SAXSdb — 2eq8

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2eq8
沉积日期 deposition_date	2007-03-30
结构标题 title	Crystal structure of lipoamide dehydrogenase from thermus thermophilus HB8 with psbdp
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	49.45 Å
回转半径 Rg (电子) rg_electron	49.92 Å
零角强度 I(0) i0	588891000.00
分子量 molecular_weight	205150.0 kDa
排除体积 excluded_volume	258920 Å³
包络体积 envelope_volume	344130 Å³
水化壳体积 shell_volume	59353 Å³
包络直径 envelope_diameter	174.4 Å
壳层 Rg shell_rg	50.41 Å
包络 Rg envelope_rg	49.41 Å
形状 Rg shape_rg	49.92 Å
总 Rg total_rg	49.96 Å
总原子数 total_atoms	14438
残基数 n_residues	1906
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	173.8 Å
Rg (实空间) rg_real	49.99 Å
Rg 误差 (实空间) rg_real_error	1.68 Å
I(0) (实空间) i0_real	5.8890e+08
I(0) 误差 (实空间) i0_real_error	1.0390e+07
Rg (倒空间) rg_reciprocal	49.45 Å
I(0) (倒空间) i0_reciprocal	588500000.0000
解质量估计 total_estimate	0.5846
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	38.0 Å
偏度 Skewness skewness	0.440
峰度 Kurtosis kurtosis	-0.588
角度范围 angular_range	— – 0.1600 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	82090000.0000
实空间数据点数 n_real_points	33
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.655; Stabil: 1.000; Sysdev: 0.087; Positv: 1.000; Valcen: 0.679; Smooth: 0.691

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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	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,D,E
原子数 atom_count	16327

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	4292.9 kDa
EC 编号 ec_number	2.3.1.12
来源方法 src_method	syn
拷贝数 entity_count	2

聚合体 Polymer

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

PAAPSIRRLARELGVDLTRLRGTGLAGRITEEDVRRAAGL

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	4

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	1889

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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	2eq8A01
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	2eq8A02
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	2eq8A03
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	2eq8B01
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	2eq8B02
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	2eq8B03
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	2eq8D01
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	2eq8D02
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	2eq8D03
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	2eq8E01
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	2eq8E02
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	2eq8E03
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 (1)

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晶胞边长 a length_a	85.758 Å
晶胞边长 b length_b	104.082 Å
晶胞边长 c length_c	112.856 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	107.30 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

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	1.940 Å
最低分辨率 resolution_low	46.860 Å
R 因子 r_factor	0.2070
R_work r_work	0.2070
R_free r_free	0.2440

fit	/app/data/saxs_computation/eq/2eq8/2eq8.fit
pddf	/app/data/pr_computation/eq/2eq8/2eq8.pr.out
profile	/app/data/saxs_computation/eq/2eq8/2eq8.dat

Crystal structure of lipoamide dehydrogenase from thermus thermophilus HB8 with psbdp

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

Entity 3 non-polymer

Entity 4 water

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)