1h6v

Mammalian thioredoxin reductase

Method: X-RAY DIFFRACTION D_max: 198.5 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	1h6v
沉积日期 deposition_date	2001-06-27
结构标题 title	Mammalian thioredoxin reductase
关键词 keywords	OXIDOREDUCTASE, PYRIDINE NUCLEOTIDE-DISULFIDE OXIDOREDUCTASE, FLAVOPROTEIN; OXIDOREDUCTASE
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	55.86 Å
回转半径 Rg (电子) rg_electron	56.62 Å
零角强度 I(0) i0	1569800000.00
分子量 molecular_weight	328790.0 kDa
排除体积 excluded_volume	410760 Å³
包络体积 envelope_volume	559840 Å³
水化壳体积 shell_volume	88328 Å³
包络直径 envelope_diameter	216.7 Å
壳层 Rg shell_rg	52.93 Å
包络 Rg envelope_rg	55.92 Å
形状 Rg shape_rg	56.62 Å
总 Rg total_rg	56.54 Å
总原子数 total_atoms	23066
残基数 n_residues	2927
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	198.5 Å
Rg (实空间) rg_real	56.44 Å
Rg 误差 (实空间) rg_real_error	2.39 Å
I(0) (实空间) i0_real	1.5700e+09
I(0) 误差 (实空间) i0_real_error	3.6410e+07
Rg (倒空间) rg_reciprocal	55.36 Å
I(0) (倒空间) i0_reciprocal	1567000000.0000
解质量估计 total_estimate	0.7941
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	49.6 Å
偏度 Skewness skewness	0.622
峰度 Kurtosis kurtosis	-0.194
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	164400000.0000
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: 0.644; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.841; Smooth: 0.550

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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 (4)

Entity 1 polymer

描述 description	THIOREDOXIN REDUCTASE
分子量 formula_weight	54646.3 kDa
EC 编号 ec_number	1.6.4.5
突变 mutation	YES
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,C,D,E,F
原子数 atom_count	23075

MNDSKDAPKSYDFDLIIIGGGSGGLAAAKEAAKFDKKVMVLDFVTPTPLGTNWGLGGTCVNVGCIPKKLMHQAALLGQALKDSRNYGWKLEDTVKHDWEKMTESVQNHIGSLNWGYRVALREKKVVYENAYGKFIGPHKIMATNNKGKEKVYSAERFLIATGERPRYLGIPGDKEYCISSDDLFSLPYCPGKTLVVGASYVALECAGFLAGIGLDVTVMVRSILLRGFDQDMANKIGEHMEEHGIKFIRQFVPTKIEQIEAGTPGRLKVTAKSTNSEETIEDEFNTVLLAVGRDSCTRTIGLETVGVKINEKTGKIPVTDEEQTNVPYIYAIGDILEGKLELTPVAIQAGRLLAQRLYGGSTVKCDYDNVPTTVFTPLEYGCCGLSEEKAVEKFGEENIEVYHSFFWPLEWTVPSRDNNKCYAKVICNLKDNERVVGFHVLGPNAGEVTQGFAAALKCGLTKQQLDSTIGIHPVCAEIFTTLSVTKRSGGDILQSGCCG

来源 Source

来源生物 organism	RATTUS NORVEGICUS
通用名 common_name	RAT
NCBI 分类编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 non-polymer

描述 description	FLAVIN-ADENINE DINUCLEOTIDE
分子量 formula_weight	785.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

Entity 3 non-polymer

描述 description	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
分子量 formula_weight	745.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

Entity 4 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	9

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6. 折叠分类 (SCOP + CATH) 36 domains

SCOP 2.08 (18 domains)

结构域编号 domain_id	d1h6va1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.3 — FAD/NAD(P)-binding domain
超家族 Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
家族 Family family	c.3.1.5 — FAD/NAD-linked reductases, N-terminal and central domains

