SAXSdb — 1y8p

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1y8p
沉积日期 deposition_date	2004-12-13
结构标题 title	Crystal structure of the PDK3-L2 complex
关键词 keywords	pyruvate dehydrogenase kinase 3, lipoyl-bearing domain, protein-protein complex, TRANSFERASE; TRANSFERASE
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	26.67 Å
回转半径 Rg (电子) rg_electron	25.76 Å
零角强度 I(0) i0	48410700.00
分子量 molecular_weight	55184.0 kDa
排除体积 excluded_volume	69537 Å³
包络体积 envelope_volume	89629 Å³
水化壳体积 shell_volume	29233 Å³
包络直径 envelope_diameter	96.8 Å
壳层 Rg shell_rg	32.56 Å
包络 Rg envelope_rg	26.33 Å
形状 Rg shape_rg	25.76 Å
总 Rg total_rg	26.52 Å
总原子数 total_atoms	3881
残基数 n_residues	478
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	92.7 Å
Rg (实空间) rg_real	26.65 Å
Rg 误差 (实空间) rg_real_error	0.72 Å
I(0) (实空间) i0_real	4.8410e+07
I(0) 误差 (实空间) i0_real_error	7.1940e+05
Rg (倒空间) rg_reciprocal	26.66 Å
I(0) (倒空间) i0_reciprocal	48410000.0000
解质量估计 total_estimate	0.7935
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	33.0 Å
偏度 Skewness skewness	0.350
峰度 Kurtosis kurtosis	-0.200
角度范围 angular_range	— – 0.2950 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	11230000.0000
实空间数据点数 n_real_points	60
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.790; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.943; Smooth: 0.000

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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 (7)

Entity 1 polymer

描述 description	[Pyruvate dehydrogenase [lipoamide]] kinase isozyme 3
分子量 formula_weight	48291.0 kDa
EC 编号 ec_number	2.7.1.99
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	3949

GGSHHHHHHGMARLENLYFQGKQPVPKQIERYSRFSPSPLSIKQFLDFGRDNACEKTSYMFLRKELPVRLANTMREVNLLPDNLLNRPSVGLVQSWYMQSFLELLEYENKSPEDPQVLDNFLQVLIKVRNRHNDVVPTMAQGVIEYKEKFGFDPFISTNIQYFLDRFYTNRISFRMLINQHTLLFGGDTNPVHPKHIGSIDPTCNVADVVKDAYETAKMLCEQYYLVAPELEVEEFNAKAPDKPIQVVYVPSHLFHMLFELFKNSMRATVELYEDRKEGYPAVKTLVTLGKEDLSIKISDLGGGVPLRKIDRLFNYMYSTAPRPSLEPTRAAPLAGFGYGLPISRLYARYFQGDLKLYSMEGVGTDAVIYLKALSSESFERLPVFNKSAWRHYKTTPEADDWSNPSSEPRDASKYKAKQ

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 BL21

Entity 2 polymer

描述 description	Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
分子量 formula_weight	14192.1 kDa
EC 编号 ec_number	2.3.1.12
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B

GGSHHHHHHGMARLENLYFQGSSYPPHMQVLLPALSPTMTMGTVQRWEKKVGEKLSEGDLLAEIETDKATIGFEVQEEGYLAKILVPEGTRDVPLGTPLCIIVEKEADISAFADYRPTEVTDLKPQVP

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 BL21

Entity 3 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	POTASSIUM ION
分子量 formula_weight	39.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 5 non-polymer

描述 description	ADENOSINE-5'-TRIPHOSPHATE
分子量 formula_weight	507.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 6 non-polymer

描述 description	DIHYDROLIPOIC ACID
分子量 formula_weight	208.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 7 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	56

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6. 折叠分类 (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

结构域编号 domain_id	d1y8pa1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.29 — Bromodomain-like
超家族 Superfamily superfamily	a.29.5 — alpha-ketoacid dehydrogenase kinase, N-terminal domain
家族 Family family	a.29.5.1 — alpha-ketoacid dehydrogenase kinase, N-terminal domain

结构域编号 domain_id	d1y8pa3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.122 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
超家族 Superfamily superfamily	d.122.1 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
家族 Family family	d.122.1.4 — alpha-ketoacid dehydrogenase kinase, C-terminal domain

结构域编号 domain_id	d1y8pb_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.84 — Barrel-sandwich hybrid
超家族 Superfamily superfamily	b.84.1 — Single hybrid motif
家族 Family family	b.84.1.1 — Biotinyl/lipoyl-carrier proteins and domains

CATH v4.4 (3 domains)

结构域编号 domain_id	1y8pA01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
同源超家族 H-superfamily homologous superfamily	20 — Alpha-ketoacid/pyruvate dehydrogenase kinase, N-terminal domain

结构域编号 domain_id	1y8pA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	565 — Heat Shock Protein 90
同源超家族 H-superfamily homologous superfamily	10 — Histidine kinase-like ATPase, C-terminal domain

结构域编号 domain_id	1y8pB00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain

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7. 引用文献 (1)

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晶胞边长 a length_a	120.904 Å
晶胞边长 b length_b	120.904 Å
晶胞边长 c length_c	240.085 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	120.00 °
晶胞分子数 Z z_pdb	12

空间群 space_group	P 65 2 2
空间群编号 int_tables_number	179
晶系 crystal_system	—

分辨率 resolution	2.630 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	0.2049
R_work r_work	0.2036
R_free r_free	0.2302

fit	/app/data/saxs_computation/y8/1y8p/1y8p.fit
pddf	/app/data/pr_computation/y8/1y8p/1y8p.pr.out
profile	/app/data/saxs_computation/y8/1y8p/1y8p.dat

Crystal structure of the PDK3-L2 complex

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 (7)

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 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 water

6. 折叠分类 (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)