SAXSdb — 8rfe

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8rfe
沉积日期 deposition_date	2023-12-12
结构标题 title	CgsiGP2 sample in nanodisc
关键词 keywords	cgs, cyclic glucan, ANTIBIOTIC; ANTIBIOTIC
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	55.74 Å
回转半径 Rg (电子) rg_electron	56.36 Å
零角强度 I(0) i0	1409190000.00
分子量 molecular_weight	308190.0 kDa
排除体积 excluded_volume	383130 Å³
包络体积 envelope_volume	556950 Å³
水化壳体积 shell_volume	84782 Å³
包络直径 envelope_diameter	199.5 Å
壳层 Rg shell_rg	55.67 Å
包络 Rg envelope_rg	55.50 Å
形状 Rg shape_rg	56.35 Å
总 Rg total_rg	56.40 Å
总原子数 total_atoms	21754
残基数 n_residues	2765
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	199.1 Å
Rg (实空间) rg_real	56.13 Å
Rg 误差 (实空间) rg_real_error	2.44 Å
I(0) (实空间) i0_real	1.4090e+09
I(0) 误差 (实空间) i0_real_error	3.2420e+07
Rg (倒空间) rg_reciprocal	55.39 Å
I(0) (倒空间) i0_reciprocal	1408000000.0000
解质量估计 total_estimate	0.8178
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	49.8 Å
偏度 Skewness skewness	0.492
峰度 Kurtosis kurtosis	-0.458
角度范围 angular_range	— – 0.1400 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	175800000.0000
实空间数据点数 n_real_points	29
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.678; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.851; Smooth: 0.742

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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 (3)

Entity 1 polymer

描述 description	Cyclic beta 1-2 glucan synthetase
分子量 formula_weight	313358.7 kDa
EC 编号 ec_number	2.4.1.20
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	21776

