9mcc

;Cryo-EM structure of violaxanthin-chlorophyll-a-binding protein with red shifted Chl a (rVCP) from Trachydiscus minutus at 2.4 angstrom ;

Method: ELECTRON MICROSCOPY D_max: 105.8 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	9mcc
沉积日期 deposition_date	2025-03-17
结构标题 title	;Cryo-EM structure of violaxanthin-chlorophyll-a-binding protein with red shifted Chl a (rVCP) from Trachydiscus minutus at 2.4 angstrom ;
关键词 keywords	violaxanthin, vaucheriaxanthin, chlorophyll a, VCP, tetramer, red Chlorophyll, PHOTOSYNTHESIS; PHOTOSYNTHESIS
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	33.85 Å
回转半径 Rg (电子) rg_electron	32.94 Å
零角强度 I(0) i0	300673000.00
分子量 molecular_weight	115070.0 kDa
排除体积 excluded_volume	123190 Å³
包络体积 envelope_volume	194900 Å³
水化壳体积 shell_volume	48045 Å³
包络直径 envelope_diameter	107.9 Å
壳层 Rg shell_rg	41.06 Å
包络 Rg envelope_rg	32.67 Å
形状 Rg shape_rg	32.91 Å
总 Rg total_rg	33.53 Å
总原子数 total_atoms	8910
残基数 n_residues	700
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	105.8 Å
Rg (实空间) rg_real	33.70 Å
Rg 误差 (实空间) rg_real_error	0.56 Å
I(0) (实空间) i0_real	3.0070e+08
I(0) 误差 (实空间) i0_real_error	4.1340e+06
Rg (倒空间) rg_reciprocal	33.79 Å
I(0) (倒空间) i0_reciprocal	300700000.0000
解质量估计 total_estimate	0.9045
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	42.8 Å
偏度 Skewness skewness	0.122
峰度 Kurtosis kurtosis	-0.502
角度范围 angular_range	— – 0.2350 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	11730000.0000
实空间数据点数 n_real_points	48
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.932; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.964

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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 (6)

Entity 1 polymer

描述 description	Light-harvesting complex
分子量 formula_weight	24611.4 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,C
原子数 atom_count	8978

SDNTRTLPDRENSCPGLLLLLLPIMKTAIALLPFLGAATAFVTPMSKTSMARGRSLQMSFDDEAGAIQWFPPSPGYWDPLGFVADGDTEKFSKYRAIEIKHGRVAMLGALDYFIKTPSGWHLPGKLGDVDIDSIPVGLGAIKAVPPLGWVQILLFASALEFLAPQKEDQPPGAVQPATPSFEQPGTLEYQTKEINNGRLAMIALAGLWLGELASGGTDPIVAFKTWVGI

Entity 2 polymer

描述 description	light-harvesting complex
分子量 formula_weight	23934.5 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

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

MVAKSAALVVMGLSMASAFLAPTPNNRASAQAPMKMAKSAATKEFPFDDQPGGVKWFPSSAPYWDPLGFTNEKTEDEYWRIAHGEIKNGRLAMLAVTHYFVVGSGLRFPFKFGSVSTADVPLGLGAIKALPWAVWLQIAAFCLVLEVLTENPGFGERVPGRVPGNLQPDTPSFNAPGDLEIRTKELNNARLAMISIWGLWVGEIASGGVDPFTSFANWLKL

Entity 3 non-polymer

描述 description	CHLOROPHYLL A
分子量 formula_weight	893.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	46

Entity 4 non-polymer

描述 description	;[(2~{Z},4~{E},6~{E},8~{E},10~{E},12~{E},14~{E})-17-[(4~{S},6~{R})-4-acetyloxy-2,2,6-trimethyl-6-oxidanyl-cyclohexylidene]-6,11,15-trimethyl-2-[(~{E})-2-[(1~{S},4~{S},6~{R})-2,2,6-trimethyl-4-oxidanyl-7-oxabicyclo[4.1.0]heptan-1-yl]ethenyl]heptadeca-2,4,6,8,10,12,14,16-octaenyl] octanoate ;
分子量 formula_weight	785.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

Entity 5 non-polymer

描述 description	;(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL ;
分子量 formula_weight	600.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	10

Entity 6 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	68

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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	2.420 Å
最低分辨率 resolution_low	— Å
R 因子 r_factor	—
R_work r_work	—
R_free r_free	—

分辨率 resolution	2.42 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	290174

fit	/app/data/saxs_computation/mc/9mcc/9mcc.fit
pddf	/app/data/pr_computation/mc/9mcc/9mcc.pr.out
profile	/app/data/saxs_computation/mc/9mcc/9mcc.dat

;Cryo-EM structure of violaxanthin-chlorophyll-a-binding protein with red shifted Chl a (rVCP) from Trachydiscus minutus at 2.4 angstrom ;

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

精修参数 Refinement

冷冻电镜 EM 3D

5. 实体与聚合体信息 (6)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 water

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)