SAXSdb — 9i8m

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9i8m
沉积日期 deposition_date	2025-02-05
结构标题 title	NEDD1-bound native vertebrate gamma-tubulin ring complex from Xenopus laevis, focused reconstruction
关键词 keywords	;cytoskeleton, microtubule, microtubule nucleation, complex, template, cap, gamma-tubulin, gamma-tubulin ring complex, cell cycle, nedd1, neural precursor cell-expressed developmentally down-regulated 1 ;; CELL CYCLE
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	68.87 Å
回转半径 Rg (电子) rg_electron	68.55 Å
零角强度 I(0) i0	3720170000.00
分子量 molecular_weight	530810.0 kDa
排除体积 excluded_volume	670470 Å³
包络体积 envelope_volume	1130000 Å³
水化壳体积 shell_volume	134550 Å³
包络直径 envelope_diameter	205.7 Å
壳层 Rg shell_rg	74.10 Å
包络 Rg envelope_rg	64.98 Å
形状 Rg shape_rg	68.57 Å
总 Rg total_rg	68.58 Å
总原子数 total_atoms	37358
残基数 n_residues	4627
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	218.9 Å
Rg (实空间) rg_real	68.65 Å
Rg 误差 (实空间) rg_real_error	1.72 Å
I(0) (实空间) i0_real	3.7200e+09
I(0) 误差 (实空间) i0_real_error	6.8520e+07
Rg (倒空间) rg_reciprocal	69.50 Å
I(0) (倒空间) i0_reciprocal	3726000000.0000
解质量估计 total_estimate	0.8280
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	104.7 Å
偏度 Skewness skewness	-0.020
峰度 Kurtosis kurtosis	-0.739
角度范围 angular_range	— – 0.1150 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	252600000.0000
实空间数据点数 n_real_points	24
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.923; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; 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 (7)

Entity 1 polymer

描述 description	Gamma-tubulin complex component
分子量 formula_weight	103468.3 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,C,E,G
原子数 atom_count	37358

MSEFRIHHDVNELISLLHVFGLEGADVYIDLLQKNRTPYVTTSVSTHSAKVKIAEFSRTPDDFLKKYEELKSKNTRNLDPLVYLLSKLIEDKETLQYLQQNAKDKAELATSSVTSVSLPIAPNTSKISMQELEELRRQLETATVAVSCSHQPVEVLRKFLRDKLNKKHTGHPVPVFPSWVYERPALTGDFMSFSNPSTDVTVSIGTLPLPSQETCLVEDLLYILIGVDGRYISVQPLVGRQSRSFSVEQNLDSSVKELVNRILPVATNYSTVTRFVEENSSFEYGQVNHALGAAMRTLGKEYMILISQLEHLQRQGLLSLQKLWFYIQPTLRTMEVLASIATSLNKGECFGGATLSLLHDRTFGYTGDSQAQELCLYLTKAASAPYFDILERWIYRGIINDPYSEFMVEEHELQKEKIQEDYNDKYWDQRYTIVQQQIPSFLQKVADKILSTGKYLNVVRECGHDVTCPDAKEITYTLKEQAYVERIEKAYNYASKVLLDFLMEEEELVAHLRSIKHYFLMDQGDFFVHFMDLTEEELKKPVDDIIPTRLEALLELALRMSTANTDPFKDDLKIELMPHDLITQLLRVLAIETHQEKALINSDPTELALSGLESFSFDYIVKWPLSLIINRKALTRYQMLFRHMFYCKHVERLLCNVWISNKTAKQFSLHSAKWFAGAFTLRQRMLNFVQNIQYYMMFEVMEPTWHILEKNLKSASNIDDVLSHHTSFLDNCLKDCMLTNPELLKIFSKLMSVCVMFTNCLQRFTQSMQVQTEMEHLTLEHGTMMGPPTQCERTEEALKKKLTSKYLEEHIDKFPSSFGFESTINNFDSNFSAHLMDLLDKLSMYSTSDCEHSMINIIYRLDFNGFYTERLKQLSSERNQKSAPLLGPAQHAVSTK

Entity 2 polymer

描述 description	Gamma-tubulin complex component 3 homolog
分子量 formula_weight	103789.4 kDa
来源方法 src_method	nat
拷贝数 entity_count	9