DHNDSIRASYMTIEELHDAGAALSRDGADSLPGFMEFDFFERHRENEKEILRVYRTTAVDAENGATITPAAEWLLDNHYVIEEAIQEVRRDFPRKFYRQLPTMTVGGVTIPRVMALGWLYVAHTHSTVSRENMTALVDGYQTSQTLQIGELWALPSIIRFVLIENLRRISIRVERSRRMRQKANEVVDEIIRLNDAEASAALLKQVDSLVDDPTFATQFLYRLRNGSQTSGFAVAWLEERLHAAGTDAENVMMSEHNRLASGNVTMGNIVKSLREIDDTEWSVWFEEVSHIDKVLREETDYEILDFGSRNTYRNTIELLARRSPRTEVEVARAAVEMARSDLPAGADENHRVNVGSVLVGQRRFELEKALGYRPLASQHIVRSMRKFNWLAIAAPVLLITAVAMLAVGWFLAKAGMPWYVVTAFLLMFALPASEGATGLFNTLVTFFVKPFRLVGYEFKNGIPEDARTLVAVPCMLTSRDSVDEMMRNIEVHYLANPHGEIYFSLVSDWRDAPYEQSDEDLEILDYAKRELAALNSRYAFDGKTRFYLLHRRRIYNSAEECWMGWERKRGKLHELNMLLRGDKDTTFLGGSNIVPADVKYVMTLDADTRLMRDAVTKLVGKMHHPINRPKIDPVSGRVVEGYGLLQPRVTPSLTTGKDASVFQRVFSINRGIDPYVFTVSDVYQDLTSEGTFTGKGLYDVDAFEAALKGRIEENSILSHDLLEGSFARCALVTDVELVEDFPTRYEVEVSRQHRWARGDWQLLPFIIDRARGVTAIGRWKMVDNLRRSLTPIAWFFASILGWYFMDPLGALIWQILLIFSLFVAPTLSLLSGLVPRSTDIVPQAHFFTIWSEIRATNAQVALRIVFIADAACMMTDAIVRSLYRLLVSHKLMLEWRTAASMQSSAQGSIVDYYRQMWHAPVVAMLGLLFAALPGDNAFLIGIPFTLLWVLSPAVAWYVSQSAETEDRLFVSEHVSFELRKIARRTWRYYEAFVTPQENHLPPDNFQETPEPIVASRTSPTNIGVYLLSVISARQFGWISFADTLERIENTIQTVEKMEKHRGHLYNWYHTDTLQTLGPRYVSAVDSGNLAGHLIAVSSACRDWAEAPSAHLQGNLDGIGDVAGILRETLKALPDNRKTLRPLHRRLEERIIGFSNALASVKREHEFASIRVINLAVLARDIQKLATNVDHEVKSAQSAEVTRWAQLLVESCEAHISDSAIDLTNMEPLRQRLASLRDRSRNLAFSMDFTFLYRKDRRLLSIGYRVESKELDEACYDLLASECRLTSLFAIAKGDLPTEHWYRLGRQVVPIGAQGALVSWSGSMFEYLMPPLVMQERQGGILNQTNNLIVKEQMNHGRRLGTPWGISEAAFNARDHNMNYQYTNFGVPTLGLKRGLGQNAVIAPYASILASQYDPDGALENLDKLRKLGALGQYGFHDAVDFTPTRVPDGKVCAVVYNYYAHHHGMSIAAVANVAFDGVLRELFHSDPVIEAAELLLQEKAPREVPVMSAKYEPETPGKEQADLLRAEVRSIADPAVRDREVVFLSNGHYSTMLTSTGAGYSKWNGQAISRWKADPTDDRWGTFIFLRDTTNGQWWSATAEPRVIEGEKTKTIFTDDKAEFHKTIGDLQSVVECIVATEHDAEGRRITLLNVGSEDRYIEVTSYMEPVIASEDDDNAHPLFSRMFVQTEIGRRGDVIRAWRNRRSQNEPGTVIAHLAADNAGPSRPTEFETDRAKFIGRGRSLREAAAFDAGATLSSSDGFTLDPILSLRRTVRVPAGKKVSVIFWTIAAPSREEVDKAIDRYRHPDAFAHELVHAWTRTQVQMRHVGVTSQQAAAFQHLGRYLTYPDMHLRADSETLKTGLASQRALWPLAISGDFPIFSLRINDDMDMDIAREALSAHEYLRSRGVIFDLVIVNERAASYAQDMQHALDHISETQRRINPADGGRPHVFSVRRDLMDEETWSALLAASRVVLHVRNGKIVDQINRAVSLFAANRGPDGSSDAAQARLPVPAFPVAEPVEDAGDLDFWNGFGGFAKNGQEYVVRLNGGQSTPHPWINVISNENFGFHISAEGAGFSWSRNSRDYQLTPWTNDPVINRPGEAFYVADVETGKLYTPCAALSRDPEAMFETRHGLGYSILTGVADTLEVELTQTVDREKPVKFSQVIVRNKGSKSRRLKVYAYVEWVLGNNGQKSAPFILSRHDAGSNAIFASNPYSIDYSARTSFLTLDSEASGFTTSRREFIGRFGSAQAPQGIVAGAALSGTTEVDGDPCAALMQEIHLKPGEERHMTFILGDADNAEEAEALVKDVRQADFLSVLEESKKFWTGFTGQLQVSTPDAGFNHMVNNWLPYQALACRILARTAFYQSSGAFGFRDQLQDTLAFLLYQPDLARTQILRAAGRQFPEGDVQHWWLPLTGAGVRTTISDDVVWLAYAINQYVSATGDAAILDESIPFLKGPALMPGQHDAFFQPETSERSATLYEHAALALDLAIHRTGENGLPLILGGDWNDGMNRVGVGGKGTSVWLGWFLAGALRDFIEIAEKRGDTDRVGKWASHREKLRHVLETAGWDGSYYRRGYFDDGTPLGSASSEECQIDSLGQSWSVLSGEGEEGRSRQAMDAVMEHLVDEKTGIIRLFTPPFSRASHDPGYIKGYPPGVRENGGQYTHAATWVVLALAKQGRAQEAWNCFKLLNPVNHALDAASSETYRVEPYVVTADVYGEGAYAGRGGWSWYTGSAGWLYRAAVEGILGITRTDGKLHVSPSLPEDWSGFSIRITLDGKARDIAVSRKAGTADVSVSVDG

Entity 2 branched

描述 description	;beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose ;
分子量 formula_weight	1477.3 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	URIDINE-5'-DIPHOSPHATE-GLUCOSE
分子量 formula_weight	566.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

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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	3.80 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	171473

fit	/app/data/saxs_computation/rf/8rfe/8rfe.fit
pddf	/app/data/pr_computation/rf/8rfe/8rfe.pr.out
profile	/app/data/saxs_computation/rf/8rfe/8rfe.dat

CgsiGP2 sample in nanodisc

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 (3)

Entity 1 polymer

聚合体 Polymer

Entity 2 branched

Entity 3 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)