2eu1

Crystal structure of the chaperonin GroEL-E461K

Method: X-RAY DIFFRACTION D_max: 177.6 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	2eu1
沉积日期 deposition_date	2005-10-28
结构标题 title	Crystal structure of the chaperonin GroEL-E461K
关键词 keywords	chaperonin, GROEL, HSP60, E461K, CHAPERONE-PEPTIDE BINDING PROTEIN COMPLEX; CHAPERONE/PEPTIDE BINDING PROTEIN
实验方法 method	X-RAY DIFFRACTION

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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	66.29 Å
回转半径 Rg (电子) rg_electron	65.31 Å
零角强度 I(0) i0	8378960000.00
分子量 molecular_weight	771740.0 kDa
排除体积 excluded_volume	967360 Å³
包络体积 envelope_volume	1559700 Å³
水化壳体积 shell_volume	191920 Å³
包络直径 envelope_diameter	192.3 Å
壳层 Rg shell_rg	74.32 Å
包络 Rg envelope_rg	61.46 Å
形状 Rg shape_rg	65.31 Å
总 Rg total_rg	65.49 Å
总原子数 total_atoms	53970
残基数 n_residues	7336
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	177.6 Å
Rg (实空间) rg_real	65.96 Å
Rg 误差 (实空间) rg_real_error	0.67 Å
I(0) (实空间) i0_real	8.3790e+09
I(0) 误差 (实空间) i0_real_error	1.4230e+08
Rg (倒空间) rg_reciprocal	67.34 Å
I(0) (倒空间) i0_reciprocal	8399000000.0000
解质量估计 total_estimate	0.8400
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	96.2 Å
偏度 Skewness skewness	-0.060
峰度 Kurtosis kurtosis	-0.517
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	2560000000.0000
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: 0.981; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.973; Smooth: 0.001

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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) 42 domains

CATH v4.4 (42 domains)

结构域编号 domain_id	2eu1A01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	560 — GROEL; domain 1
同源超家族 H-superfamily homologous superfamily	10 — GroEL-like equatorial domain

结构域编号 domain_id	2eu1A02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	260 — GROEL; domain 2
同源超家族 H-superfamily homologous superfamily	10 — TCP-1-like chaperonin intermediate domain

结构域编号 domain_id	2eu1A03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	7 — GroEL
同源超家族 H-superfamily homologous superfamily	10 — GroEL

结构域编号 domain_id	2eu1B01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	560 — GROEL; domain 1
同源超家族 H-superfamily homologous superfamily	10 — GroEL-like equatorial domain

结构域编号 domain_id	2eu1B02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	260 — GROEL; domain 2
同源超家族 H-superfamily homologous superfamily	10 — TCP-1-like chaperonin intermediate domain

结构域编号 domain_id	2eu1B03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	7 — GroEL
同源超家族 H-superfamily homologous superfamily	10 — GroEL

结构域编号 domain_id	2eu1C01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	560 — GROEL; domain 1
同源超家族 H-superfamily homologous superfamily	10 — GroEL-like equatorial domain

结构域编号 domain_id	2eu1C02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	260 — GROEL; domain 2
同源超家族 H-superfamily homologous superfamily	10 — TCP-1-like chaperonin intermediate domain

结构域编号 domain_id	2eu1C03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	7 — GroEL
同源超家族 H-superfamily homologous superfamily	10 — GroEL

结构域编号 domain_id	2eu1D01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	560 — GROEL; domain 1
同源超家族 H-superfamily homologous superfamily	10 — GroEL-like equatorial domain

结构域编号 domain_id	2eu1D02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	260 — GROEL; domain 2
同源超家族 H-superfamily homologous superfamily	10 — TCP-1-like chaperonin intermediate domain

结构域编号 domain_id	2eu1D03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	7 — GroEL
同源超家族 H-superfamily homologous superfamily	10 — GroEL

结构域编号 domain_id	2eu1E01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	560 — GROEL; domain 1
同源超家族 H-superfamily homologous superfamily	10 — GroEL-like equatorial domain

结构域编号 domain_id	2eu1E02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	260 — GROEL; domain 2
同源超家族 H-superfamily homologous superfamily	10 — TCP-1-like chaperonin intermediate domain

结构域编号 domain_id	2eu1E03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	7 — GroEL
同源超家族 H-superfamily homologous superfamily	10 — GroEL

结构域编号 domain_id	2eu1F01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	560 — GROEL; domain 1
同源超家族 H-superfamily homologous superfamily	10 — GroEL-like equatorial domain

结构域编号 domain_id	2eu1F02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	260 — GROEL; domain 2
同源超家族 H-superfamily homologous superfamily	10 — TCP-1-like chaperonin intermediate domain

结构域编号 domain_id	2eu1F03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	7 — GroEL
同源超家族 H-superfamily homologous superfamily	10 — GroEL

结构域编号 domain_id	2eu1G01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	560 — GROEL; domain 1
同源超家族 H-superfamily homologous superfamily	10 — GroEL-like equatorial domain

结构域编号 domain_id	2eu1G02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	260 — GROEL; domain 2
同源超家族 H-superfamily homologous superfamily	10 — TCP-1-like chaperonin intermediate domain

结构域编号 domain_id	2eu1G03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	7 — GroEL
同源超家族 H-superfamily homologous superfamily	10 — GroEL

结构域编号 domain_id	2eu1H01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	560 — GROEL; domain 1
同源超家族 H-superfamily homologous superfamily	10 — GroEL-like equatorial domain

结构域编号 domain_id	2eu1H02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	260 — GROEL; domain 2
同源超家族 H-superfamily homologous superfamily	10 — TCP-1-like chaperonin intermediate domain

