8i7x

Crystal structure of human ClpP in complex with ZG36

Method: X-RAY DIFFRACTION D_max: 111.5 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	8i7x
沉积日期 deposition_date	2023-02-02
结构标题 title	Crystal structure of human ClpP in complex with ZG36
关键词 keywords	mitochondrial protease, HYDROLASE; HYDROLASE
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	42.08 Å
回转半径 Rg (电子) rg_electron	41.15 Å
零角强度 I(0) i0	947041000.00
分子量 molecular_weight	260160.0 kDa
排除体积 excluded_volume	328570 Å³
包络体积 envelope_volume	453700 Å³
水化壳体积 shell_volume	88573 Å³
包络直径 envelope_diameter	117.2 Å
壳层 Rg shell_rg	50.92 Å
包络 Rg envelope_rg	38.36 Å
形状 Rg shape_rg	41.17 Å
总 Rg total_rg	41.59 Å
总原子数 total_atoms	18135
残基数 n_residues	2270
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	111.5 Å
Rg (实空间) rg_real	41.66 Å
Rg 误差 (实空间) rg_real_error	0.36 Å
I(0) (实空间) i0_real	9.4700e+08
I(0) 误差 (实空间) i0_real_error	1.2590e+07
Rg (倒空间) rg_reciprocal	42.08 Å
I(0) (倒空间) i0_reciprocal	947500000.0000
解质量估计 total_estimate	0.8538
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	64.5 Å
偏度 Skewness skewness	-0.289
峰度 Kurtosis kurtosis	-0.622
角度范围 angular_range	— – 0.1900 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	178200000.0000
实空间数据点数 n_real_points	39
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.900; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.398

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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	ATP-dependent Clp protease proteolytic subunit, mitochondrial
分子量 formula_weight	24189.9 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 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	18730

PLIPIVVEQTGRGERAYDIYSRLLRERIVCVMGPIDDSVASLVIAQLLFLQSESNKKPIHMYINSPGGVVTAGLAIYDTMQYILNPICTWCVGQAASMGSLLLAAGTPGMRHSLPNSRIMIHQPSGGARGQATDIAIQAEEIMKLKKQLYNIYAKHTKQSLQVIESAMERDRYMSPMEAQEFGILDKVLVHPPQDGEDEPTLVQKEPVEAAPAAEPVPAST

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	;(6S,9aS)-N-[(4-bromophenyl)methyl]-6-[(2S)-butan-2-yl]-8-[(4-methoxynaphthalen-1-yl)methyl]-4,7-bis(oxidanylidene)-3,6,9,9a-tetrahydro-2H-pyrazino[1,2-a]pyrimidine-1-carboxamide ;
分子量 formula_weight	607.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	14

Entity 3 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	595

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6. 折叠分类 (SCOP + CATH) 14 domains

CATH v4.4 (14 domains)

结构域编号 domain_id	8i7xA01
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	8i7xB01
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	8i7xC01
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	8i7xD01
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	8i7xE01
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	8i7xF01
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	8i7xG01
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	8i7xH01
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	8i7xI01
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	8i7xJ01
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	8i7xK01
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	8i7xL01
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	8i7xM01
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	8i7xN01
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

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7. 引用文献 (2)

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晶胞边长 a length_a	113.240 Å
晶胞边长 b length_b	96.080 Å
晶胞边长 c length_c	127.000 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	92.72 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	28

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	1.990 Å
最低分辨率 resolution_low	30.850 Å
R 因子 r_factor	0.2325
R_work r_work	0.2310
R_free r_free	0.2597

fit	/app/data/saxs_computation/i7/8i7x/8i7x.fit
pddf	/app/data/pr_computation/i7/8i7x/8i7x.pr.out
profile	/app/data/saxs_computation/i7/8i7x/8i7x.dat

Crystal structure of human ClpP in complex with ZG36

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