SAXSdb — 9nmr

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9nmr
沉积日期 deposition_date	2025-03-04
结构标题 title	Structure of mouse RyR1 (including auxiliary transmembrane helix TMx; EGTA-only dataset)
关键词 keywords	Calcium, Ion Channel, TRANSPORT PROTEIN; TRANSPORT 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	104.20 Å
零角强度 I(0) i0	56359000000.00
分子量 molecular_weight	2044200.0 kDa
排除体积 excluded_volume	2562500 Å³
包络体积 envelope_volume	4684800 Å³
水化壳体积 shell_volume	366950 Å³
包络直径 envelope_diameter	363.6 Å
壳层 Rg shell_rg	104.50 Å
包络 Rg envelope_rg	100.60 Å
形状 Rg shape_rg	104.30 Å
总 Rg total_rg	104.10 Å
总原子数 total_atoms	143660
残基数 n_residues	18012
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	270.8 Å
Rg (实空间) rg_real	100.50 Å
Rg 误差 (实空间) rg_real_error	0.65 Å
I(0) (实空间) i0_real	5.3910e+10
I(0) 误差 (实空间) i0_real_error	9.5050e+08
Rg (倒空间) rg_reciprocal	104.90 Å
I(0) (倒空间) i0_reciprocal	56420000000.0000
解质量估计 total_estimate	0.9094
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	126.4 Å
偏度 Skewness skewness	0.106
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	0.7186
最高正则化参数 α highest_alpha	5453000000.0000
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: 0.954; 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 (4)

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,B,C,D
原子数 atom_count	143684

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,F,G,H

MGVQVETISPGDGRTFPKRGQTCVVHYTGMLEDGKKFDSSRDRNKPFKFTLGKQEVIRGWEEGVAQMSVGQRAKLIISSDYAYGATGHPGIIPPHATLVFDVELLKLE

Entity 3 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 4 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	2.91 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	129073

fit	/app/data/saxs_computation/nm/9nmr/9nmr.fit
pddf	/app/data/pr_computation/nm/9nmr/9nmr.pr.out
profile	/app/data/saxs_computation/nm/9nmr/9nmr.dat

Structure of mouse RyR1 (including auxiliary transmembrane helix TMx; 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 (4)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 non-polymer

Entity 4 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)