9o49

Cryo-EM structure of Rubisco with hetero small subunit 1A3B form I

Method: ELECTRON MICROSCOPY D_max: 133.1 Å Quality: REASONABLE

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	9o49
沉积日期 deposition_date	2025-04-08
结构标题 title	Cryo-EM structure of Rubisco with hetero small subunit 1A3B form I
关键词 keywords	rubisco, Arabidopsis thaliana, hetero small subunit, PLANT PROTEIN; PLANT 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	46.29 Å
回转半径 Rg (电子) rg_electron	45.66 Å
零角强度 I(0) i0	3425370000.00
分子量 molecular_weight	494740.0 kDa
排除体积 excluded_volume	619760 Å³
包络体积 envelope_volume	751670 Å³
水化壳体积 shell_volume	124010 Å³
包络直径 envelope_diameter	138.4 Å
壳层 Rg shell_rg	58.61 Å
包络 Rg envelope_rg	45.38 Å
形状 Rg shape_rg	45.65 Å
总 Rg total_rg	46.06 Å
总原子数 total_atoms	34914
残基数 n_residues	4424
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	133.1 Å
Rg (实空间) rg_real	45.84 Å
Rg 误差 (实空间) rg_real_error	0.55 Å
I(0) (实空间) i0_real	3.4250e+09
I(0) 误差 (实空间) i0_real_error	5.0840e+07
Rg (倒空间) rg_reciprocal	46.28 Å
I(0) (倒空间) i0_reciprocal	3427000000.0000
解质量估计 total_estimate	0.6449
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	62.6 Å
偏度 Skewness skewness	-0.006
峰度 Kurtosis kurtosis	-0.562
角度范围 angular_range	— – 0.1700 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	1582000000.0000
实空间数据点数 n_real_points	35
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.949; Stabil: 1.000; Sysdev: 0.021; Positv: 1.000; Valcen: 0.967; Smooth: 0.502

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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	Ribulose bisphosphate carboxylase large chain
分子量 formula_weight	53020.9 kDa
EC 编号 ec_number	4.1.1.39
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	A,B,C,D,E,F,G,H
原子数 atom_count	34914

MSPQTETKASVGFKAGVKEYKLTYYTPEYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYHIEPVPGEETQFIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALAALRLEDLRIPPAYTKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEAIYKSQAETGEIKGHYLNATAGTCEEMIKRAVFARELGVPIVMHDYLTGGFTANTSLSHYCRDNGLLLHIHRAMHAVIDRQKNHGMHFRVLAKALRLSGGDHIHAGTVVGKLEGDRESTLGFVDLLRDDYVEKDRSRGIFFTQDWVSLPGVLPVASGGIHVWHMPALTEIFGDDSVLQFGGGTLGHPWGNAPGAVANRVALEACVQARNEGRDLAVEGNEIIREACKWSPELAAACEVWKEITFNFPTIDKLDGQE

Entity 2 polymer

描述 description	Ribulose bisphosphate carboxylase small subunit 3B, chloroplastic
分子量 formula_weight	20307.3 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	I,K,L,M,N,O

MASSMLSSAAVVTSPAQATMVAPFTGLKSSAAFPVTRKTNKDITSIASNGGRVSCMKVWPPIGKKKFETLSYLPDLSDVELAKEVDYLLRNKWIPCVEFELEHGFVYREHGNTPGYYDGRYWTMWKLPLFGCTDSAQVLKEVEECKKEYPGAFIRIIGFDNTRQVQCISFIAYKPPSFTEA

Entity 3 polymer

描述 description	Ribulose bisphosphate carboxylase small subunit 1A, chloroplastic
分子量 formula_weight	20237.1 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	J,P

MASSMLSSATMVASPAQATMVAPFNGLKSSAAFPATRKANNDITSITSNGGRVNCMQVWPPIGKKKFETLSYLPDLTDSELAKEVDYLIRNKWIPCVEFELEHGFVYREHGNSPGYYDGRYWTMWKLPLFGCTDSAQVLKEVEECKKEYPNAFIRIIGFDNTRQVQCISFIAYKPPSFTG

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7. 引用文献 (1)

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分辨率 resolution	2.870 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	2.87 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	14328

fit	/app/data/saxs_computation/o4/9o49/9o49.fit
pddf	/app/data/pr_computation/o4/9o49/9o49.pr.out
profile	/app/data/saxs_computation/o4/9o49/9o49.dat

Cryo-EM structure of Rubisco with hetero small subunit 1A3B form I

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

精修参数 Refinement

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 polymer

聚合体 Polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)