SAXSdb — 9cap

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9cap
沉积日期 deposition_date	2024-06-17
结构标题 title	Structure of the LPD-3 complex
关键词 keywords	Native, membrane protein complex, BLTP, LIPID TRANSPORT; LIPID 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	48.52 Å
回转半径 Rg (电子) rg_electron	49.46 Å
零角强度 I(0) i0	552138000.00
分子量 molecular_weight	209240.0 kDa
排除体积 excluded_volume	268210 Å³
包络体积 envelope_volume	361890 Å³
水化壳体积 shell_volume	65142 Å³
包络直径 envelope_diameter	199.4 Å
壳层 Rg shell_rg	48.53 Å
包络 Rg envelope_rg	50.34 Å
形状 Rg shape_rg	49.47 Å
总 Rg total_rg	49.42 Å
总原子数 total_atoms	14705
残基数 n_residues	1730
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	185.4 Å
Rg (实空间) rg_real	49.24 Å
Rg 误差 (实空间) rg_real_error	2.32 Å
I(0) (实空间) i0_real	5.5210e+08
I(0) 误差 (实空间) i0_real_error	1.1860e+07
Rg (倒空间) rg_reciprocal	48.52 Å
I(0) (倒空间) i0_reciprocal	551600000.0000
解质量估计 total_estimate	0.7751
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	46.4 Å
偏度 Skewness skewness	0.668
峰度 Kurtosis kurtosis	0.073
角度范围 angular_range	— – 0.1600 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	62500000.0000
实空间数据点数 n_real_points	33
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.500; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.692; Smooth: 0.881

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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	Bridge-like lipid transfer protein family member 1 C-terminal domain-containing protein
分子量 formula_weight	483608.1 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	A
原子数 atom_count	14705

