1m8p

Crystal Structure of P. chrysogenum ATP Sulfurylase in the T-state

Method: X-RAY DIFFRACTION D_max: 157.6 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	1m8p
沉积日期 deposition_date	2002-07-25
结构标题 title	Crystal Structure of P. chrysogenum ATP Sulfurylase in the T-state
关键词 keywords	Rossmann fold, phosphosulfate binding, T-state, 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	48.48 Å
回转半径 Rg (电子) rg_electron	47.98 Å
零角强度 I(0) i0	565240000.00
分子量 molecular_weight	192900.0 kDa
排除体积 excluded_volume	239790 Å³
包络体积 envelope_volume	335680 Å³
水化壳体积 shell_volume	59194 Å³
包络直径 envelope_diameter	154.1 Å
壳层 Rg shell_rg	51.40 Å
包络 Rg envelope_rg	46.41 Å
形状 Rg shape_rg	47.95 Å
总 Rg total_rg	48.18 Å
总原子数 total_atoms	13596
残基数 n_residues	1719
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	157.6 Å
Rg (实空间) rg_real	48.37 Å
Rg 误差 (实空间) rg_real_error	1.46 Å
I(0) (实空间) i0_real	5.6520e+08
I(0) 误差 (实空间) i0_real_error	1.0740e+07
Rg (倒空间) rg_reciprocal	48.48 Å
I(0) (倒空间) i0_reciprocal	565300000.0000
解质量估计 total_estimate	0.9006
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	62.1 Å
偏度 Skewness skewness	0.130
峰度 Kurtosis kurtosis	-0.683
角度范围 angular_range	— – 0.1650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	22530000.0000
实空间数据点数 n_real_points	34
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.929; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.918

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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	sulfate adenylyltransferase
分子量 formula_weight	64062.5 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	14054

MANAPHGGVLKDLLARDAPRQAELAAEAESLPAVTLTERQLCDLELIMNGGFSPLEGFMNQADYDRVCEDNRLADGNVFSMPITLDASQEVIDEKKLQAASRITLRDFRDDRNLAILTIDDIYRPDKTKEAKLVFGGDPEHPAIVYLNNTVKEFYIGGKIEAVNKLNHYDYVALRYTPAELRVHFDKLGWSRVVAFQTRNPMHRAHRELTVRAARSRQANVLIHPVVGLTKPGDIDHFTRVRAYQALLPRYPNGMAVLGLLGLAMRMGGPREAIWHAIIRKNHGATHFIVGRDHAGPGSNSKGEDFYGPYDAQHAVEKYKDELGIEVVEFQMVTYLPDTDEYRPVDQVPAGVKTLNISGTELRRRLRSGAHIPEWFSYPEVVKILRESNPPRATQGFTIFLTGYMNSGKDAIARALQVTLNQQGGRSVSLLLGDTVRHELSSELGFTREDRHTNIQRIAFVATELTRAGAAVIAAPIAPYEESRKFARDAVSQAGSFFLVHVATPLEHCEQSDKRGIYAAARRGEIKGFTGVDDPYETPEKADLVVDFSKQSVRSIVHEIILVLESQGFLERQ

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	;3'-PHOSPHATE-ADENOSINE-5'-PHOSPHATE SULFATE ;
分子量 formula_weight	507.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

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	458

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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	d1m8pa1
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	d1m8pa2
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	d1m8pa3
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	d1m8pb1
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	d1m8pb2
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	d1m8pb3
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	d1m8pc1
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	d1m8pc2
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	d1m8pc3
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	1m8pA01
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	1m8pA02
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	1m8pA03
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	1m8pB01
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	1m8pB02
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	1m8pB03
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	1m8pC01
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	1m8pC02
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	1m8pC03
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	135.449 Å
晶胞边长 b length_b	135.449 Å
晶胞边长 c length_c	234.587 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	120.00 °
晶胞分子数 Z z_pdb	18

空间群 space_group	P 31 2 1
空间群编号 int_tables_number	152
晶系 crystal_system	—

分辨率 resolution	2.600 Å
最低分辨率 resolution_low	29.330 Å
R 因子 r_factor	0.2180
R_work r_work	0.2180
R_free r_free	0.2720

fit	/app/data/saxs_computation/m8/1m8p/1m8p.fit
pddf	/app/data/pr_computation/m8/1m8p/1m8p.pr.out
profile	/app/data/saxs_computation/m8/1m8p/1m8p.dat