SAXSdb — 1u5b

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1u5b
沉积日期 deposition_date	2004-07-27
结构标题 title	Crystal structure of the human mitochondrial branched-chain alpha-ketoacid dehydrogenase
关键词 keywords	;OXIDOREDUCTASE, KETOACID DEHYDROGENASE, BRANCHED-CHAIN, MULTI-ENZYME COMPLEX, ACYLATION, OXIDATIVE DECARBOXYLATION MAPLE SYRUP URINE DISEASE, THIAMIN DIPHOSPHATE, PHOSPHORYLATION, 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	30.17 Å
回转半径 Rg (电子) rg_electron	29.58 Å
零角强度 I(0) i0	106406000.00
分子量 molecular_weight	81474.0 kDa
排除体积 excluded_volume	101740 Å³
包络体积 envelope_volume	125360 Å³
水化壳体积 shell_volume	35372 Å³
包络直径 envelope_diameter	104.5 Å
壳层 Rg shell_rg	36.60 Å
包络 Rg envelope_rg	29.91 Å
形状 Rg shape_rg	29.58 Å
总 Rg total_rg	30.19 Å
总原子数 total_atoms	5732
残基数 n_residues	720
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	101.1 Å
Rg (实空间) rg_real	30.22 Å
Rg 误差 (实空间) rg_real_error	0.96 Å
I(0) (实空间) i0_real	1.0640e+08
I(0) 误差 (实空间) i0_real_error	1.6020e+06
Rg (倒空间) rg_reciprocal	30.20 Å
I(0) (倒空间) i0_reciprocal	106400000.0000
解质量估计 total_estimate	0.8829
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	32.4 Å
偏度 Skewness skewness	0.376
峰度 Kurtosis kurtosis	-0.380
角度范围 angular_range	— – 0.2650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	21850000.0000
实空间数据点数 n_real_points	54
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.857; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.966; Smooth: 0.942

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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	2-oxoisovalerate dehydrogenase alpha subunit
分子量 formula_weight	45571.1 kDa
EC 编号 ec_number	1.2.4.4
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	6381

SSLDDKPQFPGASAEFIDKLEFIQPNVISGIPIYRVMDRQGQIINPSEDPHLPKEKVLKLYKSMTLLNTMDRILYESQRQGRISFYMTNYGEEGTHVGSAAALDNTDLVFGQYREAGVLMYRDYPLELFMAQCYGNISDLGKGRQMPVHYGCKERHFVTISSPLATQIPQAVGAAYAAKRANANRVVICYFGEGAASEGDAHAGFNFAATLECPIIFFCRNNGYAISTPTSEQYRGDGIAARGPGYGIMSIRVDGNDVFAVYNATKEARRRAVAENQPFLIEAMTYRIGHHSTSDDSSAYRSVDEVNYWDKQDHPISRLRHYLLSQGWWDEEQEKAWRKQSRRKVMEAFEQAERKPKPNPNLLFSDVYQEMPAQLRKQQESLARHLQTYGEHYPLDHFDK

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	2-oxoisovalerate dehydrogenase beta subunit
分子量 formula_weight	37902.3 kDa
EC 编号 ec_number	1.2.4.4
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

VAHFTFQPDPEPREYGQTQKMNLFQSVTSALDNSLAKDPTAVIFGEDVAFGGVFRCTVGLRDKYGKDRVFNTPLCEQGIVGFGIGIAVTGATAIAEIQFADYIFPAFDQIVNEAAKYRYRSGDLFNCGSLTIRSPWGCVGHGALYHSQSPEAFFAHCPGIKVVIPRSPFQAKGLLLSCIEDKNPCIFFEPKILYRAAAEEVPIEPYNIPLSQAEVIQEGSDVTLVAWGTQVHVIREVASMAKEKLGVSCEVIDLRTIIPWDVDTICKSVIKTGRLLISHEAPLTGGFASEISSTVQEECFLNLEAPISRVCGYDTPFPHIFEPFYIPDKWKCYDALRKMINY

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

Entity 4 non-polymer

描述 description	MANGANESE (II) ION
分子量 formula_weight	54.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 non-polymer

描述 description	THIAMINE DIPHOSPHATE
分子量 formula_weight	425.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 6 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 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	479

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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	d1u5ba_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.36 — Thiamin diphosphate-binding fold (THDP-binding)
超家族 Superfamily superfamily	c.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
家族 Family family	c.36.1.11 — Branched-chain alpha-keto acid dehydrogenase PP module

结构域编号 domain_id	d1u5bb1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.36 — Thiamin diphosphate-binding fold (THDP-binding)
超家族 Superfamily superfamily	c.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
家族 Family family	c.36.1.7 — Branched-chain alpha-keto acid dehydrogenase Pyr module

结构域编号 domain_id	d1u5bb2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.48 — TK C-terminal domain-like
超家族 Superfamily superfamily	c.48.1 — TK C-terminal domain-like
家族 Family family	c.48.1.2 — Branched-chain alpha-keto acid dehydrogenase beta-subunit, C-terminal-domain

CATH v4.4 (3 domains)

结构域编号 domain_id	1u5bA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

结构域编号 domain_id	1u5bB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

结构域编号 domain_id	1u5bB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	920 —

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7. 引用文献 (3)

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晶胞边长 a length_a	143.315 Å
晶胞边长 b length_b	143.315 Å
晶胞边长 c length_c	69.294 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	6

空间群 space_group	P 31 2 1
空间群编号 int_tables_number	152
晶系 crystal_system	—

分辨率 resolution	1.830 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	0.1560
R_work r_work	0.1560
R_free r_free	0.1934

fit	/app/data/saxs_computation/u5/1u5b/1u5b.fit
pddf	/app/data/pr_computation/u5/1u5b/1u5b.pr.out
profile	/app/data/saxs_computation/u5/1u5b/1u5b.dat

Crystal structure of the human mitochondrial branched-chain alpha-ketoacid dehydrogenase

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 (3)

8. 文件与曲线 (10)

Files (7)

Curves (3)