFTGTTEEVNVLIANSEIALQSGDVKKAISILKGVPQESPYFLRARQILADVYLDQLRDRRNYAKCYADLIEIDPSFDNYKMLGDALMKIREPEEASRAYEKAALIKPDDEQIIQLLGLSLCQTHDYNKALTYYENALRMNPKRLDLIIDLGKLCIQIKNFNRAEEILKPDIFSDEYQLPTYQNLKRNQEGFYLIAKLNIKRTPPGVFTPIDMYRKALKKSIQIQIDVIEKAKQEGEDVEKERKTLADMYIELAKYTNQYEKNEKATLDILAEASKYTNNQDTMSKTVGNQEKILELEVQMYFKSNQKLECENKCNLLLKLNPNNDLACLTLAELLLQKDEYSQAIEQFKKILQDRPNNYGILAKLIDFFRRSFQINEAKTYIERAEKKATNTNDPGLCYCRGLYHKYNRSPKDALNEFSKAKKSSQYAEESLVNMIDIYLNPDQDLYYSNVEEGPKVVDEVNLRACESLLREMQIRASYLRYIVMESYVFFLGGPRYKGGLEQGLKNLNDILKTNNDYIPAMLALAVGKFIQKKSTDAKNLLKLLWKRQYTTEYGEDLERAWLLSADSFIAIQKYDSAEEILKKCLKYNQSCGKAEEYMGLIKEKEQSYVDAATHYEKAYKLTNEKSASIAFRLSFNYLKAKRYVDCINICKKILVLFPNYPKIEKDCLEKARQALK

Entity 4 polymer

描述 description	Intraflagellar transport protein 43 homolog
分子量 formula_weight	16711.2 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	F

MAAKGKQGWGFGGKDQNVKIDTSQQDQKKQNIWEQNNEDLIFVPDLTQEAQEQEVSKVSAPPNQPTVQVQDINELQKFTKINTLPQTEEGVDLSQLMQILSPVEDIKEKDEAWEFLQLKTQIYEIVSNMYGGNELIDDDDEDDENQ

Entity 5 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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6. 折叠分类 (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

结构域编号 domain_id	8hmcA01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	130 — 7 Propeller
拓扑 Topology topology	10 — Methylamine Dehydrogenase; Chain H
同源超家族 H-superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

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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	3.60 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	538078

fit	/app/data/saxs_computation/hm/8hmc/8hmc.fit
pddf	/app/data/pr_computation/hm/8hmc/8hmc.pr.out
profile	/app/data/saxs_computation/hm/8hmc/8hmc.dat

base module state 1 of Tetrahymena IFT-A

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 non-polymer

6. 折叠分类 (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)