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B,D,F,H,O,Q,R,S,T

MAVPDQKSPNVLLQNLCCRILGKGEADVAQQFQYAVRVIGSNFAPTVERDEFLVTEKIKKEFVRQRREADGALFSELHRKLQSQGVLKNRWSILYLLLSLSEDPRKQPNKTSSFAALFAQALPRDAHSTPYYYARPQSLPLSYQDRNVQCAQNAASIGSSGISSIGMYALNGPTPQSIIQGQSNQTPNMGDALRQQLGSRLAWTLAAGQQPSQQSTTTKGLPNTVSRNVPRTRREGDSSGSVEITETSLVRDLLYVFQGIDGKFVKMCNSENCYKVDGKVAVSKSLKDITSKLSELGWLHNKIKKYTDQRSLDRAFGLVGQSFCAALHQELKEYYRLLSVLHSQLQVEDDQGVNLGVESSLTLRRLLVWTFDPKIRLKTLAALVDHCQGRKGGELASAVHAYTKTGDPYMRSLVQHILGLVAYPILNFLYRWIYDGELEDTYHEFFVASDPVVKTDRLWHDKYSLRKSMIPSFMTMDQSRKVLLIGKSINFLHQVCHDQTPASKAMAVGKSAESPKDAAELFTDLENAFQTKIDAAYFDTSKYLLDVLNKNYNLLEHMQAMRRYLLLGQGDFIRHLMDLLKPELVRPATTLYQHNLTGILETAVRATNAQFDNPEILKRLDVRLLEVSPGDTGWDVFSLDYHVDGPIATVFTRECMSHYLRVFNFLWRAKRMEYILTDIWKGHMCNAKLLKGMPELSGVLHQCHILASEMVHFIHQMQYYITFEVLECSWDELWNKVLKAQDLDHIIAAHDVFLDTIISRCLLDSESRALLNQLRAVFDQIIEFQNAQDALYRAALEELQQRLQFEERKKERESEGEWGVTAAEEDVENKRIQEFQESIPKMRSQLRILTHFYQGIVQQFLVLLTTSTDESLRFLSFRLDFNEHYKAREPRLRVSMGTRGRRSFHV

Entity 3 polymer

描述 description	Gamma-tubulin complex component
分子量 formula_weight	76123.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	I,K

MIHELLLALSGYPGSIFTWNKRTGLQVSQDIPFLHPGETSVLNRLCKLGTDYIRFTEFIEQYTGHVQQQDHHPSQQGQVGLHGIYLRAFCRGLDSILQPYRQALLDLEQEFLADPHLSISHINYSLDQFHLLFPSIMVVVEQIKSQKIHGCQILETVYKHSCGGLPPVRSALEKTLAVCHGVMYKQLSAWMLHGLLLDQYEEFFVRQGSSSGNLAAAFEEEEDDLGIGGLTGKQLRELQDLRLIEEENMLAPSLKQFSLRAEMLPSYIPVRVAEKILFVGESVQMFENQNVNMSRTGSILKNQEDTFAAELHRLKQQPLFSLVDFESVLDRIRSTVAEHLWKLMVEESDLLGQLKIIKDFYLLGRGELFQAFIDVAQNMLKTPPTAVTEHDVNVAFQLSAHKVLLDDDNLLPLLNLTIDYHGKEHKDTSQPREGPFRDMSPREAPTSGWAALGLSYKVQWPLHILFTPAVLEKYNVVFKYLLSVRRVQSELQHCWALQMQRKHLESNKTDAIKWRLQNHMAFLVDNLQYYLQVDVLESQFSQLLQQINSTRDFESIRLAHDHFLSNLLAQSFILLKPVFHCLNEILELCHSFCSLVSQNLGPLDERGAGQLDILVKGFSCQSSLLFRILSSVRNHQINPDLAQLLLRLDYNKYYTQAGGTLGSFGL

Entity 4 polymer

描述 description	Gamma-tubulin complex component
分子量 formula_weight	117577.6 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	J

