1i2d

CRYSTAL STRUCTURE OF ATP SULFURYLASE FROM PENICILLIUM CHRYSOGENUM

Method: X-RAY DIFFRACTION D_max: 151.7 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	1i2d
沉积日期 deposition_date	2001-02-07
结构标题 title	CRYSTAL STRUCTURE OF ATP SULFURYLASE FROM PENICILLIUM CHRYSOGENUM
关键词 keywords	nucleotide binding, allosteric, hexamer, 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	46.81 Å
回转半径 Rg (电子) rg_electron	46.42 Å
零角强度 I(0) i0	568480000.00
分子量 molecular_weight	192440.0 kDa
排除体积 excluded_volume	238830 Å³
包络体积 envelope_volume	322290 Å³
水化壳体积 shell_volume	57906 Å³
包络直径 envelope_diameter	149.4 Å
壳层 Rg shell_rg	50.60 Å
包络 Rg envelope_rg	45.31 Å
形状 Rg shape_rg	46.41 Å
总 Rg total_rg	46.62 Å
总原子数 total_atoms	13569
残基数 n_residues	1716
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	151.7 Å
Rg (实空间) rg_real	46.74 Å
Rg 误差 (实空间) rg_real_error	1.53 Å
I(0) (实空间) i0_real	5.6850e+08
I(0) 误差 (实空间) i0_real_error	1.1240e+07
Rg (倒空间) rg_reciprocal	46.81 Å
I(0) (倒空间) i0_reciprocal	568500000.0000
解质量估计 total_estimate	0.9031
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	58.0 Å
偏度 Skewness skewness	0.158
峰度 Kurtosis kurtosis	-0.690
角度范围 angular_range	— – 0.1700 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	26950000.0000
实空间数据点数 n_real_points	35
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.948; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.893

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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	ATP SULFURYLASE
分子量 formula_weight	64048.5 kDa
EC 编号 ec_number	2.7.7.4
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C
原子数 atom_count	13851

MANAPHGGVLKDLLARDAPRQAELAAEAESLPAVTLTERQLCDLELIMNGGFSPLEGFMNQADYDRVCEDNRLADGNVFSMPITLDASQEVIDEKKLQAGSRITLRDFRDDRNLAILTIDDIYRPDKTKEAKLVFGGDPEHPAIVYLNNTVKEFYIGGKIEAVNKLNHYDYVALRYTPAELRVHFDKLGWSRVVAFQTRNPMHRAHRELTVRAARSRQANVLIHPVVGLTKPGDIDHFTRVRAYQALLPRYPNGMAVLGLLGLAMRMGGPREAIWHAIIRKNHGATHFIVGRDHAGPGSNSKGEDFYGPYDAQHAVEKYKDELGIEVVEFQMVTYLPDTDEYRPVDQVPAGVKTLNISGTELRRRLRSGAHIPEWFSYPEVVKILRESNPPRATQGFTIFLTGYMNSGKDAIARALQVTLNQQGGRSVSLLLGDTVRHELSSELGFTREDRHTNIQRIAFVATELTRAGAAVIAAPIAPYEESRKFARDAVSQAGSFFLVHVATPLEHCEQSDKRGIYAAARRGEIKGFTGVDDPYETPEKADLVVDFSKQSVRSIVHEIILVLESQGFLERQ

来源 Source

来源生物 organism	Penicillium chrysogenum
NCBI 分类编号 ncbi_taxonomy_id	5076
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	ADENOSINE-5'-PHOSPHOSULFATE
分子量 formula_weight	427.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

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	282

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6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (9 domains)

结构域编号 domain_id	d1i2da1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.122 — PUA domain-like
超家族 Superfamily superfamily	b.122.1 — PUA domain-like
家族 Family family	b.122.1.3 — ATP sulfurylase N-terminal domain

结构域编号 domain_id	d1i2da2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
超家族 Superfamily superfamily	c.26.1 — Nucleotidylyl transferase
家族 Family family	c.26.1.5 — ATP sulfurylase catalytic domain

结构域编号 domain_id	d1i2da3
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.15 — ATP sulfurylase C-terminal domain

结构域编号 domain_id	d1i2db1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.122 — PUA domain-like
超家族 Superfamily superfamily	b.122.1 — PUA domain-like
家族 Family family	b.122.1.3 — ATP sulfurylase N-terminal domain

结构域编号 domain_id	d1i2db2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
超家族 Superfamily superfamily	c.26.1 — Nucleotidylyl transferase
家族 Family family	c.26.1.5 — ATP sulfurylase catalytic domain

结构域编号 domain_id	d1i2db3
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.15 — ATP sulfurylase C-terminal domain

结构域编号 domain_id	d1i2dc1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.122 — PUA domain-like
超家族 Superfamily superfamily	b.122.1 — PUA domain-like
家族 Family family	b.122.1.3 — ATP sulfurylase N-terminal domain

结构域编号 domain_id	d1i2dc2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
超家族 Superfamily superfamily	c.26.1 — Nucleotidylyl transferase
家族 Family family	c.26.1.5 — ATP sulfurylase catalytic domain

结构域编号 domain_id	d1i2dc3
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.15 — ATP sulfurylase C-terminal domain

CATH v4.4 (9 domains)

结构域编号 domain_id	1i2dA01
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	620 — HUPs

结构域编号 domain_id	1i2dA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	400 — Sulfate adenylyltransferase
同源超家族 H-superfamily homologous superfamily	10 — Sulfate adenylyltransferase

结构域编号 domain_id	1i2dA03
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	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	1i2dB01
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	620 — HUPs

结构域编号 domain_id	1i2dB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	400 — Sulfate adenylyltransferase
同源超家族 H-superfamily homologous superfamily	10 — Sulfate adenylyltransferase

结构域编号 domain_id	1i2dB03
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	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	1i2dC01
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	620 — HUPs

结构域编号 domain_id	1i2dC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	400 — Sulfate adenylyltransferase
同源超家族 H-superfamily homologous superfamily	10 — Sulfate adenylyltransferase

结构域编号 domain_id	1i2dC03
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	300 — P-loop containing nucleotide triphosphate hydrolases

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7. 引用文献 (1)

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晶胞边长 a length_a	135.670 Å
晶胞边长 b length_b	162.090 Å
晶胞边长 c length_c	273.000 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	90.00 °
晶胞分子数 Z z_pdb	24

空间群 space_group	I 2 2 2
空间群编号 int_tables_number	23
晶系 crystal_system	—

分辨率 resolution	2.810 Å
最低分辨率 resolution_low	29.080 Å
R 因子 r_factor	0.2070
R_work r_work	0.2070
R_free r_free	0.2450

fit	/app/data/saxs_computation/i2/1i2d/1i2d.fit
pddf	/app/data/pr_computation/i2/1i2d/1i2d.pr.out
profile	/app/data/saxs_computation/i2/1i2d/1i2d.dat