1u1i

Myo-inositol phosphate synthase mIPS from A. fulgidus

Method: X-RAY DIFFRACTION D_max: 110.2 Å Quality: REASONABLE

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	1u1i
沉积日期 deposition_date	2004-07-15
结构标题 title	Myo-inositol phosphate synthase mIPS from A. fulgidus
关键词 keywords	NAD cofactor, metal ions, ISOMERASE; ISOMERASE
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	36.75 Å
回转半径 Rg (电子) rg_electron	35.69 Å
零角强度 I(0) i0	443962000.00
分子量 molecular_weight	177930.0 kDa
排除体积 excluded_volume	224910 Å³
包络体积 envelope_volume	262490 Å³
水化壳体积 shell_volume	59396 Å³
包络直径 envelope_diameter	113.8 Å
壳层 Rg shell_rg	43.77 Å
包络 Rg envelope_rg	35.75 Å
形状 Rg shape_rg	35.68 Å
总 Rg total_rg	36.24 Å
总原子数 total_atoms	12534
残基数 n_residues	1568
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	36.80 Å
Rg 误差 (实空间) rg_real_error	0.23 Å
I(0) (实空间) i0_real	4.3250e+08
I(0) 误差 (实空间) i0_real_error	4.7860e+06
Rg (倒空间) rg_reciprocal	36.66 Å
I(0) (倒空间) i0_reciprocal	444000000.0000
解质量估计 total_estimate	0.7313
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	53.8 Å
偏度 Skewness skewness	0.073
峰度 Kurtosis kurtosis	-0.620
角度范围 angular_range	— – 0.2150 Å⁻¹
当前正则化参数 α current_alpha	3.3250
最高正则化参数 α highest_alpha	331100000.0000
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: 0.961; Stabil: 0.921; Sysdev: 0.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.887

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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	myo-inositol-1-phosphate synthase
分子量 formula_weight	43767.2 kDa
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	13553

MKVWLVGAYGIVSTTAMVGARAIERGIAPKIGLVSELPHFEGIEKYAPFSFEFGGHEIRLLSNAYEAAKEHWELNRHFDREILEAVKSDLEGIVARKGTALNCGSGIKELGDIKTLEGEGLSLAEMVSRIEEDIKSFADDETVVINVASTEPLPNYSEEYHGSLEGFERMIDEDRKEYASASMLYAYAALKLGLPYANFTPSPGSAIPALKELAEKKGVPHAGNDGKTGETLVKTTLAPMFAYRNMEVVGWMSYNILGDYDGKVLSARDNKESKVLSKDKVLEKMLGYSPYSITEIQYFPSLVDNKTAFDFVHFKGFLGKLMKFYFIWDAIDAIVAAPLILDIARFLLFAKKKGVKGVVKEMAFFFKSPMDTNVINTHEQFVVLKEWYSNLK

来源 Source

来源生物 organism	Archaeoglobus fulgidus
NCBI 分类编号 ncbi_taxonomy_id	224325
宿主生物 host_organism	Escherichia coli BL21

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	4

Entity 3 non-polymer

描述 description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
分子量 formula_weight	663.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 4 non-polymer

描述 description	POTASSIUM ION
分子量 formula_weight	39.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	1019

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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	d1u1ia1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family family	c.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain

结构域编号 domain_id	d1u1ia2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.81 — FwdE/GAPDH domain-like
超家族 Superfamily superfamily	d.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
家族 Family family	d.81.1.3 — Dihydrodipicolinate reductase-like

结构域编号 domain_id	d1u1ib1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family family	c.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain

结构域编号 domain_id	d1u1ib2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.81 — FwdE/GAPDH domain-like
超家族 Superfamily superfamily	d.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
家族 Family family	d.81.1.3 — Dihydrodipicolinate reductase-like

结构域编号 domain_id	d1u1ic1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family family	c.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain

结构域编号 domain_id	d1u1ic2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.81 — FwdE/GAPDH domain-like
超家族 Superfamily superfamily	d.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
家族 Family family	d.81.1.3 — Dihydrodipicolinate reductase-like

结构域编号 domain_id	d1u1id1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family family	c.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain

结构域编号 domain_id	d1u1id2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.81 — FwdE/GAPDH domain-like
超家族 Superfamily superfamily	d.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
家族 Family family	d.81.1.3 — Dihydrodipicolinate reductase-like

CATH v4.4 (8 domains)

结构域编号 domain_id	1u1iA01
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	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	1u1iA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

结构域编号 domain_id	1u1iB01
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	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	1u1iB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

结构域编号 domain_id	1u1iC01
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	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	1u1iC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

结构域编号 domain_id	1u1iD01
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	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	1u1iD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

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7. 引用文献 (1)

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晶胞边长 a length_a	62.770 Å
晶胞边长 b length_b	83.940 Å
晶胞边长 c length_c	91.790 Å
晶胞夹角 α angle_alpha	65.79 °
晶胞夹角 β angle_beta	72.43 °
晶胞夹角 γ angle_gamma	74.98 °
晶胞分子数 Z z_pdb	4

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	1.900 Å
最低分辨率 resolution_low	37.600 Å
R 因子 r_factor	0.2130
R_work r_work	0.2110
R_free r_free	0.2840

fit	/app/data/saxs_computation/u1/1u1i/1u1i.fit
pddf	/app/data/pr_computation/u1/1u1i/1u1i.pr.out
profile	/app/data/saxs_computation/u1/1u1i/1u1i.dat