1tyf

THE STRUCTURE OF CLPP AT 2.3 ANGSTROM RESOLUTION SUGGESTS A MODEL FOR ATP-DEPENDENT PROTEOLYSIS

Method: X-RAY DIFFRACTION D_max: 110.2 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	1tyf
沉积日期 deposition_date	1997-10-13
结构标题 title	THE STRUCTURE OF CLPP AT 2.3 ANGSTROM RESOLUTION SUGGESTS A MODEL FOR ATP-DEPENDENT PROTEOLYSIS
关键词 keywords	PEPTIDASE; PEPTIDASE
实验方法 method	X-RAY DIFFRACTION

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	43.27 Å
回转半径 Rg (电子) rg_electron	42.38 Å
零角强度 I(0) i0	1232810000.00
分子量 molecular_weight	286430.0 kDa
排除体积 excluded_volume	357630 Å³
包络体积 envelope_volume	509150 Å³
水化壳体积 shell_volume	96942 Å³
包络直径 envelope_diameter	120.3 Å
壳层 Rg shell_rg	51.83 Å
包络 Rg envelope_rg	39.44 Å
形状 Rg shape_rg	42.41 Å
总 Rg total_rg	42.74 Å
总原子数 total_atoms	20062
残基数 n_residues	2562
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	110.2 Å
Rg (实空间) rg_real	42.82 Å
Rg 误差 (实空间) rg_real_error	0.54 Å
I(0) (实空间) i0_real	1.2330e+09
I(0) 误差 (实空间) i0_real_error	2.0150e+07
Rg (倒空间) rg_reciprocal	43.27 Å
I(0) (倒空间) i0_reciprocal	1233000000.0000
解质量估计 total_estimate	0.8349
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	64.3 Å
偏度 Skewness skewness	-0.239
峰度 Kurtosis kurtosis	-0.607
角度范围 angular_range	— – 0.1800 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	792700000.0000
实空间数据点数 n_real_points	37
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.953; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.001

▶

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

▶

5. 实体与聚合体信息 (2)

▼

6. 折叠分类 (SCOP + CATH) 28 domains

SCOP 2.08 (14 domains)

结构域编号 domain_id	d1tyfa_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.14 — ClpP/crotonase
超家族 Superfamily superfamily	c.14.1 — ClpP/crotonase
家族 Family family	c.14.1.1 — Clp protease, ClpP subunit

结构域编号 domain_id	d1tyfb_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.14 — ClpP/crotonase
超家族 Superfamily superfamily	c.14.1 — ClpP/crotonase
家族 Family family	c.14.1.1 — Clp protease, ClpP subunit

结构域编号 domain_id	d1tyfc_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.14 — ClpP/crotonase
超家族 Superfamily superfamily	c.14.1 — ClpP/crotonase
家族 Family family	c.14.1.1 — Clp protease, ClpP subunit

结构域编号 domain_id	d1tyfd_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.14 — ClpP/crotonase
超家族 Superfamily superfamily	c.14.1 — ClpP/crotonase
家族 Family family	c.14.1.1 — Clp protease, ClpP subunit

结构域编号 domain_id	d1tyfe_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.14 — ClpP/crotonase
超家族 Superfamily superfamily	c.14.1 — ClpP/crotonase
家族 Family family	c.14.1.1 — Clp protease, ClpP subunit

结构域编号 domain_id	d1tyff_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.14 — ClpP/crotonase
超家族 Superfamily superfamily	c.14.1 — ClpP/crotonase
家族 Family family	c.14.1.1 — Clp protease, ClpP subunit

结构域编号 domain_id	d1tyfg_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.14 — ClpP/crotonase
超家族 Superfamily superfamily	c.14.1 — ClpP/crotonase
家族 Family family	c.14.1.1 — Clp protease, ClpP subunit

结构域编号 domain_id	d1tyfh_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.14 — ClpP/crotonase
超家族 Superfamily superfamily	c.14.1 — ClpP/crotonase
家族 Family family	c.14.1.1 — Clp protease, ClpP subunit

结构域编号 domain_id	d1tyfi_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.14 — ClpP/crotonase
超家族 Superfamily superfamily	c.14.1 — ClpP/crotonase
家族 Family family	c.14.1.1 — Clp protease, ClpP subunit

结构域编号 domain_id	d1tyfj_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.14 — ClpP/crotonase
超家族 Superfamily superfamily	c.14.1 — ClpP/crotonase
家族 Family family	c.14.1.1 — Clp protease, ClpP subunit

结构域编号 domain_id	d1tyfk_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.14 — ClpP/crotonase
超家族 Superfamily superfamily	c.14.1 — ClpP/crotonase
家族 Family family	c.14.1.1 — Clp protease, ClpP subunit

结构域编号 domain_id	d1tyfl_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.14 — ClpP/crotonase
超家族 Superfamily superfamily	c.14.1 — ClpP/crotonase
家族 Family family	c.14.1.1 — Clp protease, ClpP subunit

结构域编号 domain_id	d1tyfm_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.14 — ClpP/crotonase
超家族 Superfamily superfamily	c.14.1 — ClpP/crotonase
家族 Family family	c.14.1.1 — Clp protease, ClpP subunit

结构域编号 domain_id	d1tyfn_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.14 — ClpP/crotonase
超家族 Superfamily superfamily	c.14.1 — ClpP/crotonase
家族 Family family	c.14.1.1 — Clp protease, ClpP subunit

CATH v4.4 (14 domains)

结构域编号 domain_id	1tyfA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

结构域编号 domain_id	1tyfB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

结构域编号 domain_id	1tyfC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

结构域编号 domain_id	1tyfD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

结构域编号 domain_id	1tyfE00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

结构域编号 domain_id	1tyfF00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

结构域编号 domain_id	1tyfG00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

结构域编号 domain_id	1tyfH00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

结构域编号 domain_id	1tyfI00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

结构域编号 domain_id	1tyfJ00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

结构域编号 domain_id	1tyfK00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

结构域编号 domain_id	1tyfL00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

结构域编号 domain_id	1tyfM00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

结构域编号 domain_id	1tyfN00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

▶

7. 引用文献 (2)

▶

晶胞边长 a length_a	193.320 Å
晶胞边长 b length_b	102.460 Å
晶胞边长 c length_c	157.080 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	97.80 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	56

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	2.300 Å
最低分辨率 resolution_low	80.000 Å
R 因子 r_factor	0.2190
R_work r_work	0.2190
R_free r_free	0.2920

描述 description	CLP PEPTIDASE
分子量 formula_weight	21586.9 kDa
EC 编号 ec_number	3.4.21.92
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	21308

THE STRUCTURE OF CLPP AT 2.3 ANGSTROM RESOLUTION SUGGESTS A MODEL FOR ATP-DEPENDENT PROTEOLYSIS

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 (2)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 water

6. 折叠分类 (SCOP + CATH) 28 domains

SCOP 2.08 (14 domains)

CATH v4.4 (14 domains)

7. 引用文献 (2)

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

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	1246

fit	/app/data/saxs_computation/ty/1tyf/1tyf.fit
pddf	/app/data/pr_computation/ty/1tyf/1tyf.pr.out
profile	/app/data/saxs_computation/ty/1tyf/1tyf.dat