MAHWTRFERDQEGDIKKLVSLMSGIQDDQDGNFQQALQFAWSNFRFHRYLDVSSHTVLRTLEGIFEKLVVHSDLEKAESWKRLTEEFLLLPLPNTEGTKTDSHFAVLSLLLCLSDSPSNHDYTEKPRKKENDEQEPFDWGKYLREGEDIEFSPDADTPEWSEASEEEDAQEPPSREDSGIQVDRTPLEDPEKKGAPPLVSWKVGEPDARSWLEQHIVHQYWTSRAPRFSHSSHLHSNLSAIWDQHLYTTDPLYTPDDKTIVTETQVIRETLWLLSGVKKLLIFQLNDGKVNVRNDIIVTHMTQNCLRSVLEQIAAYGQVVFRLQKFIDEITGHGSEVPLPGTLPTAKKTTEAPFRTYQAFMWALYKYFISFKEELTEIEKCIINKDETVTLAIVLDKLAPRLAQLKVLHRVFSTGIAEVPPDTRNVVRASHLLNTLYKAILDYDNVGEASEQTVSLLFCLWVETVRPYLEIVDEWIVHGNLFDPAKEFIIQRNKDVPFNHRDFWYATYTLYSVSEKTENEDKMSDNASASSGSDQAPAGRQHTMVSFLKPVLKQIIMAGKSMQLLKNLKCRTALQQDSSRDSDRKSLYTLFLESVQSRLQHGNDSVPDIITEQQVNKLSLIKMQSIVAKHLELDEVHDPLLAINFVRLYLEQSDFLETFTCNEVCVDRSSESVTCQSFELTLRSCLYPHIGKQYLECCGNLMYTLKKDYRLVEYLQAMRNFFLLEAGDTMYDFYTPIFDKIREKEPWLNLSYLNVQIQEAVGQRYPDDSTRLSVSFESVDLAKKKLPVHTLDGLILSYKVPWPVDIVISSECQKIYNQVFLLLLLIKWAKYSLDVLQFNELGNASENESTKEGATVEPFPLPPLTSPSEPKGQQIHRMFLLRVKLMHFVNSLHNYLMTRILHSTGLEFQHQVEEAKDLDQLIKIHYRYLSTIHDRCLLREKVSSVKEAIMKVLNVVLMFADRWHAGLGAWKKESIVKMESDFTNCHKFLVKVLNKAVCRGSFPHLESLALSLMAGMEQS

Entity 5 polymer

描述 description	Gamma-tubulin complex component 6
分子量 formula_weight	193069.1 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	L

MDSITKLFGDLCESHMVGFPWRTALNSRKHSKNRTKQTLKKLAYDTLFVHLFQDEARKLQPNCTRLPVKNKIIMLSFNLRICGMSSEADRLEELVEYLEQSNGIQISDLHAVLELLVELSGTGPPQLLPPKRDYFKNNKYVGRNVKYQGYDYYDVQVFEADLGTTVAYQELEISTTIQRTLQIMEAAPGTGLPALSFFSQNDLSTDKFEKETRGSLFGALVHSRTNDMDIKLDMPPVPENADLSGLAIKVPQSIDQSEDEGFQSASNMTPDSQSEPSMTPDIDVWEAVLTYGPSKRRCWERIGCPPGKREEPYVTEAGREAFDKLYKLHEGGLQILSATTLQPQLVLLEETDLVKAVLNVLIGVVSSTFSYNQALQSFAVKQGVYISGTSPDNVSSLLTQVAEYGTYYTRLSHFSLLTVLDSSHSNGLVFQAFTSGLRKYLQYYRACVLSTPASLTLLTISFLFRKLGRQLRYLAELCCIGTLVTSATRGISTAFPTGVKLLSYLYKEALENSSNENYPVLLSLLKTSCEPYTRFIYDWVYSGVFRDVCGEFMIQVNEDYLGFRDKRYWTHGYVLISKEVEDCVPVFLKHVANEIYICGKTINLLKLCCPKHYICWSDIPVPRISVTFSLEELKEMEKDCAVYVARMERIARHSCISKEQKALQTEIARQELIIQARETTEKVFETFKDRKLAEKLSLDTKKRELFQKLKDQYEKEQERRLTTKQEEADDDFSYAREIRDREKRLKALEEELELKTRQELIEHYSRLSEEATRKEQRALWKLQRHKLETIRLKFFLEEQKRMQDLVANFPVDICEENLGVLPDGEISHQTDNTNDAGLGNIENEKSVPEQHALHNNNDEVYTAQNCISKSESLCVDVTLPTENVHSQTSNASVLGVPSFDSNLCTPDVDIIDFLPTLPSENQEVAVVQSLVDDALISIGSDLNTDTKDKESLCALKSDLQESSTGSEYDFKTILKPIACTQVSQGHIKIGEYSSNVQPARPRWSTHGHSSDSNIKIGNYVSDINVHQPKHSQHGHSSDSNINISDHMSDVEPRLPRLNLHGHISTGHIKVGEYASDVEPSTPRHSVHGHASQGNIKIGENVSDVKLSRPRWNIHGHVSDANIKIGENTSEIAPLRPRWNIHGHASQSHIKIGELVSDIEPSQPRRTPFGHPSQSSIPIGDQPVEKYAQKSESEVHSSNSTIQHLLYSNIPDKNKDTGGTLTDSPVPVPDQGNSNDDTEKRSSTLEQRVQAADSVCDGEASPNTAQSLPCMSDTLDFGTNGEENVGNDDHTWEKQQEYLKGLAEKYCLEKYQDSYELMSHPPVLHLYSNVMPNRFSFPTDSDIKSATDETTVQLIELLSLPVLMKYSVTAPMVSHVYLVNKAIVDYYFVELKMERHFEAMRHFLLMEDGEFAQSLSDMLFEKLGSGQTPSELLNPLVLNSILNKALQYSLHGDSSLASNLTFALKYLPEVFTPTAPDALSCLELKYKVDWPLNIVITDTCMNKYSRIFSFLLQLKHMVWTLRDVWFHLKRTALVNQASNSVQYRQLQLYRHEMQHFVKVIQGYIANQILHVTWCEFRNKLSAVSNLEEIYKTHADYLNKALFRGLLTEKAAPLMNIIHSIFSLILKFRLQLISQSWICDTGKQMAVHPNFGLMQQSYNTFKYYSDFLFEVVSKLVNRGYQPHLEDFLLRINFNSYYKQS

