SAXSdb — 1n1e

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1n1e
沉积日期 deposition_date	2002-10-17
结构标题 title	Crystal structure of Leishmania mexicana Glycerol-3-phosphate dehydrogenase complexed with DHAP and NAD
关键词 keywords	NAD BINDING DOMAIN, 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	27.61 Å
回转半径 Rg (电子) rg_electron	26.83 Å
零角强度 I(0) i0	90818400.00
分子量 molecular_weight	76585.0 kDa
排除体积 excluded_volume	96724 Å³
包络体积 envelope_volume	112660 Å³
水化壳体积 shell_volume	34640 Å³
包络直径 envelope_diameter	95.1 Å
壳层 Rg shell_rg	34.52 Å
包络 Rg envelope_rg	27.12 Å
形状 Rg shape_rg	26.86 Å
总 Rg total_rg	27.48 Å
总原子数 total_atoms	5362
残基数 n_residues	698
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	91.4 Å
Rg (实空间) rg_real	27.65 Å
Rg 误差 (实空间) rg_real_error	0.67 Å
I(0) (实空间) i0_real	9.0820e+07
I(0) 误差 (实空间) i0_real_error	1.3770e+06
Rg (倒空间) rg_reciprocal	27.64 Å
I(0) (倒空间) i0_reciprocal	90820000.0000
解质量估计 total_estimate	0.6826
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	30.5 Å
偏度 Skewness skewness	0.437
峰度 Kurtosis kurtosis	-0.200
角度范围 angular_range	— – 0.2850 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	31190000.0000
实空间数据点数 n_real_points	58
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.830; Stabil: 1.000; Sysdev: 0.177; Positv: 1.000; Valcen: 0.992; Smooth: 0.858

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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 (3)

Entity 1 polymer

描述 description	glycerol-3-phosphate dehydrogenase
分子量 formula_weight	39317.8 kDa
EC 编号 ec_number	1.1.1.8
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	5668

MSTKQHSAKDELLYLNKAVVFGSGAFGTALAMVLSKKCREVCVWHMNEEEVRLVNEKRENVLFLKGVQLASNITFTSDVEKAYNGAEIILFVIPTQFLRGFFEKSGGNLIAYAKEKQVPVLVCTKGIERSTLKFPAEIIGEFLPSPLLSVLAGPSFAIEVATGVFTCVSIASADINVARRLQRIMSTGDRSFVCWATTDTVGCEVASAVKNVLAIGSGVANGLGMGLNARAALIMRGLLEIRDLTAALGGDGSAVFGLAGLGDLQLTCSSELSRNFTVGKKLGKGLPIEEIQRTSKAVAEGVATADPLMRLAKQLKVKMPLCHQIYEIVYKKKNPRDALADLLSCGLQDEGLPPLFKRSASTPSKL

来源 Source

来源生物 organism	Leishmania mexicana
NCBI 分类编号 ncbi_taxonomy_id	5665
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	;ADENOSINE 5'-(TRIHYDROGEN DIPHOSPHATE) P'-5'-ESTER WITH 3-(AMINOCARBONYL)-4-(1-HYDROXYL-2-OXO-3-PHOSPHONOOXY-PROPYL)-1-BETA-D-RIBOFURANOSYLPYRIDINIUM INNER SALT ;
分子量 formula_weight	831.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 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	306

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1n1ea1
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.100.1.6 — Glycerol-3-phosphate dehydrogenase

结构域编号 domain_id	d1n1ea2
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	d1n1eb1
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.100.1.6 — Glycerol-3-phosphate dehydrogenase

结构域编号 domain_id	d1n1eb2
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

CATH v4.4 (4 domains)

结构域编号 domain_id	1n1eA01
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	1n1eA02
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

结构域编号 domain_id	1n1eB01
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	1n1eB02
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	77.745 Å
晶胞边长 b length_b	77.745 Å
晶胞边长 c length_c	266.631 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
空间群编号 int_tables_number	170
晶系 crystal_system	—

分辨率 resolution	1.900 Å
最低分辨率 resolution_low	47.370 Å
R 因子 r_factor	0.1745
R_work r_work	0.1734
R_free r_free	0.1951

fit	/app/data/saxs_computation/n1/1n1e/1n1e.fit
pddf	/app/data/pr_computation/n1/1n1e/1n1e.pr.out
profile	/app/data/saxs_computation/n1/1n1e/1n1e.dat

Crystal structure of Leishmania mexicana Glycerol-3-phosphate dehydrogenase complexed with DHAP and NAD

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