1yp2

Crystal structure of potato tuber ADP-glucose pyrophosphorylase

Method: X-RAY DIFFRACTION D_max: 110.3 Å Quality: EXCELLENT

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	1yp2
沉积日期 deposition_date	2005-01-29
结构标题 title	Crystal structure of potato tuber ADP-glucose pyrophosphorylase
关键词 keywords	ADP-glucose synthase, ADP-glucose pyrophosphorylase, AGPASE B, Alpha-D-glucose-1-phosphate adenyl transferase, 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	36.88 Å
回转半径 Rg (电子) rg_electron	36.07 Å
零角强度 I(0) i0	554399000.00
分子量 molecular_weight	192020.0 kDa
排除体积 excluded_volume	240250 Å³
包络体积 envelope_volume	302860 Å³
水化壳体积 shell_volume	66671 Å³
包络直径 envelope_diameter	116.5 Å
壳层 Rg shell_rg	44.99 Å
包络 Rg envelope_rg	35.68 Å
形状 Rg shape_rg	36.04 Å
总 Rg total_rg	36.70 Å
总原子数 total_atoms	13429
残基数 n_residues	1709
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	110.3 Å
Rg (实空间) rg_real	36.60 Å
Rg 误差 (实空间) rg_real_error	0.84 Å
I(0) (实空间) i0_real	5.5440e+08
I(0) 误差 (实空间) i0_real_error	1.0180e+07
Rg (倒空间) rg_reciprocal	36.78 Å
I(0) (倒空间) i0_reciprocal	554500000.0000
解质量估计 total_estimate	0.9010
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	48.7 Å
偏度 Skewness skewness	0.056
峰度 Kurtosis kurtosis	-0.539
角度范围 angular_range	— – 0.2150 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	142900000.0000
实空间数据点数 n_real_points	44
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.938; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; Smooth: 0.926

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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	Glucose-1-phosphate adenylyltransferase small subunit
分子量 formula_weight	49795.7 kDa
EC 编号 ec_number	2.7.7.27
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	14643

MAVSDSQNSQTCLDPDASRSVLGIILGGGAGTRLYPLTKKRAKPAVPLGANYRLIDIPVSNCLNSNISKIYVLTQFNSASLNRHLSRAYASNMGGYKNEGFVEVLAAQQSPENPDWFQGTADAVRQYLWLFEEHTVLEYLILAGDHLYRMDYEKFIQAHRETDADITVAALPMDEKRATAFGLMKIDEEGRIIEFAEKPQGEQLQAMKVDTTILGLDDKRAKEMPFIASMGIYVISKDVMLNLLRDKFPGANDFGSEVIPGATSLGMRVQAYLYDGYWEDIGTIEAFYNANLGITKKPVPDFSFYDRSAPIYTQPRYLPPSKMLDADVTDSVIGEGCVIKNCKIHHSVVGLRSCISEGAIIEDSLLMGADYYETDADRKLLAAKGSVPIGIGKNCHIKRAIIDKNARIGDNVKIINKDNVQEAARETDGYFIKSGIVTVIKDALIPSGIII

来源 Source

来源生物 organism	Solanum tuberosum
通用名 common_name	potato
NCBI 分类编号 ncbi_taxonomy_id	4113
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	12

Entity 3 non-polymer

描述 description	PARA-MERCURY-BENZENESULFONIC ACID
分子量 formula_weight	357.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

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	1214

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6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1yp2a1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.81 — Single-stranded left-handed beta-helix
超家族 Superfamily superfamily	b.81.1 — Trimeric LpxA-like enzymes
家族 Family family	b.81.1.4 — GlmU C-terminal domain-like

结构域编号 domain_id	d1yp2a2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.68 — Nucleotide-diphospho-sugar transferases
超家族 Superfamily superfamily	c.68.1 — Nucleotide-diphospho-sugar transferases
家族 Family family	c.68.1.6 — glucose-1-phosphate thymidylyltransferase

结构域编号 domain_id	d1yp2b1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.81 — Single-stranded left-handed beta-helix
超家族 Superfamily superfamily	b.81.1 — Trimeric LpxA-like enzymes
家族 Family family	b.81.1.4 — GlmU C-terminal domain-like

结构域编号 domain_id	d1yp2b2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.68 — Nucleotide-diphospho-sugar transferases
超家族 Superfamily superfamily	c.68.1 — Nucleotide-diphospho-sugar transferases
家族 Family family	c.68.1.6 — glucose-1-phosphate thymidylyltransferase

结构域编号 domain_id	d1yp2c1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.81 — Single-stranded left-handed beta-helix
超家族 Superfamily superfamily	b.81.1 — Trimeric LpxA-like enzymes
家族 Family family	b.81.1.4 — GlmU C-terminal domain-like

结构域编号 domain_id	d1yp2c2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.68 — Nucleotide-diphospho-sugar transferases
超家族 Superfamily superfamily	c.68.1 — Nucleotide-diphospho-sugar transferases
家族 Family family	c.68.1.6 — glucose-1-phosphate thymidylyltransferase

结构域编号 domain_id	d1yp2d1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.81 — Single-stranded left-handed beta-helix
超家族 Superfamily superfamily	b.81.1 — Trimeric LpxA-like enzymes
家族 Family family	b.81.1.4 — GlmU C-terminal domain-like

结构域编号 domain_id	d1yp2d2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.68 — Nucleotide-diphospho-sugar transferases
超家族 Superfamily superfamily	c.68.1 — Nucleotide-diphospho-sugar transferases
家族 Family family	c.68.1.6 — glucose-1-phosphate thymidylyltransferase

CATH v4.4 (8 domains)

结构域编号 domain_id	1yp2A01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

结构域编号 domain_id	1yp2A02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	160 — 3 Solenoid
拓扑 Topology topology	10 — UDP N-Acetylglucosamine Acyltransferase; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Hexapeptide repeat proteins

结构域编号 domain_id	1yp2B01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

结构域编号 domain_id	1yp2B02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	160 — 3 Solenoid
拓扑 Topology topology	10 — UDP N-Acetylglucosamine Acyltransferase; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Hexapeptide repeat proteins

结构域编号 domain_id	1yp2C01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

结构域编号 domain_id	1yp2C02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	160 — 3 Solenoid
拓扑 Topology topology	10 — UDP N-Acetylglucosamine Acyltransferase; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Hexapeptide repeat proteins

结构域编号 domain_id	1yp2D01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

结构域编号 domain_id	1yp2D02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	160 — 3 Solenoid
拓扑 Topology topology	10 — UDP N-Acetylglucosamine Acyltransferase; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Hexapeptide repeat proteins

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7. 引用文献 (1)

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晶胞边长 a length_a	79.465 Å
晶胞边长 b length_b	137.551 Å
晶胞边长 c length_c	91.623 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	112.53 °
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	2.110 Å
最低分辨率 resolution_low	19.940 Å
R 因子 r_factor	0.1720
R_work r_work	0.1720
R_free r_free	0.2290

fit	/app/data/saxs_computation/yp/1yp2/1yp2.fit
pddf	/app/data/pr_computation/yp/1yp2/1yp2.pr.out
profile	/app/data/saxs_computation/yp/1yp2/1yp2.dat