结构域编号 domain_id	d1h6va2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.3 — FAD/NAD(P)-binding domain
超家族 Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
家族 Family family	c.3.1.5 — FAD/NAD-linked reductases, N-terminal and central domains

结构域编号 domain_id	d1h6va3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.87 — CO dehydrogenase flavoprotein C-domain-like
超家族 Superfamily superfamily	d.87.1 — FAD/NAD-linked reductases, dimerisation (C-terminal) domain
家族 Family family	d.87.1.1 — FAD/NAD-linked reductases, dimerisation (C-terminal) domain

结构域编号 domain_id	d1h6vb1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.3 — FAD/NAD(P)-binding domain
超家族 Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
家族 Family family	c.3.1.5 — FAD/NAD-linked reductases, N-terminal and central domains

结构域编号 domain_id	d1h6vb2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.3 — FAD/NAD(P)-binding domain
超家族 Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
家族 Family family	c.3.1.5 — FAD/NAD-linked reductases, N-terminal and central domains

结构域编号 domain_id	d1h6vb3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.87 — CO dehydrogenase flavoprotein C-domain-like
超家族 Superfamily superfamily	d.87.1 — FAD/NAD-linked reductases, dimerisation (C-terminal) domain
家族 Family family	d.87.1.1 — FAD/NAD-linked reductases, dimerisation (C-terminal) domain

结构域编号 domain_id	d1h6vc1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.3 — FAD/NAD(P)-binding domain
超家族 Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
家族 Family family	c.3.1.5 — FAD/NAD-linked reductases, N-terminal and central domains

结构域编号 domain_id	d1h6vc2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.3 — FAD/NAD(P)-binding domain
超家族 Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
家族 Family family	c.3.1.5 — FAD/NAD-linked reductases, N-terminal and central domains

结构域编号 domain_id	d1h6vc3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.87 — CO dehydrogenase flavoprotein C-domain-like
超家族 Superfamily superfamily	d.87.1 — FAD/NAD-linked reductases, dimerisation (C-terminal) domain
家族 Family family	d.87.1.1 — FAD/NAD-linked reductases, dimerisation (C-terminal) domain

结构域编号 domain_id	d1h6vd1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.3 — FAD/NAD(P)-binding domain
超家族 Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
家族 Family family	c.3.1.5 — FAD/NAD-linked reductases, N-terminal and central domains

结构域编号 domain_id	d1h6vd2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.3 — FAD/NAD(P)-binding domain
超家族 Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
家族 Family family	c.3.1.5 — FAD/NAD-linked reductases, N-terminal and central domains

结构域编号 domain_id	d1h6vd3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.87 — CO dehydrogenase flavoprotein C-domain-like
超家族 Superfamily superfamily	d.87.1 — FAD/NAD-linked reductases, dimerisation (C-terminal) domain
家族 Family family	d.87.1.1 — FAD/NAD-linked reductases, dimerisation (C-terminal) domain

结构域编号 domain_id	d1h6ve1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.3 — FAD/NAD(P)-binding domain
超家族 Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
家族 Family family	c.3.1.5 — FAD/NAD-linked reductases, N-terminal and central domains

结构域编号 domain_id	d1h6ve2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.3 — FAD/NAD(P)-binding domain
超家族 Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
家族 Family family	c.3.1.5 — FAD/NAD-linked reductases, N-terminal and central domains

结构域编号 domain_id	d1h6ve3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.87 — CO dehydrogenase flavoprotein C-domain-like
超家族 Superfamily superfamily	d.87.1 — FAD/NAD-linked reductases, dimerisation (C-terminal) domain
家族 Family family	d.87.1.1 — FAD/NAD-linked reductases, dimerisation (C-terminal) domain

结构域编号 domain_id	d1h6vf1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.3 — FAD/NAD(P)-binding domain
超家族 Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
家族 Family family	c.3.1.5 — FAD/NAD-linked reductases, N-terminal and central domains

