1olm

;Supernatant Protein Factor in Complex with RRR-alpha-Tocopherylquinone: A Link between Oxidized Vitamin E and Cholesterol Biosynthesis ;

Method: X-RAY DIFFRACTION D_max: 133.1 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	1olm
沉积日期 deposition_date	2003-08-08
结构标题 title	;Supernatant Protein Factor in Complex with RRR-alpha-Tocopherylquinone: A Link between Oxidized Vitamin E and Cholesterol Biosynthesis ;
关键词 keywords	;LIPID-BINDING PROTEIN, CHOLESTEROL BIOSYNTHESIS, OXIDIZED VITAMIN E, LIPID-BINDING, TRANSPORT, TRANSCRIPTION REGULATION, ACTIVATOR, LIPID BINDING PROTEIN ;; LIPID BINDING PROTEIN
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	39.72 Å
回转半径 Rg (电子) rg_electron	39.30 Å
零角强度 I(0) i0	264812000.00
分子量 molecular_weight	136210.0 kDa
排除体积 excluded_volume	172270 Å³
包络体积 envelope_volume	231570 Å³
水化壳体积 shell_volume	51656 Å³
包络直径 envelope_diameter	141.1 Å
壳层 Rg shell_rg	42.63 Å
包络 Rg envelope_rg	38.92 Å
形状 Rg shape_rg	39.28 Å
总 Rg total_rg	39.56 Å
总原子数 total_atoms	9589
残基数 n_residues	1177
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	133.1 Å
Rg (实空间) rg_real	39.86 Å
Rg 误差 (实空间) rg_real_error	1.27 Å
I(0) (实空间) i0_real	2.6480e+08
I(0) 误差 (实空间) i0_real_error	4.5640e+06
Rg (倒空间) rg_reciprocal	39.78 Å
I(0) (倒空间) i0_reciprocal	264800000.0000
解质量估计 total_estimate	0.6560
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	43.3 Å
偏度 Skewness skewness	0.397
峰度 Kurtosis kurtosis	-0.298
角度范围 angular_range	— – 0.2000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	31320000.0000
实空间数据点数 n_real_points	41
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.893; Stabil: 1.000; Sysdev: 0.062; Positv: 1.000; Valcen: 0.969; Smooth: 0.691

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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	SEC14-LIKE PROTEIN 2
分子量 formula_weight	46208.2 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,C
原子数 atom_count	10464

MSGRVGDLSPRQKEALAKFRENVQDVLPALPNPDDYFLLRWLRARSFDLQKSEAMLRKHVEFRKQKDIDNIISWQPPEVIQQYLSGGMCGYDLDGCPVWYDIIGPLDAKGLLFSASKQDLLRTKMRECELLLQECAHQTTKLGRKVETITIIYDCEGLGLKHLWKPAVEAYGEFLCMFEENYPETLKRLFVVKAPKLFPVAYNLIKPFLSEDTRKKIMVLGANWKEVLLKHISPDQVPVEYGGTMTDPDGNPKCKSKINYGGDIPRKYYVRDQVKQQYEHSVQISRGSSHQVEYEILFPGCVLRWQFMSDGADVGFGIFLKTKMGERQRAGEMTEVLPNQRYNSHLVPEDGTLTCSDPGIYVLRFDNTYSFIHAKKVNFTVEVLLPDKASEEKMKQLGAGTPK

来源 Source

来源生物 organism	HOMO SAPIENS
通用名 common_name	HUMAN
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 polymer

描述 description	SEC14-LIKE PROTEIN 2
分子量 formula_weight	46236.2 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	E

MSGRVGDLSPRQKEALAKFRENVQDVLPALPNPDDYFLLRWLRARSFDLQKSEAMLRKHVEFRKQKDIDNIISWQPPEVIQQYLSGGMCGYDLDGCPVWYDIIGPLDAKGLLFSASKQDLLRTKMRECELLLQECAHQTTKLGRKVETITIIYDCEGLGLKHLWKPAVEAYGEFLCMFEENYPETLKRLFVVKAPKLFPVAYNLIKPFLSEDTRKKIMVLGANWKEVLLKHISPDQVPVEYGGTMTDPDGNPKCKSKINYGGDIPRKYYVRDQVKQQYEHSVQISRGSSHQVEYEILFPGCVLRWQFMSDGADVGFGIFLKKKMGERQRAGEMTEVLPNQRYNSHLVPEDGTLTCSDPGIYVLRFDNTYSFIHAKKVNFTVEVLLPDKASEEKMKQLGAGTPK

来源 Source

来源生物 organism	HOMO SAPIENS
通用名 common_name	HUMAN
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	ESCHERICHIA COLI

Entity 3 non-polymer

描述 description	RRR-ALPHA-TOCOPHERYLQUINONE
分子量 formula_weight	446.7 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

