1yp4

Crystal structure of potato tuber ADP-glucose pyrophosphorylase in complex with ADP-glucose

Method: X-RAY DIFFRACTION D_max: 110.2 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	1yp4
沉积日期 deposition_date	2005-01-29
结构标题 title	Crystal structure of potato tuber ADP-glucose pyrophosphorylase in complex with ADP-glucose
关键词 keywords	ADP-glucose pyrophosphorylase-ADP-glucose complex, 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	36.73 Å
回转半径 Rg (电子) rg_electron	35.92 Å
零角强度 I(0) i0	566415000.00
分子量 molecular_weight	193180.0 kDa
排除体积 excluded_volume	241630 Å³
包络体积 envelope_volume	304440 Å³
水化壳体积 shell_volume	67094 Å³
包络直径 envelope_diameter	116.5 Å
壳层 Rg shell_rg	44.91 Å
包络 Rg envelope_rg	35.61 Å
形状 Rg shape_rg	35.89 Å
总 Rg total_rg	36.55 Å
总原子数 total_atoms	13550
残基数 n_residues	1725
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	110.2 Å
Rg (实空间) rg_real	36.44 Å
Rg 误差 (实空间) rg_real_error	0.64 Å
I(0) (实空间) i0_real	5.6640e+08
I(0) 误差 (实空间) i0_real_error	8.2450e+06
Rg (倒空间) rg_reciprocal	36.62 Å
I(0) (倒空间) i0_reciprocal	566500000.0000
解质量估计 total_estimate	0.9009
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	105.1 Å
偏度 Skewness skewness	0.056
峰度 Kurtosis kurtosis	-0.536
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	226500000.0000
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: 0.934; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.935

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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 (5)

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	14021

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	16

Entity 3 non-polymer

描述 description	ADENOSINE-5'-DIPHOSPHATE
分子量 formula_weight	427.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	ADENOSINE-5'-DIPHOSPHATE-GLUCOSE
分子量 formula_weight	589.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 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	471

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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	d1yp4a1
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	d1yp4a2
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	d1yp4b1
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	d1yp4b2
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	d1yp4c1
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	d1yp4c2
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	d1yp4d1
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	d1yp4d2
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	1yp4A01
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	1yp4A02
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	1yp4B01
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	1yp4B02
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	1yp4C01
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	1yp4C02
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	1yp4D01
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	1yp4D02
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	79.857 Å
晶胞边长 b length_b	137.964 Å
晶胞边长 c length_c	90.832 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	112.91 °
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	2.300 Å
最低分辨率 resolution_low	19.990 Å
R 因子 r_factor	0.1830
R_work r_work	0.1830
R_free r_free	0.2440

fit	/app/data/saxs_computation/yp/1yp4/1yp4.fit
pddf	/app/data/pr_computation/yp/1yp4/1yp4.pr.out
profile	/app/data/saxs_computation/yp/1yp4/1yp4.dat