Entity 6 polymer

描述 description	NEDD1 gamma-tubulin ring complex targeting factor L homeolog
分子量 formula_weight	73215.2 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	U,V,W,X

MESRGGGGRVRLPGTTMQDNIRFVSAGDDVKIWDYSSMTTVEQFNPHSASHPVSSLCWSSNNHFLVTASGSGDKIVVSSCKSKPVPLLELAEGKKQTCVNLNSSSQYVVSGGLDNTVNIWDLKSKRLHRSLKDHKDEVTCVTFNANDCYVASGSMSGEIILHNVTTNLSSTPFGHGSSQPIRHLKYSYVKKSLLGTVSDSGSVTLWDANSQNPYHVFESAHKAPASGICFSPVNDLLLVTVGLDKRIICYDVSSKILLQTVVAESPLTAVDFMPDGATLAVGSSRGKIYLYDLRMLSSPVKTVSAHKTSVQCIQFQHSNIYKSSKGPSSKSSILSTAVNKKPSTKTAAGGTQSANITKDLPPSAISSLPQPVMPVDSKVLRVNDDKSGFPRSTSLDIIPSKETDFAKTSDYKSIDSFGRSSLGDIFSPVRDDASHFRGAEDLSCKGNDLDYLPQFSTIPSSRRNPVGANTQGIHGSPLHLIIESPIKEEDESQDSELKTRKPQLLKQDFRESSSKPASVDQNNLNNSPINSVTRTPEAIEKTGHQILSQLKSDVPAHGTKIASPKVAATMSTQLASSLSEKIADTLASDRTGAPLTAIQINFIKNMIEETLDDFREACHRDIVNLQVEMIKQFHIQSSEIQMLLERYSLNESLVSEIEKLREENKRLRANF

Entity 7 polymer

描述 description	Mitotic-spindle organizing protein 1
分子量 formula_weight	7749.9 kDa
来源方法 src_method	nat
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	o,p,q,r,s,t

MANASGNMSAVRETMDVLLEISRLLNTGLDMETLSICVRLCEQGINPEALSSVIKELRRASDTLKASESTAS

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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	4.30 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	299022

fit	/app/data/saxs_computation/i8/9i8m/9i8m.fit
pddf	/app/data/pr_computation/i8/9i8m/9i8m.pr.out
profile	/app/data/saxs_computation/i8/9i8m/9i8m.dat

NEDD1-bound native vertebrate gamma-tubulin ring complex from Xenopus laevis, focused reconstruction

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 (7)

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 polymer

聚合体 Polymer

Entity 6 polymer

聚合体 Polymer

Entity 7 polymer

聚合体 Polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)