MSDFDIQIKIDDAQLDLKGVSFWVTASVVTLFLAWSTFVVLFFSRVSALFFTFVIDKYLRLSKNGIHFKIGGISISGLHAGKIMFRNVIYDNGDMTIKVNDGHLLFKYWKSVEHRHLNLSTKRASRLHLVLNGLHVNIYNNLTKYTEIARIRRFDWFFENTNMNDARRPQTKPPDTCRSPPSSVWENMWNLLGIVHIEVSAGCILVGNKFLPYALWTRFENLNSKTSVTESANDRALLTFEGETENVAVSLIKNEQFDFTAKDKDPPRTMGNDGCPLLQSASLEFVYKQDLLGYVTDDEPQSITLKLPLWSSEWRFGNNTVLSYGPWAEQQRFLIYSFFYPPDFQNSTATAMPTRGKKRIHVKHDVKIILTKETCMDIWFMRGEQLESIRTRCGPLSSLDMSILWITTEKGFYWNMKAEFLNFEATTSLIFTKLFSCKKFNVDGSFVYPLTWNGEQTWTIDYAFTKANAWFVWDHKRLFTDLINDWIGDDPSDISKFVPFRVHNRMKVVDGFEVIMLLNESNWVDTADMNAENVEVAIVGEKLSFECELPFVDFLPQTQMVKYEMRGEKSVAMRAKFPPDSATAPIRAALSRLARCNSYAPPSKHGTHSLDTDVWFELWRTELVKMDFDHHYRPLIVKSNIPSDIPFSILSDYLPPPANHPWDLEPDYLGVDILIEGSDVKFTGLLVKLLFELKNNYFGWYDSMTSVDDEKIDDPIKLKASFDKTNANGMKPVEYFRTMNVDVTVRVCNVRAEMLLYSPAIDEGAEPEKVPVVFVEEVAVEVKKTKTQALIQVGVSPACAYLDKSSQGSGPGCITLSGFQFRGHAMYSAKEVAWNMGLVEYGWIMEILVGDIAGTLDFPAHAHVLHQIMESLLMFVISPDDATKVPDRMQFCQHGQLIKACSIAGKKTNEILGPCKTEEQMKYRQIRISVDSVNLTFVEEKTILQISADPVRVTICNAHESRFTEHVCIRVPGISIRQAVRIKEKPENIWIEGANAAIEGVSLDIELPTPKSASPTIGKERLEFVRMHDADTKRLHFLWADHSVWGCACFGNTCFFGDVDEIGSTFMETLTKKKFFVPGIERNPEKQPQVMQSVILKNKPILSNQPHMFYKKPKNADVVITIRKESTGDTESFHSARSQQSPGLRILQSMEMSSSYATFVDNVRVELPSAITVPQFGEPGAILEWCQAHQATRIINDVNTSGVNEVRFLSKPKKSQDIEYNTSRDTLGKRRLAINGVAATSLDLFVTPIGIEAFERLVTAASHSVPAINPCILVHMCYRDCVLKKHRQPLTESLFADEDNDSEPISEVDITVDLPRVSIGLFQCGVKKNIVKSNHTDHITANMGLLLIDRAFIQSKLIPAESVSQDFSADTSNLSSTLYQLNGSAITVQLLQLTNRDAPDFGSSGTATTPNNWEHCAISRRMNNLEPRVMMDFNVSDTLIILERRPIILLLPDKSTTAITPIHSPANAPTPTAMNRTPTLTLTPSAGAGGGERAEPMRKKKKMICEHYLKADIGSVTTALVMARPQELTAGDEFPIYEALAPVMVSWLSVVENFLRTVDKFIHTVECWKSVAMAKVLKLALDSTDEKVVVKVGKNRMGRTRVLSAHQASCPSCILLKTLFRWFAYAGNAPGAINHRLDIRPEFEIEETRKTALMALLSHWQSDVGKELKLVSYEDAHRFKVTRPDEAAIVALTKSKRLKRKMLEKKESSKKETRVVMEVKPEQPKAKRGRMSPAPLLKKLRKKAGDDDFDDDSMKFLSDVEMQEFNTLPLYEDYEDDEMLENLDSEPKIDDKVDLYTWMRNAQRESTLRRRKLAGGAEGSVKDDLNLKGYINPMDIQQKAYYYNIYRWAQLQWTSLDGIEKDHWHLDYSVTLREVDVRMMAKSIKNSSDHLRQYITPAQQKVMQVRNAAVNGGMVWKMERDERRKIPLHGQWNISYSGNVEGIRFLIGMATVSLGKELSLVLRVAMEAKNELRMHSTAESTPRNEVKVFKPVVPNQYDLAVEWDEKVLDMTRDYEKHMQRMRTNKEDVVEKVKVMVNGSAMVSSIVLESVLNDLYVSVTISQIVLAHSKNPMPDIPVVVHAVTLSTTPTAAAAEDKKTATLTKKSVSSTFKIDDLTVSLTKMKLTLSEADSSNKKSDILRCTLNSSSFNVHTNLKTLTSAKESNRPKNNLINSNIATTATLRLGALEGTMPMAAYSLHDVVMRHGKELEQQLNRLAAQPASTPLSSSTPFPSAEQSLLAKVADMKTAPEPVVITQAEFKPLTTLPATAAHVQDAKGQIVRRVPVAVVSFSIELTSIEMNIQLLPSLQAKYRINRATSNGITGVQANWSILLDEHFFEFCVTGQGGKTETFRLQLPSVTSDGLYQAEQGVSSQKPSTDKKLIYREGGSLQMTVVLGRVNHIFTTELLNQLMFAEHSFRTELTALINRIRSSSFASTNSSRSAQSTNDRVNSTANLKLLLPVQTTSTPVHIEKPPLLFSIKIQTKEIPRKDEKTDKDAKTPKASGASGNLDQSQHPSHSTHVKSTPWLQLTAATPTQTAVRLTVDSLEGELTNKWVVKEEGSKERIYGNAVIHFNAKLGQLIKPVPTGDSVAATDVTDLQEFATFMTQVRVENKERNMFNSSYSYHISLNRPIFLVKAAAIDKAILLWLNYKNTYDYWRNEREKVVQEKTTTKLSNAGMFSPTQIAEDADMNLSLAINNGMYMCMPLYSHDVTEGMPALVLSLQKSNLSVLVKKELTCKASFNGFKCSFVDDFDEQALTQSFLDATHSDQSNCIFFPEGTYQLCSKAEATKGPAKWVLSVSAEMQGVEIDLDTRIGKLAKLLVNTFSMIRTDDDDDMSFWGDEGELDSDEEKVEGASELKKLKAEEKVPWMENKMHEHSRAVFELAARGVSNKLIEAEKHKLRQYELIRFKAFRRNVVEKLKKGTTASRQHTETPPPQPRPDTTSRRNSRTTSTSQKNSEDLTTPGDIETVNFNLDVKVNITSGTCTLRTQKKEGANQLALPGILKRLNLGTKDIKAMFEPQIITTTTFSIPSVEIKAYHVSDPSNRSTDEFCKDKREKISKGLAKDADKLHRDLHNKSRFGNTYINGGGGPKTSTVPPPPKRGCFYIFVGLASMPSETVVTPHLATYFEQVLEPLPPSAVFQSQNNTREASVPDDGKGDANNEVHNIMAMDTAAFPIDFVFYLDVQSSTIRFDGKQPTSRSQTQADCLLTLPRLTLELTSKRTRDNIDNYVGGIHISGQFKGFMLKIYNPLELEPDSSRALQLSLDLLSFVISRNKNSSTEPDNRVRFVFSSQISKASFEYNFRRLGELIQFPKPWYRAAIARRVFFGDQAAPRQKDDASDITGTTRSRLPTDPKSLQPPAASTASTGSGSFVPHQRKPWTALVLAAIQWNEFEVTAFMSNTMGKTTWKATKGLVWGDAKLNSLNERDVSISFVLGSSELCARDGAISGTIMLNNLKVSADHSLSADVKRVPVNKAKIRLEWITANIEWMSRRVLIAKWCGPSFKVNDYYKGLKEGDHFALSELGMNVQASWKDLQVVITKSTVDDVAAIVNRLISFIDEQLKNSRILLGNLSASTNLKKQAQALIESRKPTTHFWEKVLDYMSEMQMNEQLMGLMEREGAKVGGHIELKAGGISLVMMKGDMNADTWAVFHLRDACILFDPEARMDFLDNSSQQKIGILLKQTFCLQLGSRHGNQTENRANVCRVQTRFNNSRHLQKAEDILEFFIGDVMKIIGSADHSEKKKLKEVEVIQSPISENENTAKSPTSTFSRFRSPGTSKTKESGPATNHNVMELFQFPGLEAKMSSQQLNGVDDGDKYESVFQMPMDVLTTFVCDFFSEVAIETNFNAQVSFLPELLKSYLKESHSGTSSSHSTNSSPAVSSSKESVVSETSKDPRIFTCQEWKVEPRVRFIDRIKWTPPVLDDILKKLQIFDHRNTIPKVIQRAVLDPLDATLAASVIATLQIVDNKKTIQKFKKSRTDSMAPTPKRRDSRRSSEEVSVSIDIPDIITDISDASFRPKHNGSGVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKLICTTGKLPVPWPTLVTTLGYGLMCFARYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYITADKQKNGIKANFKIRHNIEDGGVQLADHYQQNTPIGDGPVLLPDNHYLSYQSKLSKDPNEKRDHMVLLEFVTAAGITLGMDELYKGSGLEVLFQGPANSGVDYKDHDGDYKDHDIDYKDDDDK

