9gtp

;Cryo-EM structure of a contractile injection system in Streptomyces coelicolor, the baseplate complex in extended state applied 6-fold symmetry. ;

Method: ELECTRON MICROSCOPY D_max: 230.9 Å Quality: EXCELLENT

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	9gtp
沉积日期 deposition_date	2024-09-18
结构标题 title	;Cryo-EM structure of a contractile injection system in Streptomyces coelicolor, the baseplate complex in extended state applied 6-fold symmetry. ;
关键词 keywords	Contractile injection system, STRUCTURAL PROTEIN; STRUCTURAL 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	91.50 Å
回转半径 Rg (电子) rg_electron	90.53 Å
零角强度 I(0) i0	55837200000.00
分子量 molecular_weight	1986600.0 kDa
排除体积 excluded_volume	2472200 Å³
包络体积 envelope_volume	4415800 Å³
水化壳体积 shell_volume	381340 Å³
包络直径 envelope_diameter	281.1 Å
壳层 Rg shell_rg	103.10 Å
包络 Rg envelope_rg	87.25 Å
形状 Rg shape_rg	90.52 Å
总 Rg total_rg	90.64 Å
总原子数 total_atoms	140250
残基数 n_residues	18262
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	230.9 Å
Rg (实空间) rg_real	89.27 Å
Rg 误差 (实空间) rg_real_error	0.27 Å
I(0) (实空间) i0_real	5.3550e+10
I(0) 误差 (实空间) i0_real_error	9.0380e+08
Rg (倒空间) rg_reciprocal	93.71 Å
I(0) (倒空间) i0_reciprocal	56240000000.0000
解质量估计 total_estimate	0.9100
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	122.3 Å
偏度 Skewness skewness	0.043
峰度 Kurtosis kurtosis	-0.584
角度范围 angular_range	— – 0.0850 Å⁻¹
当前正则化参数 α current_alpha	0.9945
最高正则化参数 α highest_alpha	8026000000.0000
实空间数据点数 n_real_points	18
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 1.000; Stabil: 0.955; Sysdev: 1.000; Positv: 1.000; Valcen: 0.965; 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	Phage tail protein
分子量 formula_weight	16493.7 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,k,l,m,n
原子数 atom_count	140250

MSLPKPEDVLVAPNFGIQIDGVMVEYLNSVSNLQIEQDVIRYQQNQGTTGRNNVTLMPGVAKDGSVQVERGMSQSSVFTQWINDSMAGRMATARKNATIIVMDYEDNPVKRWNLRNAWCSKVVAGTLKAGDTNALTETITIVFEELVVE

Entity 2 polymer

描述 description	Phage tail sheath family protein
分子量 formula_weight	57009.6 kDa
来源方法 src_method	nat
拷贝数 entity_count	18

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	1h,2i,3i,1i,2j,3j,1j,2e,3e,1e,2f,3f,1f,2g,3g,1g,2h,3h

MPSYLSPGVYVEEVASGSRPIEGVGTSVAAFVGLAPTGPLNEPTLVTNWTQYVAAFGDFTGGYYLAHSVYGFFNNGGSAAYVVRVGGSAEDAAADGSVNGAAAPAAVTGSTAKALPAAEPKQLGTFAVTATAAGQSGPLTVEVADPEGEGPAERFKLIVKDGDKPVETFDVSAKKGNRSYVVTQVKERSKLITVTEAAPSAQLVRPENQSLTLPAPPSAAPAVPAGQAESAHPGPAQYLGDSSDRTGFGGLEAIDEISMVAVPDLMAAYQRGAIDLEAVKAVQLGLIAHCELMGDRVAIIDPPPNQNARQIRVWRQETAGYDSKYAALYYPWIKSFDPATGQSRLVPPSGHVAGIWARNDSERGVHKAPANEVVRGAVDLELQITRGEQDLLNPIGVNCIRSFPGRGIRVWGARTLSSDPAWRYLNIRRYFNYLEESILIGTQWVVFEPNDHNLWARIRRNVSAFLVNEWRNGALFGQSPDQAYYVKCDEETNPPESVDLGRVVCEIGIAPVKPAEFVIFRLAQFSSGGGELDE

Entity 3 polymer

描述 description	Baseplate protein J-like domain-containing protein
分子量 formula_weight	70889.4 kDa
来源方法 src_method	nat
拷贝数 entity_count	12

