9fnn

;Cryo-EM structure of the c-di-GMP-saturated 'crown'less Bcs macrocomplex for cellulose secretion in E. coli ;

Method: ELECTRON MICROSCOPY D_max: 171.7 Å Quality: GOOD

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9fnn
沉积日期 deposition_date	2024-06-10
结构标题 title	;Cryo-EM structure of the c-di-GMP-saturated 'crown'less Bcs macrocomplex for cellulose secretion in E. coli ;
关键词 keywords	Bacterial cellulose secretion, 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	51.31 Å
回转半径 Rg (电子) rg_electron	51.91 Å
零角强度 I(0) i0	1526950000.00
分子量 molecular_weight	336080.0 kDa
排除体积 excluded_volume	424750 Å³
包络体积 envelope_volume	651410 Å³
水化壳体积 shell_volume	102240 Å³
包络直径 envelope_diameter	178.9 Å
壳层 Rg shell_rg	56.84 Å
包络 Rg envelope_rg	51.54 Å
形状 Rg shape_rg	51.95 Å
总 Rg total_rg	51.94 Å
总原子数 total_atoms	23714
残基数 n_residues	2895
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	171.7 Å
Rg (实空间) rg_real	51.23 Å
Rg 误差 (实空间) rg_real_error	1.51 Å
I(0) (实空间) i0_real	1.5270e+09
I(0) 误差 (实空间) i0_real_error	3.3380e+07
Rg (倒空间) rg_reciprocal	51.36 Å
I(0) (倒空间) i0_reciprocal	1527000000.0000
解质量估计 total_estimate	0.8829
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	60.9 Å
偏度 Skewness skewness	0.261
峰度 Kurtosis kurtosis	-0.399
角度范围 angular_range	— – 0.1550 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	137100000.0000
实空间数据点数 n_real_points	32
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.879; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.837

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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 (10)

Entity 1 polymer

描述 description	Cellulose synthase catalytic subunit [UDP-forming]
分子量 formula_weight	104015.7 kDa
EC 编号 ec_number	2.4.1.12
突变 mutation	HA-FLAG-tagged at C-terminue
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
原子数 atom_count	23714

MSILTRWLLIPPVNARLIGRYRDYRRHGASAFSATLGCFWMILAWIFIPLEHPRWQRIRAEHKNLYPHINASRPRPLDPVRYLIQTCWLLIGASRKETPKPRRRAFSGLQNIRGRYHQWMNELPERVSHKTQHLDEKKELGHLSAGARRLILGIIVTFSLILALICVTQPFNPLAQFIFLMLLWGVALIVRRMPGRFSALMLIVLSLTVSCRYIWWRYTSTLNWDDPVSLVCGLILLFAETYAWIVLVLGYFQVVWPLNRQPVPLPKDMSLWPSVDIFVPTYNEDLNVVKNTIYASLGIDWPKDKLNIWILDDGGREEFRQFAQNVGVKYIARTTHEHAKAGNINNALKYAKGEFVSIFDCDHVPTRSFLQMTMGWFLKEKQLAMMQTPHHFFSPDPFERNLGRFRKTPNEGTLFYGLVQDGNDMWDATFFCGSCAVIRRKPLDEIGGIAVETVTEDAHTSLRLHRRGYTSAYMRIPQAAGLATESLSAHIGQRIRWARGMVQIFRLDNPLTGKGLKFAQRLCYVNAMFHFLSGIPRLIFLTAPLAFLLLHAYIIYAPALMIALFVLPHMIHASLTNSKIQGKYRHSFWSEIYETVLAWYIAPPTLVALINPHKGKFNVTAKGGLVEEEYVDWVISRPYIFLVLLNLVGVAVGIWRYFYGPPTEMLTVVVSMVWVFYNLIVLGGAVAVSVESKQVRRSHRVEMTMPAAIAREDGHLFSCTVQDFSDGGLGIKINGQAQILEGQKVNLLLKRGQQEYVFPTQVARVMGNEVGLKLMPLTTQQHIDFVQCTFARADTWALWQDSYPEDKPLESLLDILKLGFRGYRHLAEFAPSSVKGIFRVLTSLVSWVVSFIPRRPERSETAQPSDQALAQQGSARSSGRTGLEFEEFYPYDVPDYAADYKDDDDKRS

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	Cyclic di-GMP-binding protein
分子量 formula_weight	86184.4 kDa
突变 mutation	C-terminal tail only in refined structure
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B,X,Y,Z

MKRKLFWICAVAMGMSAFPSFMTQATPATQPLINAEPAVAAQTEQNPQVGQVMPGVQGADAPVVAQNGPSRDVKLTFAQIAPPPGSMVLRGINPNGSIEFGMRSDEVVTKAMLNLEYTPSPSLLPVQSQLKVYLNDELMGVLPVTKEQLGKKTLAQMPINPLFITDFNRVRLEFVGHYQDVCENPASTTLWLDVGRSSGLDLTYQTLNVKNDLSHFPVPFFDPRDNRTNTLPMVFAGAPDVGLQQASAIVASWFGSRSGWRGQNFPVLYNQLPDRNAIVFATNDKRPDFLRDHPAVKAPVIEMINHPQNPYVKLLVVFGRDDKDLLQAAKGIAQGNILFRGESVVVNEVKPLLPRKPYDAPNWVRTDRPVTFGELKTYEEQLQSSGLEPAAINVSLNLPPDLYLMRSTGIDMDINYRYTMPPVKDSSRMDISLNNQFLQSFNLSSKQEANRLLLRIPVLQGLLDGKTDVSIPALKLGATNQLRFDFEYMNPMPGGSVDNCITFQPVQNHVVIGDDSTIDFSKYYHFIPMPDLRAFANAGFPFSRMADLSQTITVMPKAPNEAQMETLLNTVGFIGAQTGFPAINLTVTDDGSTIQGKDADIMIIGGIPDKLKDDKQIDLLVQATESWVKTPMRQTPFPGIVPDESDRAAETRSTLTSSGAMAAVIGFQSPYNDQRSVIALLADSPRGYEMLNDAVNDSGKRATMFGSVAVIRESGINSLRVGDVYYVGHLPWFERLWYALANHPILLAVLAAISVILLAWVLWRLLRIISRRRLNPDNE

