8hla

;Heteromeric ring comprised of peroxiredoxin from Thermococcus kodakaraensis (TkPrx) F42C/C46S/C205S/C211S mutant modified with 2-(bromoacetyl)naphthalene (Naph@TkPrxF42C) and TkPrx C46S/F76C/C205S/C211S mutant modified with 2-(bromoacetyl)naphthalene (Naph@TkPrxF76C) (Naph@(MIX|3:3)) ;

Method: ELECTRON MICROSCOPY D_max: 162.7 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	8hla
沉积日期 deposition_date	2022-11-29
结构标题 title	;Heteromeric ring comprised of peroxiredoxin from Thermococcus kodakaraensis (TkPrx) F42C/C46S/C205S/C211S mutant modified with 2-(bromoacetyl)naphthalene (Naph@TkPrxF42C) and TkPrx C46S/F76C/C205S/C211S mutant modified with 2-(bromoacetyl)naphthalene (Naph@TkPrxF76C) (Naph@(MIX\|3:3)) ;
关键词 keywords	Peroxiredoxin, Complex, Protein protein interactions, OXIDOREDUCTASE; OXIDOREDUCTASE
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	56.77 Å
回转半径 Rg (电子) rg_electron	55.97 Å
零角强度 I(0) i0	1081990000.00
分子量 molecular_weight	294830.0 kDa
排除体积 excluded_volume	375440 Å³
包络体积 envelope_volume	541660 Å³
水化壳体积 shell_volume	77229 Å³
包络直径 envelope_diameter	159.1 Å
壳层 Rg shell_rg	67.22 Å
包络 Rg envelope_rg	52.00 Å
形状 Rg shape_rg	56.00 Å
总 Rg total_rg	56.11 Å
总原子数 total_atoms	20868
残基数 n_residues	2580
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	162.7 Å
Rg (实空间) rg_real	56.48 Å
Rg 误差 (实空间) rg_real_error	1.31 Å
I(0) (实空间) i0_real	1.0820e+09
I(0) 误差 (实空间) i0_real_error	2.2470e+07
Rg (倒空间) rg_reciprocal	56.97 Å
I(0) (倒空间) i0_reciprocal	1083000000.0000
解质量估计 total_estimate	0.8081
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	98.8 Å
偏度 Skewness skewness	-0.183
峰度 Kurtosis kurtosis	-1.019
角度范围 angular_range	— – 0.1400 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	43060000.0000
实空间数据点数 n_real_points	29
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.742; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.282

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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	Peroxiredoxin
分子量 formula_weight	24585.1 kDa
EC 编号 ec_number	1.11.1.24
突变 mutation	C46S,F76C,C205S,C211S
来源方法 src_method	man
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,E,F,I,J
原子数 atom_count	20868

MVVIGEKFPEVEVKTTHGVIKLPDYFAEQGKWFVLFSHPADFTPVSTTEFYAMQKRVDQFRELGVEPIGLSVDQVCSHIKWMEWIKENLGEEITFPVIADDRGELADKLGMIPSGATITARAVFIVDDKGIIRAIVYYPAEVGRDWDEILRLVKALKVSDEKGVALPHKWPNNELIGDKAIVPPASTVDEVKQREEAKAKGEIESYDWWFSYKKLE

来源 Source

来源生物 organism	Thermococcus kodakarensis KOD1
NCBI 分类编号 ncbi_taxonomy_id	69014
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	Peroxiredoxin
分子量 formula_weight	24585.1 kDa
EC 编号 ec_number	1.11.1.24
突变 mutation	F42C,C46S,C205S,C211S
来源方法 src_method	man
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C,D,G,H,K,L

MVVIGEKFPEVEVKTTHGVIKLPDYFAEQGKWFVLFSHPADCTPVSTTEFYAMQKRVDQFRELGVEPIGLSVDQVFSHIKWMEWIKENLGEEITFPVIADDRGELADKLGMIPSGATITARAVFIVDDKGIIRAIVYYPAEVGRDWDEILRLVKALKVSDEKGVALPHKWPNNELIGDKAIVPPASTVDEVKQREEAKAKGEIESYDWWFSYKKLE

