1gru

SOLUTION STRUCTURE OF GROES-ADP7-GROEL-ATP7 COMPLEX BY CRYO-EM

Method: ELECTRON MICROSCOPY D_max: 194.1 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

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1gru
沉积日期 deposition_date	2001-12-16
结构标题 title	SOLUTION STRUCTURE OF GROES-ADP7-GROEL-ATP7 COMPLEX BY CRYO-EM
关键词 keywords	CHAPERONE, CHAPERONIN, HSP60, GROEL-GROES, MOLECULAR CHAPERONE, ADP; CHAPERONE
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	68.80 Å
回转半径 Rg (电子) rg_electron	68.51 Å
零角强度 I(0) i0	9899920000.00
分子量 molecular_weight	838840.0 kDa
排除体积 excluded_volume	1051000 Å³
包络体积 envelope_volume	1811300 Å³
水化壳体积 shell_volume	213930 Å³
包络直径 envelope_diameter	209.5 Å
壳层 Rg shell_rg	77.46 Å
包络 Rg envelope_rg	64.54 Å
形状 Rg shape_rg	68.54 Å
总 Rg total_rg	68.55 Å
总原子数 total_atoms	58688
残基数 n_residues	8029
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	194.1 Å
Rg (实空间) rg_real	68.53 Å
Rg 误差 (实空间) rg_real_error	0.84 Å
I(0) (实空间) i0_real	9.8990e+09
I(0) 误差 (实空间) i0_real_error	1.9450e+08
Rg (倒空间) rg_reciprocal	69.63 Å
I(0) (倒空间) i0_reciprocal	9920000000.0000
解质量估计 total_estimate	0.8295
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	92.8 Å
偏度 Skewness skewness	0.130
峰度 Kurtosis kurtosis	-0.309
角度范围 angular_range	— – 0.1150 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	2757000000.0000
实空间数据点数 n_real_points	24
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: 0.941; Smooth: 0.043

▶

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

▶

5. 实体与聚合体信息 (2)

Entity 1 polymer

描述 description	GROEL
分子量 formula_weight	57260.5 kDa
来源方法 src_method	man
拷贝数 entity_count	14

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,I,J,K,L,M,N
原子数 atom_count	58688

AAKDVKFGNDARVKMLRGVNVLADAVKVTLGPKGRNVVLDKSFGAPTITKDGVSVAREIELEDKFENMGAQMVKEVASKANDAAGDGTTTATVLAQAIITEGLKAVAAGMNPMDLKRGIDKAVTAAVEELKALSVPCSDSKAIAQVGTISANSDETVGKLIAEAMDKVGKEGVITVEDGTGLQDELDVVEGMQFDRGYLSPYFINKPETGAVELESPFILLADKKISNIREMLPVLEAVAKAGKPLLIIAEDVEGEALATLVVNTMRGIVKVAAVKAPGFGDRRKAMLQDIATLTGGTVISEEIGMELEKATLEDLGQAKRVVINKDTTTIIDGVGEEAAIQGRVAQIRQQIEEATSDYDREKLQERVAKLAGGVAVIKVGAATEVEMKEKKARVEDALHATRAAVEEGVVAGGGVALIRVASKLADLRGQNEDQNVGIKVALRAMEAPLRQIVLNCGEEPSVVANTVKGGDGNYGYNAATEEYGNMIDMGILDPTKVTRSALQYAASVAGLMITTECMVTDLPKNDAADLGAAGGMGGMGGMGGMM

来源 Source

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

Entity 2 polymer

描述 description	GROES
分子量 formula_weight	10400.9 kDa
来源方法 src_method	man
拷贝数 entity_count	7

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	O,P,Q,R,S,T,U

MNIRPLHDRVIVKRKEVETKSAGGIVLTGSAAAKSTRGEVLAVGNGRILENGEVKPLDVKVGDIVIFNDGYGVKSEKIDNEEVLIMSESDILAIVEA

来源 Source

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

▼

6. 折叠分类 (SCOP + CATH) 21 domains

SCOP 2.08 (21 domains)

结构域编号 domain_id	d1grua_
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	d1grub_
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	d1gruc_
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	d1grud_
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	d1grue_
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	d1gruf_
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	d1grug_
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	d1gruh_
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	d1grui_
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	d1gruj_
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	d1gruk_
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	d1grul_
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	d1grum_
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	d1grun_
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	d1gruo_
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	d1grup_
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	d1gruq_
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	d1grur_
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	d1grus_
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	d1grut_
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	d1gruu_
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

▶

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	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	12.500 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	12.50 Å
分辨率测定方法 resolution_method	MODEL BASED ANGULAR REFINEMENT
颗粒数 num_particles	1448

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

SOLUTION STRUCTURE OF GROES-ADP7-GROEL-ATP7 COMPLEX BY CRYO-EM

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 (2)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

6. 折叠分类 (SCOP + CATH) 21 domains

SCOP 2.08 (21 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)