SAXSdb — 8wjn

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8wjn
沉积日期 deposition_date	2023-09-26
结构标题 title	Cryo-EM structure of 6-subunit Smc5/6 head region
关键词 keywords	CELL CYCLE; 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	46.28 Å
回转半径 Rg (电子) rg_electron	46.24 Å
零角强度 I(0) i0	652523000.00
分子量 molecular_weight	209960.0 kDa
排除体积 excluded_volume	263300 Å³
包络体积 envelope_volume	396890 Å³
水化壳体积 shell_volume	73488 Å³
包络直径 envelope_diameter	183.4 Å
壳层 Rg shell_rg	48.62 Å
包络 Rg envelope_rg	47.16 Å
形状 Rg shape_rg	46.22 Å
总 Rg total_rg	46.41 Å
总原子数 total_atoms	29655
残基数 n_residues	1842
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	124.8 Å
Rg (实空间) rg_real	43.78 Å
Rg 误差 (实空间) rg_real_error	0.37 Å
I(0) (实空间) i0_real	6.2830e+08
I(0) 误差 (实空间) i0_real_error	9.8030e+06
Rg (倒空间) rg_reciprocal	46.29 Å
I(0) (倒空间) i0_reciprocal	652300000.0000
解质量估计 total_estimate	0.7223
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	55.1 Å
偏度 Skewness skewness	0.302
峰度 Kurtosis kurtosis	-0.346
角度范围 angular_range	— – 0.1700 Å⁻¹
当前正则化参数 α current_alpha	0.1493
最高正则化参数 α highest_alpha	73750000.0000
实空间数据点数 n_real_points	35
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.966; Stabil: 0.970; Sysdev: 0.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.600

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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	Structural maintenance of chromosomes protein 6
分子量 formula_weight	128199.7 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B
原子数 atom_count	29655

MISTTISGKRPIEQVDDELLSLTAQQENEEQQQQRKRRRHQFAPMTQFNSNTLDEDSGFRSSSDVATADQDNFLEESPSGYIKKVILRNFMCHEHFELELGSRLNFIVGNNGSGKSAILTAITIGLGAKASETNRGSSLKDLIREGCYSAKIILHLDNSKYGAYQQGIFGNEIIVERIIKRDGPASFSLRSENGKEISNKKKDIQTVVDYFSVPVSNPMCFLSQDAARSFLTASTSQDKYSHFMKGTLLQEITENLLYASAIHDSAQENMALHLENLKSLKAEYEDAKKLLRELNQTSDLNERKMLLQAKSLWIDVAHNTDACKNLENEISGIQQKVDEVTEKIRNRQEKIERYTSDGTTIEAQIDAKVIYVNEKDSEHQNARELLRDVKSRFEKEKSNQAEAQSNIDQGRKKVDALNKTIAHLEEELTKEMGGDKDQMRQELEQLEKANEKLREVNNSLVVSLQDVKNEERDIQHERESELRTISRSIQNKKVELQNIAKGNDTFLMNFDRNMDRLLRTIEQRKNEFETPAIGPLGSLVTIRKGFEKWTRSIQRAISSSLNAFVVSNPKDNRLFRDIMRSCGIRSNIPIVTYCLSQFDYSKGRAHGNYPTIVDALEFSKPEIECLFVDLSRIERIVLIEDKNEARNFLQRNPVNVNMALSLRDRRSGFQLSGGYRLDTVTYQDKIRLKVNSSSDNGTQYLKDLIEQETKELQNIRDRYEEKLSEVRSRLKEIDGRLKSTKNEMRKTNFRMTELKMNVGKVVDTGILNSKINERKNQEQAIASYEAAKEELGLKIEQIAQEAQPIKEQYDSTKLALVEAQDELQQLKEDINSRQSKIQKYKDDTIYYEDKKKVYLENIKKIEVNVAALKEGIQRQIQNACAFCSKERIENVDLPDTQEEIKRELDKVSRMIQKAEKSLGLSQEEVIALFEKCRNKYKEGQKKYMEIDEALNRLHNSLKARDQNYKNAEKGTCFDADMDFRASLKVRKFSGNLSFIKDTKSLEIYILTTNDEKARNVDTLSGGEKSFSQMALLLATWKPMRSRIIALDEFDVFMDQVNRKIGTTLIVKKLKDIARTQTIIITPQDIGKIADIDSSGVSIHRMRDPERQNNSNFYN

来源 Source

来源生物 organism	Saccharomyces cerevisiae S288C
NCBI 分类编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 polymer

描述 description	Structural maintenance of chromosomes protein 5
分子量 formula_weight	126237.2 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A

