SAXSdb — 1dli

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1dli
沉积日期 deposition_date	1999-12-09
结构标题 title	THE FIRST STRUCTURE OF UDP-GLUCOSE DEHYDROGENASE (UDPGDH) REVEALS THE CATALYTIC RESIDUES NECESSARY FOR THE TWO-FOLD OXIDATION
关键词 keywords	ROSSMANN FOLD, TERNARY COMPLEX, CRYSTALLOGRAPHIC DIMER, OXIDOREDUCTASE; 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	23.54 Å
回转半径 Rg (电子) rg_electron	22.79 Å
零角强度 I(0) i0	37004600.00
分子量 molecular_weight	47249.0 kDa
排除体积 excluded_volume	59354 Å³
包络体积 envelope_volume	70293 Å³
水化壳体积 shell_volume	25597 Å³
包络直径 envelope_diameter	82.3 Å
壳层 Rg shell_rg	29.79 Å
包络 Rg envelope_rg	23.09 Å
形状 Rg shape_rg	22.78 Å
总 Rg total_rg	23.65 Å
总原子数 total_atoms	3314
残基数 n_residues	402
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	77.7 Å
Rg (实空间) rg_real	23.52 Å
Rg 误差 (实空间) rg_real_error	0.61 Å
I(0) (实空间) i0_real	3.7000e+07
I(0) 误差 (实空间) i0_real_error	5.7710e+05
Rg (倒空间) rg_reciprocal	23.52 Å
I(0) (倒空间) i0_reciprocal	37000000.0000
解质量估计 total_estimate	0.8073
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	27.9 Å
偏度 Skewness skewness	0.356
峰度 Kurtosis kurtosis	-0.299
角度范围 angular_range	— – 0.3350 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	7927000.0000
实空间数据点数 n_real_points	65
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.834; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; 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 (6)

Entity 1 polymer

描述 description	UDP-GLUCOSE DEHYDROGENASE
分子量 formula_weight	45537.1 kDa
EC 编号 ec_number	1.1.1.22
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	3607

MKIAVAGSGYVGLSLGVLLSLQNEVTIVDILPSKVDKINNGLSPIQDEYIEYYLKSKQLSIKATLDSKAAYKEAELVIIATPTNYNSRINYFDTQHVETVIKEVLSVNSHATLIIKSTIPIGFITEMRQKFQTDRIIFSPEFLRESKALYDNLYPSRIIVSCEENDSPKVKADAEKFALLLKSAAKKNNVPVLIMGASEAEAVKLFANTYLALRVAYFNELDTYAESRKLNSHMIIQGISYDDRIGMHYNNPSFGYGGYCLPKDTKQLLANYNNIPQTLIEAIVSSNNVRKSYIAKQIINVLKEQESPVKVVGVYRLIMKSNSDNFRESAIKDVIDILKSKDIKIIIYEPMLNKLESEDQSVLVNDLENFKKQANIIVTNRYDNELQDVKNKVYSRDIFGRD

来源 Source

来源生物 organism	Streptococcus pyogenes
NCBI 分类编号 ncbi_taxonomy_id	1314
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 3 non-polymer

描述 description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
分子量 formula_weight	663.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	URIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE
分子量 formula_weight	536.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 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	3

Entity 6 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	280

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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	d1dlia1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.100 — 6-phosphogluconate dehydrogenase C-terminal domain-like
超家族 Superfamily superfamily	a.100.1 — 6-phosphogluconate dehydrogenase C-terminal domain-like
家族 Family family	a.100.1.4 — UDP-glucose/GDP-mannose dehydrogenase dimerisation domain

结构域编号 domain_id	d1dlia2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family family	c.2.1.6 — 6-phosphogluconate dehydrogenase-like, N-terminal domain

结构域编号 domain_id	d1dlia3
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
超家族 Superfamily superfamily	c.26.3 — UDP-glucose/GDP-mannose dehydrogenase C-terminal domain
家族 Family family	c.26.3.1 — UDP-glucose/GDP-mannose dehydrogenase C-terminal domain

CATH v4.4 (3 domains)

结构域编号 domain_id	1dliA01
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	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	1dliA02
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	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	1dliA03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1040 — N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2

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7. 引用文献 (1)

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晶胞边长 a length_a	106.601 Å
晶胞边长 b length_b	106.601 Å
晶胞边长 c length_c	81.592 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	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	P 4 21 2
空间群编号 int_tables_number	90
晶系 crystal_system	—

分辨率 resolution	2.310 Å
最低分辨率 resolution_low	24.230 Å
R 因子 r_factor	0.1860
R_work r_work	0.1860
R_free r_free	0.2590

fit	/app/data/saxs_computation/dl/1dli/1dli.fit
pddf	/app/data/pr_computation/dl/1dli/1dli.pr.out
profile	/app/data/saxs_computation/dl/1dli/1dli.dat

THE FIRST STRUCTURE OF UDP-GLUCOSE DEHYDROGENASE (UDPGDH) REVEALS THE CATALYTIC RESIDUES NECESSARY FOR THE TWO-FOLD OXIDATION

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution