SAXSdb — 8vk3

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8vk3
沉积日期 deposition_date	2024-01-08
结构标题 title	Structure of mouse RyR1 in complex with S100A1 (EGTA-only dataset)
关键词 keywords	Calcium, Ion Channel, MEMBRANE PROTEIN; MEMBRANE PROTEIN
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	105.00 Å
零角强度 I(0) i0	60508000000.00
分子量 molecular_weight	2117800.0 kDa
排除体积 excluded_volume	2654100 Å³
包络体积 envelope_volume	4838500 Å³
水化壳体积 shell_volume	374950 Å³
包络直径 envelope_diameter	364.0 Å
壳层 Rg shell_rg	105.70 Å
包络 Rg envelope_rg	101.20 Å
形状 Rg shape_rg	105.10 Å
总 Rg total_rg	104.90 Å
总原子数 total_atoms	148828
残基数 n_residues	18668
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	272.9 Å
Rg (实空间) rg_real	101.40 Å
Rg 误差 (实空间) rg_real_error	0.65 Å
I(0) (实空间) i0_real	5.7840e+10
I(0) 误差 (实空间) i0_real_error	1.1800e+09
Rg (倒空间) rg_reciprocal	105.70 Å
I(0) (倒空间) i0_reciprocal	60560000000.0000
解质量估计 total_estimate	0.9095
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	127.3 Å
偏度 Skewness skewness	0.119
峰度 Kurtosis kurtosis	-0.682
角度范围 angular_range	— – 0.0750 Å⁻¹
当前正则化参数 α current_alpha	0.8000
最高正则化参数 α highest_alpha	7211000000.0000
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: 0.000; Oscil: 0.999; Stabil: 0.957; Sysdev: 1.000; Positv: 1.000; Valcen: 0.957; Smooth: 0.000

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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	Ryanodine receptor 1
分子量 formula_weight	565692.6 kDa
来源方法 src_method	nat
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,D,B,C
原子数 atom_count	148852