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	875

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6. 折叠分类 (SCOP + CATH) 15 domains

SCOP 2.08 (9 domains)

结构域编号 domain_id	d1olma1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.5 — RuvA C-terminal domain-like
超家族 Superfamily superfamily	a.5.3 — CRAL/TRIO N-terminal domain
家族 Family family	a.5.3.1 — CRAL/TRIO N-terminal domain

结构域编号 domain_id	d1olma2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.132 — Supernatant protein factor (SPF), C-terminal domain
超家族 Superfamily superfamily	b.132.1 — Supernatant protein factor (SPF), C-terminal domain
家族 Family family	b.132.1.1 — Supernatant protein factor (SPF), C-terminal domain

结构域编号 domain_id	d1olma3
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.13 — SpoIIaa-like
超家族 Superfamily superfamily	c.13.1 — CRAL/TRIO domain
家族 Family family	c.13.1.1 — CRAL/TRIO domain

结构域编号 domain_id	d1olmc1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.5 — RuvA C-terminal domain-like
超家族 Superfamily superfamily	a.5.3 — CRAL/TRIO N-terminal domain
家族 Family family	a.5.3.1 — CRAL/TRIO N-terminal domain

结构域编号 domain_id	d1olmc2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.132 — Supernatant protein factor (SPF), C-terminal domain
超家族 Superfamily superfamily	b.132.1 — Supernatant protein factor (SPF), C-terminal domain
家族 Family family	b.132.1.1 — Supernatant protein factor (SPF), C-terminal domain

结构域编号 domain_id	d1olmc3
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.13 — SpoIIaa-like
超家族 Superfamily superfamily	c.13.1 — CRAL/TRIO domain
家族 Family family	c.13.1.1 — CRAL/TRIO domain

结构域编号 domain_id	d1olme1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.5 — RuvA C-terminal domain-like
超家族 Superfamily superfamily	a.5.3 — CRAL/TRIO N-terminal domain
家族 Family family	a.5.3.1 — CRAL/TRIO N-terminal domain

结构域编号 domain_id	d1olme2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.132 — Supernatant protein factor (SPF), C-terminal domain
超家族 Superfamily superfamily	b.132.1 — Supernatant protein factor (SPF), C-terminal domain
家族 Family family	b.132.1.1 — Supernatant protein factor (SPF), C-terminal domain

结构域编号 domain_id	d1olme3
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.13 — SpoIIaa-like
超家族 Superfamily superfamily	c.13.1 — CRAL/TRIO domain
家族 Family family	c.13.1.1 — CRAL/TRIO domain

CATH v4.4 (6 domains)

结构域编号 domain_id	1olmA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	525 — Phosphatidylinositol Transfer Protein Sec14p
同源超家族 H-superfamily homologous superfamily	10 — CRAL-TRIO lipid binding domain

结构域编号 domain_id	1olmA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	680 — GOLD domain

结构域编号 domain_id	1olmC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	525 — Phosphatidylinositol Transfer Protein Sec14p
同源超家族 H-superfamily homologous superfamily	10 — CRAL-TRIO lipid binding domain

结构域编号 domain_id	1olmC02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	680 — GOLD domain

结构域编号 domain_id	1olmE01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	525 — Phosphatidylinositol Transfer Protein Sec14p
同源超家族 H-superfamily homologous superfamily	10 — CRAL-TRIO lipid binding domain

结构域编号 domain_id	1olmE02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	680 — GOLD domain

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7. 引用文献 (1)

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晶胞边长 a length_a	60.856 Å
晶胞边长 b length_b	84.621 Å
晶胞边长 c length_c	87.452 Å
晶胞夹角 α angle_alpha	116.20 °
晶胞夹角 β angle_beta	102.64 °
晶胞夹角 γ angle_gamma	100.24 °
晶胞分子数 Z z_pdb	2

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

分辨率 resolution	1.950 Å
最低分辨率 resolution_low	19.650 Å
R 因子 r_factor	0.1810
R_work r_work	0.1800
R_free r_free	0.2110

fit	/app/data/saxs_computation/ol/1olm/1olm.fit
pddf	/app/data/pr_computation/ol/1olm/1olm.pr.out
profile	/app/data/saxs_computation/ol/1olm/1olm.dat

;Supernatant Protein Factor in Complex with RRR-alpha-Tocopherylquinone: A Link between Oxidized Vitamin E and Cholesterol Biosynthesis ;

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

1. 结构基本信息 1. Structure Basics

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

4. 晶体学与实验 4. Crystallography & Experiment

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

衍射实验 Diffraction

5. 实体与聚合体信息 (4)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

Entity 4 water

6. 折叠分类 (SCOP + CATH) 15 domains

SCOP 2.08 (9 domains)

CATH v4.4 (6 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)