1n7d

Extracellular domain of the LDL receptor

Method: X-RAY DIFFRACTION D_max: 129.9 Å Quality: GOOD

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	1n7d
沉积日期 deposition_date	2002-11-13
结构标题 title	Extracellular domain of the LDL receptor
关键词 keywords	LDL-Receptor, familial hypercholesterolemia, LDL, cholesterol metabolism, LIPID TRANSPORT; LIPID TRANSPORT
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	34.85 Å
回转半径 Rg (电子) rg_electron	34.85 Å
零角强度 I(0) i0	145360000.00
分子量 molecular_weight	76844.0 kDa
排除体积 excluded_volume	86112 Å³
包络体积 envelope_volume	143310 Å³
水化壳体积 shell_volume	37270 Å³
包络直径 envelope_diameter	141.1 Å
壳层 Rg shell_rg	37.65 Å
包络 Rg envelope_rg	35.48 Å
形状 Rg shape_rg	34.62 Å
总 Rg total_rg	35.56 Å
总原子数 total_atoms	4956
残基数 n_residues	639
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	129.9 Å
Rg (实空间) rg_real	35.23 Å
Rg 误差 (实空间) rg_real_error	2.32 Å
I(0) (实空间) i0_real	1.4540e+08
I(0) 误差 (实空间) i0_real_error	3.0440e+06
Rg (倒空间) rg_reciprocal	34.99 Å
I(0) (倒空间) i0_reciprocal	145300000.0000
解质量估计 total_estimate	0.8018
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	34.6 Å
偏度 Skewness skewness	0.615
峰度 Kurtosis kurtosis	0.038
角度范围 angular_range	— – 0.2250 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	2860000.0000
实空间数据点数 n_real_points	46
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.607; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.726; Smooth: 0.875

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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	Low-density lipoprotein receptor
分子量 formula_weight	77703.6 kDa
突变 mutation	N494Q, N636Q
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	A
原子数 atom_count	4956

AVGDRCERNEFQCQDGKCISYKWVCDGSAECQDGSDESQETCLSVTCKSGDFSCGGRVNRCIPQFWRCDGQVDCDNGSDEQGCPPKTCSQDEFRCHDGKCISRQFVCDSDRDCLDGSDEASCPVLTCGPASFQCNSSTCIPQLWACDNDPDCEDGSDEWPQRCRGLYVFQGDSSPCSAFEFHCLSGECIHSSWRCDGGPDCKDKSDEENCAVATCRPDEFQCSDGNCIHGSRQCDREYDCKDMSDEVGCVNVTLCEGPNKFKCHSGECITLDKVCNMARDCRDWSDEPIKECGTNECLDNNGGCSHVCNDLKIGYECLCPDGFQLVAQRRCEDIDECQDPDTCSQLCVNLEGGYKCQCEEGFQLDPHTKACKAVGSIAYLFFTNRHEVRKMTLDRSEYTSLIPNLRNVVALDTEVASNRIYWSDLSQRMICSTQLDRAHGVSSYDTVISRDIQAPDGLAVDWIHSNIYWTDSVLGTVSVADTKGVKRKTLFREQGSKPRAIVVDPVHGFMYWTDWGTPAKIKKGGLNGVDIYSLVTENIQWPNGITLDLLSGRLYWVDSKLHSISSIDVNGGNRKTILEDEKRLAHPFSLAVFEDKVFWTDIINEAIFSANRLTGSDVNLLAENLLSPEDMVLFHQLTQPRGVNWCERTTLSNGGCQYLCLPAPQINPHSPKFTCACPDGMLLARDMRSCLTEAEAAVA

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	Trichoplusia ni

Entity 2 branched

描述 description	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	910.8 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 3 branched

描述 description	;alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	748.7 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

Entity 5 non-polymer

描述 description	12-TUNGSTOPHOSPHATE
分子量 formula_weight	2877.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

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6. 折叠分类 (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

结构域编号 domain_id	d1n7da1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.68 — 6-bladed beta-propeller
超家族 Superfamily superfamily	b.68.5 — YWTD domain
家族 Family family	b.68.5.1 — YWTD domain

结构域编号 domain_id	d1n7da2
类 Class class	g — Small proteins
折叠类型 Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
超家族 Superfamily superfamily	g.3.11 — EGF/Laminin
家族 Family family	g.3.11.1 — EGF-type module

结构域编号 domain_id	d1n7da3
类 Class class	g — Small proteins
折叠类型 Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
超家族 Superfamily superfamily	g.3.11 — EGF/Laminin
家族 Family family	g.3.11.1 — EGF-type module

结构域编号 domain_id	d1n7da4
类 Class class	g — Small proteins
折叠类型 Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
超家族 Superfamily superfamily	g.3.11 — EGF/Laminin
家族 Family family	g.3.11.1 — EGF-type module