MGDGGGEGEDEVQFLRTDDEVVLQCSATVLKEQLKLCLAAEGFGNRLCFLEPTSNAQNVPPDLAICCFILEQSLSVRALQEMLANTVEAGVESSQGGGHRTLLYGHAILLRHAHSRMYLSCLTTSRSMTDKLAFDVGLQEDATGEACWWTMHPASKQRSEGEKVRVGDDLILVSVSSERYLHLSTASGELQVDASFMQTLWNMNPICSGCEEGFVTGGHVLRLFHGHMDECLTISPSDSDDQRRLVYYEGGPVCTHARSLWRLEPLRISWSGSHLRWGQPLRIRHVTTGRYLGLTEDQGLVVVDASKAHTKATSFCFRISKEKLDVAPKRDVEGMGPPEIKYGESLCFVQHVASGLWLTYAAPDPKALRLGVLKKKAMLHQEGHMDDALSLTRCQQEESQAARMIYSTAGLYNQFIKGLDSFSGKPRGSGPPAGSALPIEGVILSLQDLIGYFEPPSEELQHEEKQTKLRSLRNRQSLFQEEGMLSLVLNCIDRLNVYTTAAHFAEFAGEEAAESWKEIVNLLYELLASLIRGNRTNCALFSTNLDWLVSKLDRLEASSGILEVLYCVLIESPEVLNIIQENHIKSIISLLDKHGRNHKVLDVLCSLCVCNGVAVRSNQDLITENLLPGRELLLQTNLINYVTSIRPNIFVGRAEGSTQYGKWYFEVMVDEVAPFLTAQATHLRVGWALSEGYSPYPGGGEGWGGNGVGDDLYSYGFDGLHLWTGHVARPVTSPGQHLLAPEDVVSCCLDLSVPSISFRINGCPVQGVFESFNLDGLFFPVVSFSAGIKVRFLLGGRHGEFKFLPPPGYAPCHEAVLPRERLHLQPIKEYRREGPRGPHLVGPSRCLSHLDFVPCPVDTIQIVLPPHLERIREKLAENIHELWALTRIEQGWTYGPVRDDNKRLHPCLVNFHSLPEPERNYNLQMSGETLKTLLALGCHVGMADEKAEDNLKKTKLPKTYMMSNGYKPAPLDLSHVRLTPAQTTLVDRLAENGHNVWARDRVAQGWSYSAVQDIPARRNPRLVPYRLLDEATKRSNRDSLCQAVRTLLGYGYNIEPPDQEPSQVDSQSRGDRARIFRAEKSYAVQSGRWYFEFEAVTTGEMRVGWARPELRPDVELGADDLAYVFNGHRGQRWHLGSEPFGRPWQSGDVVGCMIDLTENTIIFTLNGEVLMSDSGSETAFRDIEIGDGFLPVCSLGPGQVGHLNLGQDVSSLRFFAICGLQEGFEPFAINMQRPVTTWFSKSLPQFEPVPLEHPHYEVARMDGTVDTPPCLRLTHRTWGSQNSLVEMLFLRLSLPVQFHQHFRCTAGATPLASPGLQPPAEDEARAAEPDTDYENLRRSAGGWGEAEGGKDGTAKEGTPGGTAQAGVEAQPARAENEKDATTEKNKKRGFLFKAKKVAMMTQPPSTPALPRLPRDVVPADNRDDPEIILNTTTYYYSVRVFAGQEPSCVWVGWVTPDYHQHDMSFDLSKVRAVTVTMGDEQGNVHSSLKCSNCYMVWGGDFVSPGQQGRISHTDLVIGCLVDLATGLMTFTANGKESNTFFQVEPNTKLFPAVFVLPTHQNVVQFELGKQKNIMPLSAAMFLSERKNPAPQCPPRLEVQMLMPVSWSRMPNHFLQVDTRRAGERLGWAVQCQEPLMMMALHIPEENRCMDILELSERLDLQRFHSHTLSLYRSVCALGNNRVAHALCSHVDQAQLLHALEDARLPGPLRAGYYDLLISIHLESACRSRRSMLSEYIVPLTPETRAITLFPPGRSAEDGPRRHGLPGVGVTTSLRPPHHFSPPCFVVALPAAGATEAPARLSPAIPLEALRDKALRMLGEAVRDGGQHARDPVGGSVEFQFVPVLKLVSTLLVMGVFSDEDVKQILKMIEPEVFREEEEVEEEGEEEEEDEEEKEEDEEEEAHEKEDEEKEEAEDAAEEEKEELEEGLLQMKLPESVKLQMCHLLEYFCDQELQHRVESLAAFAECYVDKMQGNQRGRYGLLMKAFTMSAAETARRTREFRSPPQEQINMLLHFKNGADEEECPLPEEIRQELVNFHQDLLAHCGIQLEGEEEEPEEESTLGSRLMSLLEKVKLVKKTEEKPEEEPAPEEHKPQSLQELVSHTVVRWAQEDFVQSPELVRAMFSLLHRQYDGLGELLRALPRAYTISVSSVEDTMSLLECLGQIRSLLIVQMGPQEENLMIQSIGNIMNNKVFYQHPNLMRALGMHETVMEVMVNVLGGGESKEIRFPKMVTSCCRFLCYFCRISRQNQRSMFDHLSYLLENSGIGLGMQGSTPLDVAAASVIDNNELALALQEQDLEKVVSYLAGCGLQSCPMLLAKGYPDIGWNPCGGERYLDFLRFAVFVNGESVEENANVVVRLLIRKPECFGPALRGEGGSGLLAAIEEAIRISEDPARDGPGVRRDRRREHFGEEPPEENRVHLGHAIMSFYAALIDLLGRCAPETHLIQAGKGEALRIRAILRSLVPLDDLVGIISLPLQIPTLGKDGALVQPKMSASFVPDHKASMVLFLDRVYGIENQDFLLHVLDVGFLPDMRAAASLDTATFSTTEMALALNRYLCLAVLPLITKCAPLFAGTEHRAIMVDSMLHTVYRLSRGRSLTKAQRDVIEDCLMALCRYIRPSMLQHLLRRLVFDVPILNEFAKMPLKLLTNHYERCWKYYCLPTGWANFGVTSEEELHLTRKLFWGIFDSLAHKKYDQELYRIAMPCLCAIAGALPPDYVDASYSSKTEKKATVDAEGNFDPRPVETLNVIIPEKLDSFINKFAEYTHEKWAFDKIQNNWSYGENIDEELKTHPMLRPYKTFSEKDKEIYRWPIKESLKAMIAWEWTVEKAREGEEEKTEKKKTRKISQTAQTYDPREGYNPQPPDLSVVTLSRELQAMAEQLAENYHNTWGRKKKQELEAKGGGSHPLLVPYDTLTAKEKARDREKAQELLKFLQMNGYAVTRGLKDMELDTSSIEKRFAFGFLQQLLRWMDISQEFIAHLEAVVSSGRVEKSPHEQEIKFFAKILLPLINQYFTNHCLYFLSTPAKVLGSGGHASNKEKEMITSLFCKLAALVRHRVSLFGTDAPAVVNCLHILARSLDARTVMKSGPEIVKAGLRSFFESASEDIEKMVENLRLGKVSQARTQVKGVGQNLTYTTVALLPVLTTLFQHIAQHQFGDDVILDDVQVSCYRTLCSIYSLGTTRNPYVEKLRPALGECLARLAAAMPVAFLEPELNEYNACSVYTTKSPRERAILGLPNSVEEMCPDIPVLERLMAEIGGLAESGARYTEMPHVIEITLPMLCSYLPRWWERGPEAPPPALPAGAPPPCTAVTSDHLNSLLGNILRIIVNNLGIDEASWMKRLAVFAQPIVSRARPELLRSHFIPTIGRLRKRAGKVVAEEEQLRLEAKAEAEEGELLVRDEFSVLCRDLYALYPLLIRYVDNNRAHWLTEPNPNAEELFRMVGEIFIYWSKSHNFKREEQNFVVQNEINNMSFLTADNKSKMAKAGDVQSGGSDQERTKKKRRGDRYSVQTSLIVATLKKMLPIGLNMCAPTDQDLIVLAKARYALKDTDEEVREFLQNNLNLQGKVEGSPSLRWQMALYRGVPGREEDADDPEKIVRRVQEVSAVLYHLDQTEHPYKSKKAVWHKLLSKQRRRAVVACFRMTPLYNLPTHRACNMFLESYKASWILTEDHSFEDRMIDDLSKAGEQEEEEEEVEEKKPDPLHQLVLHFSRTALTEKSKLDEDYLYMAYADIMAKSCHLEEGGENGEEGGEEEEVEVSFEEKEMEKQRLLYQQSRLHNRGAAEMVLQMISACKGETGAMVSSTLKLGISILNGGNAEVQQKMLDYLKDKKEVGFFQSIQALMQTCSVLDLNAFERQNKAEGLGMVNEDGTVINRQNGEKVMADDEFTQDLFRFLQLLCEGHNNDFQNYLRTQTGNTTTINIIICTVDYLLRLQESISDFYWYYSGKDVIEEQGKRNFSKAMSVAKQVFNSLTEYIQGPCTGNQQSLAHSRLWDAVVGFLHVFAHMMMKLAQDSSQIELLKELLDLQKDMVVMLLSLLEGNVVNGMIARQMVDMLVESSSNVEMILKFFDMFLKLKDIVGSEAFQDYVTDPRGLISKKDFQKAMDSQKQFTGPEIQFLLSCSEADENEMINCEEFANRFQEPARDIGFNVAVLLTNLSEHVPHDPRLRNFLELAESILEYFRPYLGRIEIMGASRRIERIYFEISETNRAQWEMPQVKESKRQFIFDVVNEGGESEKMEMFVSFCEDTIFEMQIAAQISEPEGEPEEDEDEGAEEAEEGAAGSDGSGSAAAAGVWVWLAATAGRTLRGLSYRSLRRRVRRLRRLTAREAATAVAALLWALVTRAGGAGAGAAAGALRLLWGSLFGGGLVDSAKKVTVTELLAGMPDPTGDEVHGQQPSGAGSDAEGEGEGEGEGDAADGAGDEEAAADQAGTGGADGAVAVADGSPFRPEGAGGLGDMGDTTPVEPPTPEGSPILKRKLGVDGEEEEPPPEPEPEPEPEPEKADTENGEKEVPEPPPEPPKKTPPPPPPKKEEAGGAGLEEFWGELEVQRVKFLNYLSRNFYTLRFLALFLAFAINFILLFYKVSDSPPGEDDIEGSGAGDMSGAGSGDGSGWGSRAGEEVEGDEDENMVYYFLEESTGYMEPALRCLSLLHTLVAFLCIIGYNCLKVPLVIFKREKELARKLEFDGLYITEQPEDDDVKGQWDRLVLNTPSFPSNYWDKFVKRKVLDKHGDIFGRERIAELLGMDLASLEITAHNERKPDPPPGLLTWIMSIDVKYQIWKFGVIFTDNSFLYLGWYMVMSLLGHYNNFFFAAHLLDIAMGVKTLRTILSSVTHNGKQLVMTVGLLAVVVYLYTVVAFNFFRKFYNKSEDEDEPDMKCDDMMTCYLFHMYVGVRAGGGIGDEIEDPAGDEYELYRVVFDITFFFFVIVILLAIIQGLIIDAFGELRDQQEQVKEDMETKCFICGIGSDYFDTTPHGFETHTLEEHNLANYMFFLMYLINKDETEHTGQESYVWKMYQERCWDFFPAGDCFRKQYEDQLS