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 3 polymer

描述 description	Cyclic di-GMP binding protein BcsE
分子量 formula_weight	60967.5 kDa
突变 mutation	Strep-tagged at N-terminus
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	E,U

MASWSHPQFEKGSMRDIVDPVFSIGISSLWDELRHMPAGGVWWFNVDRHEDAISLANQTIASQAETAHVAVISMDSDPAKIFQLDDSQGPEKIKLFSMLNHEKGLYYLTRDLQCSIDPHNYLFILVCANNAWQNIPAERLRSWLDKMNKWSRLNHCSLLVINPGNNNDKQFSLLLEEYRSLFGLASLRFQGDQHLLDIAFWCNEKGVSARQQLSVQQQNGIWTLVQSEEAEIQPRSDEKRILSNVAVLEGAPPLSEHWQLFNNNEVLFNEARTAQAATVVFSLQQNAQIEPLARSIHTLRRQRGSAMKILVRENTASLRATDERLLLACGANMVIPWNAPLSRCLTMIESVQGQKFSRYVPEDITTLLSMTQPLKLRGFQKWDVFCNAVNNMMNNPLLPAHGKGVLVALRPVPGIRVEQALTLCRPNRTGDIMTIGGNRLVLFLSFCRINDLDTALNHIFPLPTGDIFSNRMVWFEDDQISAELVQMRLLAPEQWGMPLPLTQSSKPVINAEHDGRHWRRIPEPMRLLDDAVERSS

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 4 polymer

描述 description	Cellulose biosynthesis protein BcsF
分子量 formula_weight	7379.0 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

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

MMTISDIIEIIVVCALIFFPLGYLARHSLRRIRDTLRLFFAKPRYVKPAGTLRRTEKARATKK

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 5 polymer

描述 description	Cell division protein
分子量 formula_weight	27960.8 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	Q,W

MAVLGLQGVRGGVGTTTITAALAWSLQMLGENVLVVDACPDNLLRLSFNVDFTHRQGWARAMLDGQDWRDAGLRYTSQLDLLPFGQLSIEEQENPQHWQTRLSDICSGLQQLKASGRYQWILIDLPRDASQITHQLLSLCDHSLAIVNVDANCHIRLHQQALPDGAHILINNFRIGSQVQDDIYQLWLQSQRRLLPMLIHRDEAMAECLAAKQPVGEYRSDALAAEEILTLANWCLLNYSGLKTPVGSKS

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 6 polymer

描述 description	Protein YhjR
分子量 formula_weight	8645.5 kDa
突变 mutation	His-tagged at N-terminus
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	R,V

MGSSHHHHHHHHAAGSNNNEPDTLPDPAIGYIFQNDIVALKQAFSLPDIDYADISQREQLAAALKRWPLLAEFAQQK

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 7 polymer

描述 description	Cellulose biosynthesis protein BcsG
分子量 formula_weight	59688.0 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

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

MTQFTQNTAMPSSLWQYWRGLSGWNFYFLVKFGLLWAGYLNFHPLLNLVFAAFLLMPLPRYSLHRLRHWIALPIGFALFWHDTWLPGPESIMSQGSQVAGFSTDYLIDLVTRFINWQMIGAIFVLLVAWLFLSQWIRITVFVVAILLWLNVLTLAGPSFSLWPAGQPTTTVTTTGGNAAATVAATGGAPVVGDMPAQTAPPTTANLNAWLNNFYNAEAKRKSTFPSSLPADAQPFELLVINICSLSWSDIEAAGLMSHPLWSHFDIEFKNFNSATSYSGPAAIRLLRASCGQTSHTNLYQPANNDCYLFDNLSKLGFTQHLMMGHNGQFGGFLKEVRENGGMQSELMDQTNLPVILLGFDGSPVYDDTAVLNRWLDVTEKDKNSRSATFYNTLPLHDGNHYPGVSKTADYKARAQKFFDELDAFFTELEKSGRKVMVVVVPEHGGALKGDRMQVSGLRDIPSPSITDVPVGVKFFGMKAPHQGAPIVIEQPSSFLAISDLVVRVLDGKIFTEDNVDWKKLTSGLHKQHRSPRTQMQ

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 8 non-polymer

描述 description	;9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) ;
分子量 formula_weight	690.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

Entity 9 non-polymer

描述 description	ADENOSINE-5'-TRIPHOSPHATE
分子量 formula_weight	507.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 10 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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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	2.85 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	260501

fit	/app/data/saxs_computation/fn/9fnn/9fnn.fit
pddf	/app/data/pr_computation/fn/9fnn/9fnn.pr.out
profile	/app/data/saxs_computation/fn/9fnn/9fnn.dat

;Cryo-EM structure of the c-di-GMP-saturated 'crown'less Bcs macrocomplex for cellulose secretion in E. coli ;

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 (10)

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

Entity 6 polymer

聚合体 Polymer

来源 Source

Entity 7 polymer

聚合体 Polymer

来源 Source

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)