SAXSdb — 8yjt

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8yjt
沉积日期 deposition_date	2024-03-02
结构标题 title	Cryo-EM structure of the flagellar C ring in the CCW state
关键词 keywords	Flagellum, Flagellar motor, C ring, Switch complex, MOTOR PROTEIN; MOTOR PROTEIN
实验方法 method	ELECTRON MICROSCOPY

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	— Å
回转半径 Rg (电子) rg_electron	214.40 Å
零角强度 I(0) i0	154116000000.00
分子量 molecular_weight	3414600.0 kDa
排除体积 excluded_volume	4302400 Å³
包络体积 envelope_volume	18095000 Å³
水化壳体积 shell_volume	717900 Å³
包络直径 envelope_diameter	490.4 Å
壳层 Rg shell_rg	231.30 Å
包络 Rg envelope_rg	178.70 Å
形状 Rg shape_rg	214.40 Å
总 Rg total_rg	214.50 Å
总原子数 total_atoms	239768
残基数 n_residues	30328
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

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	509.4 Å
Rg (实空间) rg_real	214.40 Å
Rg 误差 (实空间) rg_real_error	1.67 Å
I(0) (实空间) i0_real	1.5250e+11
I(0) 误差 (实空间) i0_real_error	3.5490e+09
Rg (倒空间) rg_reciprocal	130.00 Å
I(0) (倒空间) i0_reciprocal	94880000000.0000
解质量估计 total_estimate	0.8003
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	363.9 Å
偏度 Skewness skewness	-0.337
峰度 Kurtosis kurtosis	-1.170
角度范围 angular_range	— – 0.0350 Å⁻¹
当前正则化参数 α current_alpha	0.6798
最高正则化参数 α highest_alpha	2684000000.0000
实空间数据点数 n_real_points	8
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.173; Oscil: 0.579; Stabil: 0.915; Sysdev: 1.000; Positv: 1.000; Valcen: 0.924; Smooth: 0.000

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (4)

Entity 1 polymer

描述 description	Flagellar motor switch protein FliG
分子量 formula_weight	36891.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	34

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	k,q,w,3,9,AE,AK,AQ,AW,Ac,Ai,Ao,Au,A1,A7,BC,BI,BO,BU,Ba,Bg,Bm,Bs,By,B5,CA,CG,CM,CS,CY,Ce,Ck,Cq,Cw
原子数 atom_count	239768

MSNLSGTDKSVILLMTIGEDRAAEVFKHLSTREVQALSTAMANVRQISNKQLTDVLSEFEQEAEQFAALNINANEYLRSVLVKALGEERASSLLEDILETRDTTSGIETLNFMEPQSAADLIRDEHPQIIATILVHLKRSQAADILALFDERLRHDVMLRIATFGGVQPAALAELTEVLNGLLDGQNLKRSKMGGVRTAAEIINLMKTQQEEAVITAVREFDGELAQKIIDEMFLFENLVDVDDRSIQRLLQEVDSESLLIALKGAEPPLREKFLRNMSQRAADILRDDLANRGPVRLSQVENEQKAILLIVRRLAETGEMVIGSGEDTYV

Entity 2 polymer

描述 description	Flagellar M-ring protein
分子量 formula_weight	61295.6 kDa
来源方法 src_method	nat
拷贝数 entity_count	34

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	l,r,x,4,0,AF,AL,AR,AX,Ad,Aj,Ap,Av,A2,A8,BD,BJ,BP,BV,Bb,Bh,Bn,Bt,Bz,B6,CB,CH,CN,CT,CZ,Cf,Cl,Cr,Cx