MTSLIDLGRYVERTHHGEDTEPRSKRVKIAKPDLSSFQPGSIIKIRLQDFVTYTLTEFNLSPSLNMIIGPNGSGKSTFVCAVCLGLAGKPEYIGRSKKVEDFIKNGQDVSKIEITLKNSPNVTDIEYIDARDETIKITRIITRSKRRSDYLINDYQVSESVVKTLVAQLNIQLDNLCQFLSQERVEEFARLKSVKLLVETIRSIDASLLDVLDELRELQGNEQSLQKDLDFKKAKIVHLRQESDKLRKSVESLRDFQNKKGEIELHSQLLPYVKVKDHKEKLNIYKEEYERAKANLRAILKDKKPFANTKKTLENQVEELTEKCSLKTDEFLKAKEKINEIFEKLNTIRDEVIKKKNQNEYYRGRTKKLQATIISTKEDFLRSQEILAQTHLPEKSVFEDIDIKRKEIINKEGEIRDLISEIDAKANAINHEMRSIQRQAESKTKSLTTTDKIGILNQDQDLKEVRDAVLMVREHPEMKDKILEPPIMTVSAINAQFAAYLAQCVDYNTSKALTVVDSDSYKLFANPILDKFKVNLRELSSADTTPPVPAETVRDLGFEGYLSDFITGDKRVMKMLCQTSKIHTIPVSRRELTPAQIKKLITPRPNGKILFKRIIHGNRLVDIKQSAYGSKQVFPTDVSIKQTNFYQGSIMSNEQKIRIENEIINLKNEYNDRKSTLDALSNQKSGYRHELSELASKNDDINREAHQLNEIRKKYTMRKSTIETLREKLDQLKREARKDVSQKIKDIDDQIQQLLLKQRHLLSKMASSMKSLKNCQKELISTQILQFEAQNMDVSMNDVIGFFNEREADLKSQYEDKKKFVKEMRDTPEFQSWMREIRSYDQDTKEKLNKVAEKYEEEGNFNLSFVQDVLDKLESEIAMVNHDESAVTILDQVTAELRELEHTVPQQSKDLETIKAKLKEDHAVLEPKLDDIVSKISARFARLFNNVGSAGAVRLEKPKDYAEWKIEIMVKFRDNAPLKKLDSHTQSGGERAVSTVLYMIALQEFTSAPFRVVDEINQGMDSRNERIVHKAMVENACAENTSQYFLITPKLLTGLHYHEKMRIHCVMAGSWIPNPSEDPKMIHFGETSNYSFD

来源 Source

来源生物 organism	Saccharomyces cerevisiae S288C
NCBI 分类编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Spodoptera frugiperda

Entity 3 polymer

描述 description	Non-structural maintenance of chromosomes element 1
分子量 formula_weight	38373.4 kDa
EC 编号 ec_number	2.3.2.27
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	F

MEVHEEQVSAPVTGDATAKYLLQYILSARGICHENALILALMRLETDASTLNTEWSIQQWVDKLNDYINAINVKLNLLGYKIIRINHGIGRNAVTLKAKQNFESFEDNTAIRAHNNDYAVLQSIVLPESNRFFVYVNLASTEETKLATRFNQNEIEFMKWAIEQFMISGETIVEGPALETSIIVKEVNRILVAATGDSNLAKWRKFSTFTVGSTNLFQFQELTATDIEDLLLRLCELKWFYRTQEGKFGIDLRCIAELEEYLTSMYNLNTCQNCHKLAIQGVRCGNESCREENEETGENSLSQIWHVDCFKHYITHVSKNCDRCGSSLITEGVYVI

来源 Source

来源生物 organism	Saccharomyces cerevisiae S288C
NCBI 分类编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Spodoptera frugiperda

Entity 4 polymer

描述 description	Non-structural maintenance of chromosome element 3
分子量 formula_weight	34005.5 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	G

MSSIDNDSDVDLTEDLAVAKIVKENPVARKMVRYILSRGESQNSIITRNKLQSVIHEAAREENIAKPSFSKMFMDINAILYNVYGFELQGLPSKNNMNAGGNGSNSNTNKSMPEPLGHRAQKFILLNNVPHSKNFDDFKILQSAHTYEELIVTGEYIGDDIASGTSNTLESKLSTDRDLVYKGVLSVILCIVFFSKNNILHQELIKFLETFGIPSDGSKIAILNITIEDLIKSLEKREYIVRLEEKSDTDGEVISYRIGRRTQAELGLESLEKLVQEIMGLEKEQTKSLHDDIIKSIGDSYSI

来源 Source

来源生物 organism	Saccharomyces cerevisiae S288C
NCBI 分类编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Spodoptera frugiperda

Entity 5 polymer

描述 description	Non-structural maintenance of chromosomes element 4
分子量 formula_weight	46195.9 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	H

MSSTVISRKRRNSTVTEPDSSGETRKQKKSRSDEKSSSSKDGDPQLEFKVLQGYRDLESEMHKGRAQVTRTGDIGVAMDNLNAVDSLFNKVIGIKNNGLFAHDARAMVSISELAQISVRNLKFDDSRSMVNLENIVNSLKRYMLKEHFKLNNIAENRNDLTLAADEQSAADQQEESDGDIDRTPDDNHTDKATSSFKATSMRHSYLQQFSHYNEFSQFNWFRIGALYNTISKNAPITDHLMGPLSIEKKPRVLTQRRRNNDQVGEKITAEKITQHSLNSTQQETTPEQVKKCFKKLSKKLGPEGSINLFKFIIDPNSFSRSIENLFYTSFLIKEGKLLMEHDEEGLPTIKIKQSISHTDSRSKEIERQRRRAAHQNHIIFQMDMPTWRKLIKKYNITSPFLD

来源 Source

来源生物 organism	Saccharomyces cerevisiae S288C
NCBI 分类编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Spodoptera frugiperda

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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	5.58 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	293207

fit	/app/data/saxs_computation/wj/8wjn/8wjn.fit
pddf	/app/data/pr_computation/wj/8wjn/8wjn.pr.out
profile	/app/data/saxs_computation/wj/8wjn/8wjn.dat

Cryo-EM structure of 6-subunit Smc5/6 head region

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

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 polymer

聚合体 Polymer

来源 Source

Entity 4 polymer

聚合体 Polymer

来源 Source

Entity 5 polymer

聚合体 Polymer

来源 Source

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)