2gvg

Crystal Structure of human NMPRTase and its complex with NMN

Method: X-RAY DIFFRACTION D_max: 179.3 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	2gvg
沉积日期 deposition_date	2006-05-02
结构标题 title	Crystal Structure of human NMPRTase and its complex with NMN
关键词 keywords	NMPRTase, Visfatin, PBEF, CRYSTAL, Cancer, 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	52.76 Å
回转半径 Rg (电子) rg_electron	52.61 Å
零角强度 I(0) i0	1361450000.00
分子量 molecular_weight	317160.0 kDa
排除体积 excluded_volume	400110 Å³
包络体积 envelope_volume	551920 Å³
水化壳体积 shell_volume	87279 Å³
包络直径 envelope_diameter	187.5 Å
壳层 Rg shell_rg	56.95 Å
包络 Rg envelope_rg	50.80 Å
形状 Rg shape_rg	52.62 Å
总 Rg total_rg	52.70 Å
总原子数 total_atoms	22406
残基数 n_residues	2777
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	179.3 Å
Rg (实空间) rg_real	52.78 Å
Rg 误差 (实空间) rg_real_error	1.62 Å
I(0) (实空间) i0_real	1.3610e+09
I(0) 误差 (实空间) i0_real_error	2.7980e+07
Rg (倒空间) rg_reciprocal	52.73 Å
I(0) (倒空间) i0_reciprocal	1361000000.0000
解质量估计 total_estimate	0.8813
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	65.8 Å
偏度 Skewness skewness	0.298
峰度 Kurtosis kurtosis	-0.405
角度范围 angular_range	— – 0.1500 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	75020000.0000
实空间数据点数 n_real_points	31
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.873; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.832

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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 (4)

Entity 1 polymer

描述 description	Nicotinamide phosphoribosyltransferase
分子量 formula_weight	55594.9 kDa
EC 编号 ec_number	2.4.2.12
来源方法 src_method	man
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F
原子数 atom_count	23801

MNPAAEAEFNILLATDSYKVTHYKQYPPNTSKVYSYFECREKKTENSKLRKVKYEETVFYGLQYILNKYLKGKVVTKEKIQEAKDVYKEHFQDDVFNEKGWNYILEKYDGHLPIEIKAVPEGFVIPRGNVLFTVENTDPECYWLTNWIETILVQSWYPITVATNSREQKKILAKYLLETSGNLDGLEYKLHDFGYRGVSSQETAGIGASAHLVNFKGTDTVAGLALIKKYYGTKDPVPGYSVPAAEHSTITAWGKDHEKDAFEHIVTQFSSVPVSVVSDSYDIYNACEKIWGEDLRHLIVSRSTQAPLIIRPDSGNPLDTVLKVLEILGKKFPVTENSKGYKLLPPYLRVIQGDGVDINTLQEIVEGMKQKMWSIENIAFGSGGGLLQKLTRDLLNCSFKCSYVVTNGLGINVFKDPVADPNKRSKKGRLSLHRTPAGNFVTLEEGKGDLEEYGQDLLHTVFKNGKVTKSYSFDEIRKNAQLNIELEAAHH

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

Entity 2 non-polymer

描述 description	PHOSPHATE ION
分子量 formula_weight	95.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	12

Entity 3 non-polymer

描述 description	BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE
分子量 formula_weight	335.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

Entity 4 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	1395

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6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (12 domains)

结构域编号 domain_id	d2gvga1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.41 — alpha/beta-Hammerhead
超家族 Superfamily superfamily	d.41.2 — Nicotinate/Quinolinate PRTase N-terminal domain-like
家族 Family family	d.41.2.0 — automated matches

结构域编号 domain_id	d2gvga2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.17 — Nicotinate/Quinolinate PRTase C-terminal domain-like
家族 Family family	c.1.17.2 — Nicotinate phosphoribosyltransferase C-terminal domain-like

结构域编号 domain_id	d2gvgb1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.41 — alpha/beta-Hammerhead
超家族 Superfamily superfamily	d.41.2 — Nicotinate/Quinolinate PRTase N-terminal domain-like
家族 Family family	d.41.2.0 — automated matches

结构域编号 domain_id	d2gvgb2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.17 — Nicotinate/Quinolinate PRTase C-terminal domain-like
家族 Family family	c.1.17.2 — Nicotinate phosphoribosyltransferase C-terminal domain-like

结构域编号 domain_id	d2gvgc1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.41 — alpha/beta-Hammerhead
超家族 Superfamily superfamily	d.41.2 — Nicotinate/Quinolinate PRTase N-terminal domain-like
家族 Family family	d.41.2.0 — automated matches

结构域编号 domain_id	d2gvgc2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.17 — Nicotinate/Quinolinate PRTase C-terminal domain-like
家族 Family family	c.1.17.2 — Nicotinate phosphoribosyltransferase C-terminal domain-like

结构域编号 domain_id	d2gvgd1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.41 — alpha/beta-Hammerhead
超家族 Superfamily superfamily	d.41.2 — Nicotinate/Quinolinate PRTase N-terminal domain-like
家族 Family family	d.41.2.0 — automated matches

结构域编号 domain_id	d2gvgd2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.17 — Nicotinate/Quinolinate PRTase C-terminal domain-like
家族 Family family	c.1.17.2 — Nicotinate phosphoribosyltransferase C-terminal domain-like

结构域编号 domain_id	d2gvge1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.41 — alpha/beta-Hammerhead
超家族 Superfamily superfamily	d.41.2 — Nicotinate/Quinolinate PRTase N-terminal domain-like
家族 Family family	d.41.2.0 — automated matches

结构域编号 domain_id	d2gvge2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.17 — Nicotinate/Quinolinate PRTase C-terminal domain-like
家族 Family family	c.1.17.2 — Nicotinate phosphoribosyltransferase C-terminal domain-like

结构域编号 domain_id	d2gvgf1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.41 — alpha/beta-Hammerhead
超家族 Superfamily superfamily	d.41.2 — Nicotinate/Quinolinate PRTase N-terminal domain-like
家族 Family family	d.41.2.0 — automated matches

结构域编号 domain_id	d2gvgf2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.17 — Nicotinate/Quinolinate PRTase C-terminal domain-like
家族 Family family	c.1.17.2 — Nicotinate phosphoribosyltransferase C-terminal domain-like

CATH v4.4 (6 domains)

结构域编号 domain_id	2gvgA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	70 — Aldolase class I

结构域编号 domain_id	2gvgB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	70 — Aldolase class I

结构域编号 domain_id	2gvgC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	70 — Aldolase class I

结构域编号 domain_id	2gvgD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	70 — Aldolase class I

结构域编号 domain_id	2gvgE02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	70 — Aldolase class I

结构域编号 domain_id	2gvgF02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	70 — Aldolase class I

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7. 引用文献 (1)

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晶胞边长 a length_a	253.070 Å
晶胞边长 b length_b	101.367 Å
晶胞边长 c length_c	148.200 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	125.48 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	24

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	2.200 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	—
R_work r_work	0.1970
R_free r_free	0.2460

fit	/app/data/saxs_computation/gv/2gvg/2gvg.fit
pddf	/app/data/pr_computation/gv/2gvg/2gvg.pr.out
profile	/app/data/saxs_computation/gv/2gvg/2gvg.dat