MSATASTATQPKPLEWLNRLRANPRIPLIVAGSAAVAIVVAMVLWAKTPDYRTLFSNLSDQDGGAIVAQLTQMNIPYRFANGSGAIEVPADKVHELRLRLAQQGLPKGGAVGFELLDQEKFGISQFSEQVNYQRALEGELARTIETLGPVKSARVHLAMPKPSLFVREQKSPSASVTVTLEPGRALDEGQISAVVHLVSSAVAGLPPGNVTLVDQSGHLLTQSNTSGRDLNDAQLKFANDVESRIQRRIEAILSPIVGNGNVHAQVTAQLDFANKEQTEEHYSPNGDASKATLRSRQLNISEQVGAGYPGGVPGALSNQPAPPNEAPIATPPTNQQNAQNTPQTSTSTNSNSAGPRSTQRNETSNYEVDRTIRHTKMNVGDIERLSVAVVVNYKTLADGKPLPLTADQMKQIEDLTREAMGFSDKRGDTLNVVNSPFSAVDNTGGELPFWQQQSFIDQLLAAGRWLLVLVVAWILWRKAVRPQLTRRVEEAKAAQEQAQVRQETEEAVEVRLSKDEQLQQRRANQRLGAEVMSQRIREMSDNDPRVVALVIRQWMSNDHE

Entity 3 polymer

描述 description	Flagellar motor switch protein FliM
分子量 formula_weight	37901.1 kDa
来源方法 src_method	nat
拷贝数 entity_count	34

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	m,s,y,5,AA,AG,AM,AS,AY,Ae,Ak,Aq,Aw,A3,A9,BE,BK,BQ,BW,Bc,Bi,Bo,Bu,B1,B7,CC,CI,CO,CU,Ca,Cg,Cm,Cs,Cy

MGDSILSQAEIDALLNGDSDTKDEPTPGIASDSDIRPYDPNTQRRVVRERLQALEIINERFARQFRMGLFNLLRRSPDITVGAIRIQPYHEFARNLPVPTNLNLIHLKPLRGTGLVVFSPSLVFIAVDNLFGGDGRFPTKVEGREFTHTEQRVINRMLKLALEGYSDAWKAINPLEVEYVRSEMQVKFTNITTSPNDIVVNTPFHVEIGNLTGEFNICLPFSMIEPLRELLVNPPLENSRHEDQNWRDNLVRQVQHSELELVANFADIPLRLSQILKLKPGDVLPIEKPDRIIAHVDGVPVLTSQYGTVNGQYALRVEHLINPILNSLNEEQPK

Entity 4 polymer

描述 description	Flagellar motor switch protein FliN
分子量 formula_weight	14801.8 kDa
来源方法 src_method	nat
拷贝数 entity_count	102

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	;n,o,p,t,u,v,z,1,2,6,7,8,AB,AC,AD,AH,AI,AJ,AN,AO,AP,AT,AU,AV,AZ,Aa,Ab,Af,Ag,Ah,Al,Am,An,Ar,As,At,Ax,Ay,Az,A4,A5,A6,A0,BA,BB,BF,BG,BH,BL,BM,BN,BR,BS,BT,BX,BY,BZ,Bd,Be,Bf,Bj,Bk,Bl,Bp,Bq,Br,Bv,Bw,Bx,B2,B3,B4,B8,B9,B0,CD,CE,CF,CJ,CK,CL,CP,CQ,CR,CV,CW,CX,Cb,Cc,Cd,Ch,Ci,Cj,Cn,Co,Cp,Ct,Cu,Cv,Cz,C1,C2 ;

MSDMNNPSDENTGALDDLWADALNEQKATTTKSAADAVFQQLGGGDVSGAMQDIDLIMDIPVKLTVELGRTRMTIKELLRLTQGSVVALDGLAGEPLDILINGYLIAQGEVVVVADKYGVRITDIITPSERMRRLSR

▶

7. 引用文献 (1)

▶

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	5.90 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	19627

fit	/app/data/saxs_computation/yj/8yjt/8yjt.fit
pddf	/app/data/pr_computation/yj/8yjt/8yjt.pr.out
profile	/app/data/saxs_computation/yj/8yjt/8yjt.dat

Cryo-EM structure of the flagellar C ring in the CCW state

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 (4)

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

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)