2eq9

Crystal structure of lipoamide dehydrogenase from thermus thermophilus HB8 with psbdb

Method: X-RAY DIFFRACTION D_max: 218.2 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

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2eq9
沉积日期 deposition_date	2007-03-30
结构标题 title	Crystal structure of lipoamide dehydrogenase from thermus thermophilus HB8 with psbdb
关键词 keywords	;PROTEIN-PROTEIN COMPLEX, OXIDOREDUCTASE, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI ;; 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	67.61 Å
回转半径 Rg (电子) rg_electron	68.09 Å
零角强度 I(0) i0	2263780000.00
分子量 molecular_weight	409460.0 kDa
排除体积 excluded_volume	517210 Å³
包络体积 envelope_volume	739150 Å³
水化壳体积 shell_volume	97887 Å³
包络直径 envelope_diameter	242.9 Å
壳层 Rg shell_rg	59.53 Å
包络 Rg envelope_rg	66.59 Å
形状 Rg shape_rg	68.08 Å
总 Rg total_rg	67.94 Å
总原子数 total_atoms	28820
残基数 n_residues	3816
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	218.2 Å
Rg (实空间) rg_real	67.93 Å
Rg 误差 (实空间) rg_real_error	2.04 Å
I(0) (实空间) i0_real	2.2630e+09
I(0) 误差 (实空间) i0_real_error	5.3000e+07
Rg (倒空间) rg_reciprocal	66.29 Å
I(0) (倒空间) i0_reciprocal	2257000000.0000
解质量估计 total_estimate	0.7958
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	85.4 Å
偏度 Skewness skewness	0.519
峰度 Kurtosis kurtosis	-0.198
角度范围 angular_range	— – 0.1150 Å⁻¹
当前正则化参数 α current_alpha	0.0003
最高正则化参数 α highest_alpha	93020000.0000
实空间数据点数 n_real_points	24
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.789; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.897; Smooth: 0.079

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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	Pyruvate dehydrogenase complex, dihydrolipoamide dehydrogenase E3 component
分子量 formula_weight	49151.8 kDa
EC 编号 ec_number	1.8.1.4
来源方法 src_method	man
拷贝数 entity_count	8

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,D,E,G,H,J,K
原子数 atom_count	29827

MTPMKTYDLIVIGTGPGGYHAAIRAAQLGLKVLAVEAGEVGGVCLNVGCIPTKALLHAAETLHHLKVAEGFGLKAKPELDLKKLGGWRDQVVKKLTGGVGTLLKGNGVELLRGFARLVGPKEVEVGGERYGAKSLILATGSEPLELKGFPFGEDVWDSTRALKVEEGLPKRLLVIGGGAVGLELGQVYRRLGAEVTLIEYMPEILPQGDPETAALLRRALEKEGIRVRTKTKAVGYEKKKDGLHVRLEPAEGGEGEEVVVDKVLVAVGRKPRTEGLGLEKAGVKVDERGFIRVNARMETSVPGVYAIGDAARPPLLAHKAMREGLIAAENAAGKDSAFDYQVPSVVYTSPEWAGVGLTEEEAKRAGYKVKVGKFPLAASGRALTLGGAEGMVKVVGDEETDLLLGVFIVGPQAGELIAEAALALEMGATLTDLALTVHPHPTLSESLMEAAEAFHKQAIHILNR

来源 Source

来源生物 organism	Thermus thermophilus
NCBI 分类编号 ncbi_taxonomy_id	300852
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	Pyruvate dehydrogenase complex, dihydrolipoamide acetyltransferase E2 component
分子量 formula_weight	4450.2 kDa
EC 编号 ec_number	2.3.1.168
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C,F,I,L

MLAVPAARKLARELGIPIEEVPGSGPLGRVRVEDVRAYAER

来源 Source

来源生物 organism	Thermus thermophilus
NCBI 分类编号 ncbi_taxonomy_id	300852
宿主生物 host_organism	Escherichia coli

Entity 3 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	8

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	1007

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6. 折叠分类 (SCOP + CATH) 32 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d2eq9c_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.9 — Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
超家族 Superfamily superfamily	a.9.1 — Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
家族 Family family	a.9.1.0 — automated matches

结构域编号 domain_id	d2eq9f_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.9 — Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
超家族 Superfamily superfamily	a.9.1 — Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
家族 Family family	a.9.1.0 — automated matches

结构域编号 domain_id	d2eq9i_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.9 — Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
超家族 Superfamily superfamily	a.9.1 — Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
家族 Family family	a.9.1.0 — automated matches

结构域编号 domain_id	d2eq9l_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.9 — Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
超家族 Superfamily superfamily	a.9.1 — Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
家族 Family family	a.9.1.0 — automated matches

CATH v4.4 (28 domains)

结构域编号 domain_id	2eq9A01
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	2eq9A02
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	2eq9A03
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	2eq9B01
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	2eq9B02
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	2eq9B03
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	2eq9C00
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	320 — Dihydrolipoamide Transferase
同源超家族 H-superfamily homologous superfamily	10 — E3-binding domain

结构域编号 domain_id	2eq9D01
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	2eq9D02
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	2eq9D03
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	2eq9E01
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	2eq9E02
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	2eq9E03
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	2eq9F00
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	320 — Dihydrolipoamide Transferase
同源超家族 H-superfamily homologous superfamily	10 — E3-binding domain

结构域编号 domain_id	2eq9G01
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	2eq9G02
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	2eq9G03
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	2eq9H01
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	2eq9H02
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	2eq9H03
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	2eq9I00
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	320 — Dihydrolipoamide Transferase
同源超家族 H-superfamily homologous superfamily	10 — E3-binding domain

结构域编号 domain_id	2eq9J01
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	2eq9J02
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	2eq9J03
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	2eq9K01
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	2eq9K02
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	2eq9K03
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	2eq9L00
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	320 — Dihydrolipoamide Transferase
同源超家族 H-superfamily homologous superfamily	10 — E3-binding domain

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7. 引用文献 (1)

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晶胞边长 a length_a	88.781 Å
晶胞边长 b length_b	88.877 Å
晶胞边长 c length_c	144.149 Å
晶胞夹角 α angle_alpha	89.26 °
晶胞夹角 β angle_beta	87.01 °
晶胞夹角 γ angle_gamma	70.84 °
晶胞分子数 Z z_pdb	8

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

分辨率 resolution	2.090 Å
最低分辨率 resolution_low	43.620 Å
R 因子 r_factor	0.2170
R_work r_work	0.2170
R_free r_free	0.2570

fit	/app/data/saxs_computation/eq/2eq9/2eq9.fit
pddf	/app/data/pr_computation/eq/2eq9/2eq9.pr.out
profile	/app/data/saxs_computation/eq/2eq9/2eq9.dat

Crystal structure of lipoamide dehydrogenase from thermus thermophilus HB8 with psbdb

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 (4)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

Entity 4 water

6. 折叠分类 (SCOP + CATH) 32 domains

SCOP 2.08 (4 domains)

CATH v4.4 (28 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)