Entity 2 polymer

描述 description	Peptidyl-prolyl cis-trans isomerase FKBP1A
分子量 formula_weight	11939.6 kDa
EC 编号 ec_number	5.2.1.8
来源方法 src_method	nat
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	E,H,F,G

MGVQVETISPGDGRTFPKRGQTCVVHYTGMLEDGKKFDSSRDRNKPFKFTLGKQEVIRGWEEGVAQMSVGQRAKLIISSDYAYGATGHPGIIPPHATLVFDVELLKLE

Entity 3 polymer

描述 description	Protein S100A1
分子量 formula_weight	10516.8 kDa
来源方法 src_method	man
拷贝数 entity_count	8

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	J,I,K,M,O,L,N,P

MGSELESAMETLINVFHAHSGKEGDKYKLSKKELKDLLQTELSGFLDVQKDADAVDKVMKELDENGDGEVDFKEYVVLVAALTVACNNFFWETS

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI 分类编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 4 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	4

Entity 5 non-polymer

描述 description	1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
分子量 formula_weight	787.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

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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	3.21 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	36506

fit	/app/data/saxs_computation/vk/8vk3/8vk3.fit
pddf	/app/data/pr_computation/vk/8vk3/8vk3.pr.out
profile	/app/data/saxs_computation/vk/8vk3/8vk3.dat

Structure of mouse RyR1 in complex with S100A1 (EGTA-only dataset)

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

来源 Source

Entity 4 non-polymer

Entity 5 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)