9i07

Photosynthetic A8B8 glycerldeyde-3-phosphate dehydrogenase hexadecamer (major conformer) from Spinacia oleracea.

Method: ELECTRON MICROSCOPY D_max: 216.4 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	9i07
沉积日期 deposition_date	2025-01-14
结构标题 title	Photosynthetic A8B8 glycerldeyde-3-phosphate dehydrogenase hexadecamer (major conformer) from Spinacia oleracea.
关键词 keywords	photosynthesis, Calvin-Benson cycle, redox regulation, OXIDOREDUCTASE; OXIDOREDUCTASE
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	66.59 Å
回转半径 Rg (电子) rg_electron	66.33 Å
零角强度 I(0) i0	5301200000.00
分子量 molecular_weight	614990.0 kDa
排除体积 excluded_volume	769300 Å³
包络体积 envelope_volume	1078100 Å³
水化壳体积 shell_volume	129470 Å³
包络直径 envelope_diameter	210.8 Å
壳层 Rg shell_rg	73.89 Å
包络 Rg envelope_rg	64.09 Å
形状 Rg shape_rg	66.34 Å
总 Rg total_rg	66.40 Å
总原子数 total_atoms	43184
残基数 n_residues	5552
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	216.4 Å
Rg (实空间) rg_real	66.29 Å
Rg 误差 (实空间) rg_real_error	2.16 Å
I(0) (实空间) i0_real	5.3010e+09
I(0) 误差 (实空间) i0_real_error	1.1310e+08
Rg (倒空间) rg_reciprocal	66.77 Å
I(0) (倒空间) i0_reciprocal	5305000000.0000
解质量估计 total_estimate	0.8480
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	99.2 Å
偏度 Skewness skewness	0.044
峰度 Kurtosis kurtosis	-0.733
角度范围 angular_range	— – 0.1200 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	1218000000.0000
实空间数据点数 n_real_points	25
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.804; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.609

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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	Glyceraldehyde-3-phosphate dehydrogenase B, chloroplastic
分子量 formula_weight	39404.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	8

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	O,Q,A,C,E,G,I,K
原子数 atom_count	43184

KLKVAINGFGRIGRNFLRCWHGRKDSPLDVVVVNDSGGVKSATHLLKYDSILGTFKADVKIIDNETFSIDGKPIKVVSNRDPLKLPWAELGIDIVIEGTGVFVDGPGAGKHIQAGAKKVIITAPAKGSDIPTYVVGVNEKDYGHDVANIISNASCTTNCLAPFVKVLDEELGIVKGTMTTTHSYTGDQRLLDASHRDLRRARAAALNIVPTSTGAAKAVSLVLPQLKGKLNGIALRVPTPNVSVVDLVVNIEKVGVTAEDVNNAFRKAAAGPLKGVLDVCDIPLVSVDFRCSDFSSTIDSSLTMVMGGDMVKVVAWYDNEWGYSQRVVDLADLVANKWPGLEGSVASGDPLEDFCKDNPADEECKLYE

Entity 2 polymer

描述 description	Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
分子量 formula_weight	36256.4 kDa
来源方法 src_method	nat
拷贝数 entity_count	8

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	P,R,B,D,F,H,J,L

KLKVAINGFGRIGRNFLRCWHGRKDSPLDVVVINDTGGVKQASHLLKYDSILGTFDADVKTAGDSAISVDGKVIKVVSDRNPVNLPWGDMGIDLVIEGTGVFVDRDGAGKHLQAGAKKVLITAPGKGDIPTYVVGVNEEGYTHADTIISNASCTTNCLAPFVKVLDQKFGIIKGTMTTTHSYTGDQRLLDASHRDLRRARAACLNIVPTSTGAAKAVALVLPNLKGKLNGIALRVPTPNVSVVDLVVQVSKKTFAEEVNAAFRESADNELKGILSVCDEPLVSIDFRCTDVSSTIDSSLTMVMGDDMVKVIAWYDNEWGYSQRVVDLADIVANKWQA

Entity 3 non-polymer

描述 description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
分子量 formula_weight	663.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	16

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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	3.10 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	55141

fit	/app/data/saxs_computation/i0/9i07/9i07.fit
pddf	/app/data/pr_computation/i0/9i07/9i07.pr.out
profile	/app/data/saxs_computation/i0/9i07/9i07.dat

Photosynthetic A8B8 glycerldeyde-3-phosphate dehydrogenase hexadecamer (major conformer) from Spinacia oleracea.

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 polymer

聚合体 Polymer

Entity 3 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)