SAXSdb — 1nql

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1nql
沉积日期 deposition_date	2003-01-21
结构标题 title	Structure of the extracellular domain of human epidermal growth factor (EGF) receptor in an inactive (low pH) complex with EGF.
关键词 keywords	;cell surface receptor, tyrosine kinase, glycoprotein, endosomal, growth factor, auto-inhibition, HORMONE-GROWTH FACTOR RECEPTOR COMPLEX ;; HORMONE/GROWTH FACTOR RECEPTOR
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	33.22 Å
回转半径 Rg (电子) rg_electron	32.43 Å
零角强度 I(0) i0	99839700.00
分子量 molecular_weight	74022.0 kDa
排除体积 excluded_volume	90521 Å³
包络体积 envelope_volume	132160 Å³
水化壳体积 shell_volume	34927 Å³
包络直径 envelope_diameter	104.1 Å
壳层 Rg shell_rg	38.65 Å
包络 Rg envelope_rg	31.24 Å
形状 Rg shape_rg	32.43 Å
总 Rg total_rg	32.97 Å
总原子数 total_atoms	5150
残基数 n_residues	660
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	102.6 Å
Rg (实空间) rg_real	33.12 Å
Rg 误差 (实空间) rg_real_error	0.83 Å
I(0) (实空间) i0_real	9.9840e+07
I(0) 误差 (实空间) i0_real_error	1.5920e+06
Rg (倒空间) rg_reciprocal	33.17 Å
I(0) (倒空间) i0_reciprocal	99840000.0000
解质量估计 total_estimate	0.9122
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	34.2 Å
偏度 Skewness skewness	0.113
峰度 Kurtosis kurtosis	-0.760
角度范围 angular_range	— – 0.2400 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	7480000.0000
实空间数据点数 n_real_points	49
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.973; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.944

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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	epidermal growth factor receptor
分子量 formula_weight	69213.8 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	A
原子数 atom_count	5150

LEEKKVCQGTSNKLTQLGTFEDHFLSLQRMFNNCEVVLGNLEITYVQRNYDLSFLKTIQEVAGYVLIALNTVERIPLENLQIIRGNMYYENSYALAVLSNYDANKTGLKELPMRNLQEILHGAVRFSNNPALCNVESIQWRDIVSSDFLSNMSMDFQNHLGSCQKCDPSCPNGSCWGAGEENCQKLTKIICAQQCSGRCRGKSPSDCCHNQCAAGCTGPRESDCLVCRKFRDEATCKDTCPPLMLYNPTTYQMDVNPEGKYSFGATCVKKCPRNYVVTDHGSCVRACGADSYEMEEDGVRKCKKCEGPCRKVCNGIGIGEFKDSLSINATNIKHFKNCTSISGDLHILPVAFRGDSFTHTPPLDPQELDILKTVKEITGFLLIQAWPENRTDLHAFENLEIIRGRTKQHGQFSLAVVSLNITSLGLRSLKEISDGDVIISGNKNLCYANTINWKKLFGTSGQKTKIISNRGENSCKATGQVCHALCSPEGCWGPEPRDCVSCRNVSRGRECVDKCKLLEGEPREFVENSECIQCHPECLPQAMNITCTGRGPDNCIQCAHYIDGPHCVKTCPAGVMGENNTLVWKYADAGHVCHLCHPNCTYGCTGPGLEGCPTNGPKHHHHHH

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	Spodoptera frugiperda

Entity 2 polymer

描述 description	epidermal growth factor
分子量 formula_weight	6229.0 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	B

NSDSECPLSHDGYCLHDGVCMYIEALDKYACNCVVGYIGERCQYRDLKWWELR

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 branched

描述 description	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	586.5 kDa
来源方法 src_method	man
拷贝数 entity_count	2

Entity 4 branched

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	424.4 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 5 non-polymer

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	221.2 kDa
来源方法 src_method	man
拷贝数 entity_count	5

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6. 折叠分类 (SCOP + CATH) 11 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d1nqla1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
超家族 Superfamily superfamily	c.10.2 — L domain-like
家族 Family family	c.10.2.5 — L domain

结构域编号 domain_id	d1nqla2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
超家族 Superfamily superfamily	c.10.2 — L domain-like
家族 Family family	c.10.2.5 — L domain

结构域编号 domain_id	d1nqla3
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.3.9 — Growth factor receptor domain
家族 Family family	g.3.9.1 — Growth factor receptor domain

结构域编号 domain_id	d1nqla4
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.3.9 — Growth factor receptor domain
家族 Family family	g.3.9.1 — Growth factor receptor domain

结构域编号 domain_id	d1nqla5
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d1nqlb_
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

CATH v4.4 (5 domains)

结构域编号 domain_id	1nqlA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	80 — Alpha-Beta Horseshoe
拓扑 Topology topology	20 — 24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A
同源超家族 H-superfamily homologous superfamily	20 — Receptor L-domain

结构域编号 domain_id	1nqlA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	10 — Ribbon
拓扑 Topology topology	220 — Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2
同源超家族 H-superfamily homologous superfamily	10 — Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2

结构域编号 domain_id	1nqlA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	80 — Alpha-Beta Horseshoe
拓扑 Topology topology	20 — 24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A
同源超家族 H-superfamily homologous superfamily	20 — Receptor L-domain

结构域编号 domain_id	1nqlA04
类 Class class	2 — Mainly Beta
架构 Architecture architecture	10 — Ribbon
拓扑 Topology topology	220 — Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2
同源超家族 H-superfamily homologous superfamily	10 — Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2

结构域编号 domain_id	1nqlB00
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 (1)

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晶胞边长 a length_a	119.170 Å
晶胞边长 b length_b	103.660 Å
晶胞边长 c length_c	101.490 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	119.27 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	2.800 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.2475
R_work r_work	0.2407
R_free r_free	0.3099

fit	/app/data/saxs_computation/nq/1nql/1nql.fit
pddf	/app/data/pr_computation/nq/1nql/1nql.pr.out
profile	/app/data/saxs_computation/nq/1nql/1nql.dat

Structure of the extracellular domain of human epidermal growth factor (EGF) receptor in an inactive (low pH) complex with EGF.

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 (5)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 branched

Entity 4 branched

Entity 5 non-polymer

6. 折叠分类 (SCOP + CATH) 11 domains

SCOP 2.08 (6 domains)

CATH v4.4 (5 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)