结构域编号 domain_id	2eu1H03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	7 — GroEL
同源超家族 H-superfamily homologous superfamily	10 — GroEL

结构域编号 domain_id	2eu1I01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	560 — GROEL; domain 1
同源超家族 H-superfamily homologous superfamily	10 — GroEL-like equatorial domain

结构域编号 domain_id	2eu1I02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	260 — GROEL; domain 2
同源超家族 H-superfamily homologous superfamily	10 — TCP-1-like chaperonin intermediate domain

结构域编号 domain_id	2eu1I03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	7 — GroEL
同源超家族 H-superfamily homologous superfamily	10 — GroEL

结构域编号 domain_id	2eu1J01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	560 — GROEL; domain 1
同源超家族 H-superfamily homologous superfamily	10 — GroEL-like equatorial domain

结构域编号 domain_id	2eu1J02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	260 — GROEL; domain 2
同源超家族 H-superfamily homologous superfamily	10 — TCP-1-like chaperonin intermediate domain

结构域编号 domain_id	2eu1J03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	7 — GroEL
同源超家族 H-superfamily homologous superfamily	10 — GroEL

结构域编号 domain_id	2eu1K01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	560 — GROEL; domain 1
同源超家族 H-superfamily homologous superfamily	10 — GroEL-like equatorial domain

结构域编号 domain_id	2eu1K02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	260 — GROEL; domain 2
同源超家族 H-superfamily homologous superfamily	10 — TCP-1-like chaperonin intermediate domain

结构域编号 domain_id	2eu1K03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	7 — GroEL
同源超家族 H-superfamily homologous superfamily	10 — GroEL

结构域编号 domain_id	2eu1L01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	560 — GROEL; domain 1
同源超家族 H-superfamily homologous superfamily	10 — GroEL-like equatorial domain

结构域编号 domain_id	2eu1L02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	260 — GROEL; domain 2
同源超家族 H-superfamily homologous superfamily	10 — TCP-1-like chaperonin intermediate domain

结构域编号 domain_id	2eu1L03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	7 — GroEL
同源超家族 H-superfamily homologous superfamily	10 — GroEL

结构域编号 domain_id	2eu1M01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	560 — GROEL; domain 1
同源超家族 H-superfamily homologous superfamily	10 — GroEL-like equatorial domain

结构域编号 domain_id	2eu1M02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	260 — GROEL; domain 2
同源超家族 H-superfamily homologous superfamily	10 — TCP-1-like chaperonin intermediate domain

结构域编号 domain_id	2eu1M03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	7 — GroEL
同源超家族 H-superfamily homologous superfamily	10 — GroEL

结构域编号 domain_id	2eu1N01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	560 — GROEL; domain 1
同源超家族 H-superfamily homologous superfamily	10 — GroEL-like equatorial domain

结构域编号 domain_id	2eu1N02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	260 — GROEL; domain 2
同源超家族 H-superfamily homologous superfamily	10 — TCP-1-like chaperonin intermediate domain

结构域编号 domain_id	2eu1N03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	7 — GroEL
同源超家族 H-superfamily homologous superfamily	10 — GroEL

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7. 引用文献 (8)

Crystal structure of the temperature-sensitive and allosteric-defective chaperonin GroEL(E461K).

J.Struct.Biol. (2006)

PMID: 16904907 · DOI: 10.1016/j.jsb.2006.06.008 PRIMARY

Crystal structure of wild-type chaperonin GROEL

J.Mol.Biol. (2005)

PMID: 16288915 · DOI: 10.1016/j.jmb.2005.09.096

;Ionic interactions at both inter-ring contact sites of GroEL are involved in transmission of the allosteric signal: a time-resolved infrared difference study ;

Protein Sci. (2005)

PMID: 16081650 · DOI: 10.1110/ps.051469605

A mutant chaperonin with rearranged inter-ring electrostatic contacts and temperature-sensitive dissociation

Nat.Struct.Mol.Biol. (2004)

PMID: 15475965 · DOI: 10.1038/nsmb844

GroEL stability and function. Contribution of the ionic interactions at the inter-ring contact sites

J.Biol.Chem. (2003)

PMID: 12796493 · DOI: 10.1074/jbc.M303958200

Salt bridges at the inter-ring interface regulate the thermostat of GroEL

J.Biol.Chem. (2002)

PMID: 12110685 · DOI: 10.1074/jbc.M205733200

The crystal structure of the asymmetric GroEL-GroES-(ADP)7 chaperonin complex

Nature (1997)

PMID: 9285585 · DOI: 10.1038/41944

Conformational variability in the refined structure of the chaperonin GroEL at 2.8 A resolution

Nature (1995)

PMID: 8846220 · DOI: 10.1038/nsb1295-1083

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晶胞边长 a length_a	267.695 Å
晶胞边长 b length_b	290.641 Å
晶胞边长 c length_c	247.006 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	112

空间群 space_group	C 2 2 21
空间群编号 int_tables_number	20
晶系 crystal_system	—

分辨率 resolution	3.290 Å
最低分辨率 resolution_low	15.000 Å
R 因子 r_factor	0.2760
R_work r_work	0.2760
R_free r_free	0.2960

描述 description	GROEL
分子量 formula_weight	57391.8 kDa
突变 mutation	E461K
来源方法 src_method	man
拷贝数 entity_count	14

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	53970

Crystal structure of the chaperonin GroEL-E461K

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

衍射实验 Diffraction

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) 42 domains

CATH v4.4 (42 domains)

7. 引用文献 (8)

8. 文件与曲线 (10)

Files (7)

Curves (3)

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/eu/2eu1/2eu1.fit
pddf	/app/data/pr_computation/eu/2eu1/2eu1.pr.out
profile	/app/data/saxs_computation/eu/2eu1/2eu1.dat