结构域编号 domain_id	d1n7da5
类 Class class	g — Small proteins
折叠类型 Fold fold	g.12 — LDL receptor-like module
超家族 Superfamily superfamily	g.12.1 — LDL receptor-like module
家族 Family family	g.12.1.1 — LDL receptor-like module

结构域编号 domain_id	d1n7da6
类 Class class	g — Small proteins
折叠类型 Fold fold	g.12 — LDL receptor-like module
超家族 Superfamily superfamily	g.12.1 — LDL receptor-like module
家族 Family family	g.12.1.1 — LDL receptor-like module

结构域编号 domain_id	d1n7da7
类 Class class	g — Small proteins
折叠类型 Fold fold	g.12 — LDL receptor-like module
超家族 Superfamily superfamily	g.12.1 — LDL receptor-like module
家族 Family family	g.12.1.1 — LDL receptor-like module

结构域编号 domain_id	d1n7da8
类 Class class	g — Small proteins
折叠类型 Fold fold	g.12 — LDL receptor-like module
超家族 Superfamily superfamily	g.12.1 — LDL receptor-like module
家族 Family family	g.12.1.1 — LDL receptor-like module

结构域编号 domain_id	d1n7da9
类 Class class	g — Small proteins
折叠类型 Fold fold	g.12 — LDL receptor-like module
超家族 Superfamily superfamily	g.12.1 — LDL receptor-like module
家族 Family family	g.12.1.1 — LDL receptor-like module

结构域编号 domain_id	d1n7daa
类 Class class	g — Small proteins
折叠类型 Fold fold	g.12 — LDL receptor-like module
超家族 Superfamily superfamily	g.12.1 — LDL receptor-like module
家族 Family family	g.12.1.1 — LDL receptor-like module

CATH v4.4 (10 domains)

结构域编号 domain_id	1n7dA01
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	400 — Low-density Lipoprotein Receptor
同源超家族 H-superfamily homologous superfamily	10 — Low-density Lipoprotein Receptor

结构域编号 domain_id	1n7dA02
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	1220 — Knottins (small inhibitors, toxins, lectins)
同源超家族 H-superfamily homologous superfamily	10 — EGF-type module

结构域编号 domain_id	1n7dA03
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	400 — Low-density Lipoprotein Receptor
同源超家族 H-superfamily homologous superfamily	10 — Low-density Lipoprotein Receptor

结构域编号 domain_id	1n7dA04
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	400 — Low-density Lipoprotein Receptor
同源超家族 H-superfamily homologous superfamily	10 — Low-density Lipoprotein Receptor

结构域编号 domain_id	1n7dA05
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	400 — Low-density Lipoprotein Receptor
同源超家族 H-superfamily homologous superfamily	10 — Low-density Lipoprotein Receptor

结构域编号 domain_id	1n7dA06
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	400 — Low-density Lipoprotein Receptor
同源超家族 H-superfamily homologous superfamily	10 — Low-density Lipoprotein Receptor

结构域编号 domain_id	1n7dA07
类 Class class	2 — Mainly Beta
架构 Architecture architecture	10 — Ribbon
拓扑 Topology topology	25 — Laminin
同源超家族 H-superfamily homologous superfamily	10 — Laminin

结构域编号 domain_id	1n7dA08
类 Class class	2 — Mainly Beta
架构 Architecture architecture	10 — Ribbon
拓扑 Topology topology	25 — Laminin
同源超家族 H-superfamily homologous superfamily	10 — Laminin

结构域编号 domain_id	1n7dA09
类 Class class	2 — Mainly Beta
架构 Architecture architecture	120 — 6 Propeller
拓扑 Topology topology	10 — Neuraminidase
同源超家族 H-superfamily homologous superfamily	30 — TolB, C-terminal domain

结构域编号 domain_id	1n7dA10
类 Class class	2 — Mainly Beta
架构 Architecture architecture	10 — Ribbon
拓扑 Topology topology	25 — Laminin
同源超家族 H-superfamily homologous superfamily	10 — Laminin

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7. 引用文献 (2)

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晶胞边长 a length_a	185.290 Å
晶胞边长 b length_b	185.290 Å
晶胞边长 c length_c	85.186 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	6

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	3.700 Å
最低分辨率 resolution_low	45.300 Å
R 因子 r_factor	—
R_work r_work	0.3810
R_free r_free	0.3820

fit	/app/data/saxs_computation/n7/1n7d/1n7d.fit
pddf	/app/data/pr_computation/n7/1n7d/1n7d.pr.out
profile	/app/data/saxs_computation/n7/1n7d/1n7d.dat