结构域编号 domain_id	d1h6vf2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.3 — FAD/NAD(P)-binding domain
超家族 Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
家族 Family family	c.3.1.5 — FAD/NAD-linked reductases, N-terminal and central domains

结构域编号 domain_id	d1h6vf3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.87 — CO dehydrogenase flavoprotein C-domain-like
超家族 Superfamily superfamily	d.87.1 — FAD/NAD-linked reductases, dimerisation (C-terminal) domain
家族 Family family	d.87.1.1 — FAD/NAD-linked reductases, dimerisation (C-terminal) domain

CATH v4.4 (18 domains)

结构域编号 domain_id	1h6vA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	50 — FAD/NAD(P)-binding domain
同源超家族 H-superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

结构域编号 domain_id	1h6vA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	50 — FAD/NAD(P)-binding domain
同源超家族 H-superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

结构域编号 domain_id	1h6vA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	390 — Enolase-like; domain 1
同源超家族 H-superfamily homologous superfamily	30 — FAD/NAD-linked reductase, C-terminal dimerisation domain

结构域编号 domain_id	1h6vB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	50 — FAD/NAD(P)-binding domain
同源超家族 H-superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

结构域编号 domain_id	1h6vB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	50 — FAD/NAD(P)-binding domain
同源超家族 H-superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

结构域编号 domain_id	1h6vB03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	390 — Enolase-like; domain 1
同源超家族 H-superfamily homologous superfamily	30 — FAD/NAD-linked reductase, C-terminal dimerisation domain

结构域编号 domain_id	1h6vC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	50 — FAD/NAD(P)-binding domain
同源超家族 H-superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

结构域编号 domain_id	1h6vC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	50 — FAD/NAD(P)-binding domain
同源超家族 H-superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

结构域编号 domain_id	1h6vC03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	390 — Enolase-like; domain 1
同源超家族 H-superfamily homologous superfamily	30 — FAD/NAD-linked reductase, C-terminal dimerisation domain

结构域编号 domain_id	1h6vD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	50 — FAD/NAD(P)-binding domain
同源超家族 H-superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

结构域编号 domain_id	1h6vD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	50 — FAD/NAD(P)-binding domain
同源超家族 H-superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

结构域编号 domain_id	1h6vD03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	390 — Enolase-like; domain 1
同源超家族 H-superfamily homologous superfamily	30 — FAD/NAD-linked reductase, C-terminal dimerisation domain

结构域编号 domain_id	1h6vE01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	50 — FAD/NAD(P)-binding domain
同源超家族 H-superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

结构域编号 domain_id	1h6vE02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	50 — FAD/NAD(P)-binding domain
同源超家族 H-superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

结构域编号 domain_id	1h6vE03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	390 — Enolase-like; domain 1
同源超家族 H-superfamily homologous superfamily	30 — FAD/NAD-linked reductase, C-terminal dimerisation domain

结构域编号 domain_id	1h6vF01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	50 — FAD/NAD(P)-binding domain
同源超家族 H-superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

结构域编号 domain_id	1h6vF02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	50 — FAD/NAD(P)-binding domain
同源超家族 H-superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

结构域编号 domain_id	1h6vF03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	390 — Enolase-like; domain 1
同源超家族 H-superfamily homologous superfamily	30 — FAD/NAD-linked reductase, C-terminal dimerisation domain

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7. 引用文献 (2)

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晶胞边长 a length_a	78.920 Å
晶胞边长 b length_b	140.464 Å
晶胞边长 c length_c	170.832 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	94.64 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	12

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	3.000 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	0.2256
R_work r_work	0.2236
R_free r_free	0.2630

fit	/app/data/saxs_computation/h6/1h6v/1h6v.fit
pddf	/app/data/pr_computation/h6/1h6v/1h6v.pr.out
profile	/app/data/saxs_computation/h6/1h6v/1h6v.dat