来源 Source

来源生物 organism	Thermococcus kodakarensis KOD1
NCBI 分类编号 ncbi_taxonomy_id	69014
宿主生物 host_organism	Escherichia coli

Entity 3 non-polymer

描述 description	1-naphthalen-2-ylethanone
分子量 formula_weight	170.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	12

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6. 折叠分类 (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

结构域编号 domain_id	8hlaA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	30 — Glutaredoxin
同源超家族 H-superfamily homologous superfamily	10 — Glutaredoxin

结构域编号 domain_id	8hlaB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	30 — Glutaredoxin
同源超家族 H-superfamily homologous superfamily	10 — Glutaredoxin

结构域编号 domain_id	8hlaC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	30 — Glutaredoxin
同源超家族 H-superfamily homologous superfamily	10 — Glutaredoxin

结构域编号 domain_id	8hlaD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	30 — Glutaredoxin
同源超家族 H-superfamily homologous superfamily	10 — Glutaredoxin

结构域编号 domain_id	8hlaE01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	30 — Glutaredoxin
同源超家族 H-superfamily homologous superfamily	10 — Glutaredoxin

结构域编号 domain_id	8hlaF01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	30 — Glutaredoxin
同源超家族 H-superfamily homologous superfamily	10 — Glutaredoxin

结构域编号 domain_id	8hlaG01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	30 — Glutaredoxin
同源超家族 H-superfamily homologous superfamily	10 — Glutaredoxin

结构域编号 domain_id	8hlaH01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	30 — Glutaredoxin
同源超家族 H-superfamily homologous superfamily	10 — Glutaredoxin

结构域编号 domain_id	8hlaI01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	30 — Glutaredoxin
同源超家族 H-superfamily homologous superfamily	10 — Glutaredoxin

结构域编号 domain_id	8hlaJ01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	30 — Glutaredoxin
同源超家族 H-superfamily homologous superfamily	10 — Glutaredoxin

结构域编号 domain_id	8hlaK01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	30 — Glutaredoxin
同源超家族 H-superfamily homologous superfamily	10 — Glutaredoxin

结构域编号 domain_id	8hlaL01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	30 — Glutaredoxin
同源超家族 H-superfamily homologous superfamily	10 — Glutaredoxin

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7. 引用文献 (1)

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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	—

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

分辨率 resolution	2.81 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	599283

fit	/app/data/saxs_computation/hl/8hla/8hla.fit
pddf	/app/data/pr_computation/hl/8hla/8hla.pr.out
profile	/app/data/saxs_computation/hl/8hla/8hla.dat

;Heteromeric ring comprised of peroxiredoxin from Thermococcus kodakaraensis (TkPrx) F42C/C46S/C205S/C211S mutant modified with 2-(bromoacetyl)naphthalene (Naph@TkPrxF42C) and TkPrx C46S/F76C/C205S/C211S mutant modified with 2-(bromoacetyl)naphthalene (Naph@TkPrxF76C) (Naph@(MIX|3:3)) ;

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

冷冻电镜 EM 3D

5. 实体与聚合体信息 (3)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

6. 折叠分类 (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)

;Heteromeric ring comprised of peroxiredoxin from Thermococcus kodakaraensis (TkPrx) F42C/C46S/C205S/C211S mutant modified with 2-(bromoacetyl)naphthalene (Naph@TkPrx*F42C) and TkPrx C46S/F76C/C205S/C211S mutant modified with 2-(bromoacetyl)naphthalene (Naph@TkPrx*F76C) (Naph@(MIX|3:3)) ;

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

冷冻电镜 EM 3D

5. 实体与聚合体信息 (3)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

6. 折叠分类 (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)

;Heteromeric ring comprised of peroxiredoxin from Thermococcus kodakaraensis (TkPrx) F42C/C46S/C205S/C211S mutant modified with 2-(bromoacetyl)naphthalene (Naph@TkPrxF42C) and TkPrx C46S/F76C/C205S/C211S mutant modified with 2-(bromoacetyl)naphthalene (Naph@TkPrxF76C) (Naph@(MIX|3:3)) ;