Entity 2 polymer

描述 description	Defect at low temperature protein 1
分子量 formula_weight	31564.5 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

MRIFVFDGTSVIYVCAVIILILIWVAIIGQRQIWRHRHNVARVRPQVSLSSRISSKKAVLLRETQLDTVMRLRCENQARLTDCISLQFHGEKPYVHRMIAVDEVTLEIDGQLNRIEGAVQRQAGESTYSYLKRIREKVPSIPLNLVHRIAFLQESARFRPEKFDVEQVMELRSLLNQFLRILSAEYDSLSDEPDMAAPRGVIASFYQFGQKIMPNNSGSKRRRNKFGGSDGVRLLMKEREEQLSLLSPLARASADSPAPAAHLRRQSDSHSALLPQ

Entity 3 polymer

描述 description	Vesicle transport protein
分子量 formula_weight	16205.3 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

MPENKEIITIFENSRNYTNLTSESTYSLAGALLLSGKYMNDWWEITLSIFLWMSLSFMVISLGATILSLFTLRKHPYVCFIPIPFIIMMFIIPFVFGAPTSMVLALAMYASKNAVSTWYCAIMGIIQTLLIFVTSVTRIHATL

Entity 4 non-polymer

描述 description	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
分子量 formula_weight	744.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	18

Entity 5 non-polymer

描述 description	HEXADECANE
分子量 formula_weight	226.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	12

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7. 引用文献 (2)

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分辨率 resolution	2.70 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	285377

fit	/app/data/saxs_computation/ca/9cap/9cap.fit
pddf	/app/data/pr_computation/ca/9cap/9cap.pr.out
profile	/app/data/saxs_computation/ca/9cap/9cap.dat

Structure of the LPD-3 complex

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

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 non-polymer

Entity 5 non-polymer

7. 引用文献 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)