1vsu

Crystal Structure of Apo-glyceraldehyde 3-phosphate dehydrogenase from Cryptosporidium parvum

Method: X-RAY DIFFRACTION D_max: 97.0 Å Quality: GOOD

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1vsu
沉积日期 deposition_date	2008-03-10
结构标题 title	Crystal Structure of Apo-glyceraldehyde 3-phosphate dehydrogenase from Cryptosporidium parvum
关键词 keywords	dehyrogenase, glycolysis, glycolytic enzyme, 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	33.05 Å
回转半径 Rg (电子) rg_electron	32.25 Å
零角强度 I(0) i0	294519000.00
分子量 molecular_weight	138850.0 kDa
排除体积 excluded_volume	174430 Å³
包络体积 envelope_volume	211430 Å³
水化壳体积 shell_volume	52319 Å³
包络直径 envelope_diameter	96.2 Å
壳层 Rg shell_rg	40.95 Å
包络 Rg envelope_rg	31.82 Å
形状 Rg shape_rg	32.26 Å
总 Rg total_rg	32.90 Å
总原子数 total_atoms	9724
残基数 n_residues	1300
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	97.0 Å
Rg (实空间) rg_real	32.73 Å
Rg 误差 (实空间) rg_real_error	0.55 Å
I(0) (实空间) i0_real	2.9450e+08
I(0) 误差 (实空间) i0_real_error	4.2830e+06
Rg (倒空间) rg_reciprocal	32.87 Å
I(0) (倒空间) i0_reciprocal	294600000.0000
解质量估计 total_estimate	0.8339
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	46.5 Å
偏度 Skewness skewness	-0.002
峰度 Kurtosis kurtosis	-0.607
角度范围 angular_range	— – 0.2400 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	141100000.0000
实空间数据点数 n_real_points	49
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.954; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.974; 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 (2)

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6. 折叠分类 (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

结构域编号 domain_id	1vsuA01
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	1vsuA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

结构域编号 domain_id	1vsuB01
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	1vsuB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

结构域编号 domain_id	1vsuC01
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	1vsuC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

结构域编号 domain_id	1vsuD01
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	1vsuD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

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7. 引用文献 (1)

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晶胞边长 a length_a	69.359 Å
晶胞边长 b length_b	121.646 Å
晶胞边长 c length_c	80.003 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	92.31 °
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	2.200 Å
最低分辨率 resolution_low	39.970 Å
R 因子 r_factor	0.2030
R_work r_work	0.2030
R_free r_free	0.2450

描述 description	Glyceraldehyde-3-phosphate dehydrogenase
分子量 formula_weight	38333.8 kDa
EC 编号 ec_number	1.2.1.12
来源方法 src_method	man
拷贝数 entity_count	4

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	10129

Crystal Structure of Apo-glyceraldehyde 3-phosphate dehydrogenase from Cryptosporidium parvum

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 (2)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 water

6. 折叠分类 (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)

来源生物 organism	Cryptosporidium parvum
NCBI 分类编号 ncbi_taxonomy_id	5807
宿主生物 host_organism	Escherichia coli

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	405

fit	/app/data/saxs_computation/vs/1vsu/1vsu.fit
pddf	/app/data/pr_computation/vs/1vsu/1vsu.pr.out
profile	/app/data/saxs_computation/vs/1vsu/1vsu.dat