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	1K,2K,1L,2L,1G,2G,1H,2H,1l,2l,1J,2J

MPLPSPNLDDRRFQQFVDDAKRYIQQRAPEWTDHNVSDPGVTLVETVAHMADQIVYRLNRVPDKNHLAFLDLVGITLFPPSAARTDVTFWLSAPQEDAILVPVGTEVATLRTERDEAVVFATEQDLRIVPCTMGRLVTQVSGEAVSDRTTDLAESKDVLCFAEAPNPGDCMLIGLSAAVPDCALALELDSRVDGVGVDPRQPPLVWEAWTEDGWQSCEVDRDGTGGLNRPGDVVLHIPGGHVLSRNGGHEAGWIRCRVTEPLSGQPFYTTSPTIRSAEAYTIGGTTGSIHAETVLDEPLGESTGLPGQRLRLEHAPVVAGEPSVLLQTAADDGWQDWQVVPHFSGSHPDDHHITVDATTGEIAFGPAVREADGTLRQYGAVPPKGAVIRARRYRTGGGRAGNVARGAVQVLRTSIPYVSEVVNREAALGGVDGETIEEAKLRAPITLRAQERAVTLRDYEELARRAAPETARITCLEGAENEYGAHAVRVLVVPQAVPDPGGRLRFEQLVPGDALLNRITRHLDERRLIGTRLAVGPPYYQGVTVVATVHAFRDVDADRVRRQTHDALYRHLDPLTGGSDGKGWPFGRPVQTGELFAVLQRVPGVELVDEVVLHPADPLTGKRGDPTNRIDLDAPALVFSYDHRVRVIGDSA

Entity 4 polymer

描述 description	LysM domain-containing protein
分子量 formula_weight	25716.3 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	P,Q,R,M,N,O

MAKSSKGAGKSLVRANLAIHEPPTGKSTSPGGLIKRFPFEFNPAQLSISQRSQWKATPTAAVRKAAKPQFMGAEPREMTLEIFLDSSMKPGGNTVMKKVESLLICCEVTAKSLAAKQPSPPWVIFEWGSFSTARFNAYVASIETQYTLFGTAGVPIRATCQMGLVEIPGPTPNQNPTSGALTAQRVHRVVAGDSLQSLAWSEYGSANAWRVIAEANGIDDPSHLPTGTELILPATEEVPH

Entity 5 polymer

描述 description	Secreted protein
分子量 formula_weight	20282.1 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	E,F,A,B,C,D

MKPASQRGSVDGLGSSLPIASMLPAVFADDDLALRFVAGLDDVLAPILNVLDCLDTYFDPALTPADFAQWLGTWVGAETDGTEAEPMLRAAVAAAARLHRVRGTLQGLSETVRLAFGVAPEITESGGATWNARPLGPFPGRPRPQLHVALRLPEPRPVDVHRLDALVAAARPAHMPYTVEVTASERTPER

Entity 6 polymer

描述 description	IraD/Gp25-like domain-containing protein
分子量 formula_weight	16609.5 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	V,W,X,S,T,U

MAEQFVGSGWSFPLRIGPTGGIALVSGEQEVEEAMRLILATAPGERPMRPEFGCAIHDLVFAPVNEQTAGRIQHEVYVTLDRWEPRIEVHDVDVTTGEEQNVLFIDVRYSIRGTNNPRSLVFPFYVIPSHDEPDLPDAPAGLPGSPESDR

Entity 7 polymer

描述 description	Phage tail protein
分子量 formula_weight	15194.9 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	a,b,c,d,e,f

MTRKDPGSSIWFSLAIDGESLGYFNGCEGLSTQVEVEQRQEGGNNGFVWQLPTRVTYSNIRLTRPLTPDTAKVAKWISSVQTGIQRPTAQISALRADGSLVARWGLIDVLPVSWQGPSLDPGSASVANEVLEIAHHGFTD

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7. 引用文献 (1)

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分辨率 resolution	3.50 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	22980

fit	/app/data/saxs_computation/gt/9gtp/9gtp.fit
pddf	/app/data/pr_computation/gt/9gtp/9gtp.pr.out
profile	/app/data/saxs_computation/gt/9gtp/9gtp.dat

;Cryo-EM structure of a contractile injection system in Streptomyces coelicolor, the baseplate complex in extended state applied 6-fold symmetry. ;

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

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)