1gr5

Solution Structure of apo GroEL by Cryo-Electron microscopy

Method: ELECTRON MICROSCOPY D_max: 170.3 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	1gr5
沉积日期 deposition_date	2001-12-14
结构标题 title	Solution Structure of apo GroEL by Cryo-Electron microscopy
关键词 keywords	CHAPERONE; CHAPERONE
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	64.41 Å
回转半径 Rg (电子) rg_electron	63.28 Å
零角强度 I(0) i0	7590060000.00
分子量 molecular_weight	751670.0 kDa
排除体积 excluded_volume	947720 Å³
包络体积 envelope_volume	1568800 Å³
水化壳体积 shell_volume	195770 Å³
包络直径 envelope_diameter	187.5 Å
壳层 Rg shell_rg	75.20 Å
包络 Rg envelope_rg	59.74 Å
形状 Rg shape_rg	63.31 Å
总 Rg total_rg	63.37 Å
总原子数 total_atoms	52668
残基数 n_residues	7238
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	170.3 Å
Rg (实空间) rg_real	63.69 Å
Rg 误差 (实空间) rg_real_error	0.69 Å
I(0) (实空间) i0_real	7.5900e+09
I(0) 误差 (实空间) i0_real_error	1.2690e+08
Rg (倒空间) rg_reciprocal	65.00 Å
I(0) (倒空间) i0_reciprocal	7607000000.0000
解质量估计 total_estimate	0.8391
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	92.3 Å
偏度 Skewness skewness	-0.085
峰度 Kurtosis kurtosis	-0.540
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	3229000000.0000
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: 0.977; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.974; 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 (1)

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6. 折叠分类 (SCOP + CATH) 14 domains

SCOP 2.08 (14 domains)

结构域编号 domain_id	d1gr5a_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.16 — GroE chaperon
超家族 Superfamily superfamily	i.16.1 — GroE chaperon
家族 Family family	i.16.1.1 — GroE chaperon

结构域编号 domain_id	d1gr5b_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.16 — GroE chaperon
超家族 Superfamily superfamily	i.16.1 — GroE chaperon
家族 Family family	i.16.1.1 — GroE chaperon

结构域编号 domain_id	d1gr5c_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.16 — GroE chaperon
超家族 Superfamily superfamily	i.16.1 — GroE chaperon
家族 Family family	i.16.1.1 — GroE chaperon

结构域编号 domain_id	d1gr5d_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.16 — GroE chaperon
超家族 Superfamily superfamily	i.16.1 — GroE chaperon
家族 Family family	i.16.1.1 — GroE chaperon

结构域编号 domain_id	d1gr5e_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.16 — GroE chaperon
超家族 Superfamily superfamily	i.16.1 — GroE chaperon
家族 Family family	i.16.1.1 — GroE chaperon

结构域编号 domain_id	d1gr5f_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.16 — GroE chaperon
超家族 Superfamily superfamily	i.16.1 — GroE chaperon
家族 Family family	i.16.1.1 — GroE chaperon

结构域编号 domain_id	d1gr5g_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.16 — GroE chaperon
超家族 Superfamily superfamily	i.16.1 — GroE chaperon
家族 Family family	i.16.1.1 — GroE chaperon

结构域编号 domain_id	d1gr5h_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.16 — GroE chaperon
超家族 Superfamily superfamily	i.16.1 — GroE chaperon
家族 Family family	i.16.1.1 — GroE chaperon

结构域编号 domain_id	d1gr5i_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.16 — GroE chaperon
超家族 Superfamily superfamily	i.16.1 — GroE chaperon
家族 Family family	i.16.1.1 — GroE chaperon

结构域编号 domain_id	d1gr5j_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.16 — GroE chaperon
超家族 Superfamily superfamily	i.16.1 — GroE chaperon
家族 Family family	i.16.1.1 — GroE chaperon

结构域编号 domain_id	d1gr5k_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.16 — GroE chaperon
超家族 Superfamily superfamily	i.16.1 — GroE chaperon
家族 Family family	i.16.1.1 — GroE chaperon

结构域编号 domain_id	d1gr5l_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.16 — GroE chaperon
超家族 Superfamily superfamily	i.16.1 — GroE chaperon
家族 Family family	i.16.1.1 — GroE chaperon

结构域编号 domain_id	d1gr5m_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.16 — GroE chaperon
超家族 Superfamily superfamily	i.16.1 — GroE chaperon
家族 Family family	i.16.1.1 — GroE chaperon

结构域编号 domain_id	d1gr5n_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.16 — GroE chaperon
超家族 Superfamily superfamily	i.16.1 — GroE chaperon
家族 Family family	i.16.1.1 — GroE chaperon

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7. 引用文献 (4)

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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	1

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	7.900 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	7.90 Å
分辨率测定方法 resolution_method	MODEL-BASED ANGULAR REFINEMENT
颗粒数 num_particles	8728

描述 description	60 KDA CHAPERONIN
分子量 formula_weight	57188.4 kDa
突变 mutation	YES
来源方法 src_method	man
拷贝数 entity_count	14

Solution Structure of apo GroEL by Cryo-Electron microscopy

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 (1)

Entity 1 polymer

聚合体 Polymer

来源 Source

6. 折叠分类 (SCOP + CATH) 14 domains

SCOP 2.08 (14 domains)

7. 引用文献 (4)

8. 文件与曲线 (10)

Files (7)

Curves (3)

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N
原子数 atom_count	52668

来源生物 organism	ESCHERICHIA COLI
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	ESCHERICHIA COLI

fit	/app/data/saxs_computation/gr/1gr5/1gr5.fit
pddf	/app/data/pr_computation/gr/1gr5/1gr5.pr.out
profile	/app/data/saxs_computation/gr/1gr5/1gr5.dat