1gp9

;A New Crystal Form of the Nk1 Splice Variant of Hgf/Sf Demonstrates Extensive Hinge Movement and Suggests that the Nk1 Dimer Originates by Domain Swapping ;

Method: X-RAY DIFFRACTION D_max: 99.7 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	1gp9
沉积日期 deposition_date	2001-10-31
结构标题 title	;A New Crystal Form of the Nk1 Splice Variant of Hgf/Sf Demonstrates Extensive Hinge Movement and Suggests that the Nk1 Dimer Originates by Domain Swapping ;
关键词 keywords	;HORMONE/GROWTH FACTOR, HGF/SF, NK1, MET, DOMAIN SWAPPING, PROTEIN ENGINEERING, GROWTH FACTOR, KRINGLE, GLYCOPROTEIN, HORMONE-GROWTH FACTOR complex ;; HORMONE/GROWTH FACTOR
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	30.89 Å
回转半径 Rg (电子) rg_electron	30.63 Å
零角强度 I(0) i0	103920000.00
分子量 molecular_weight	79099.0 kDa
排除体积 excluded_volume	98477 Å³
包络体积 envelope_volume	126970 Å³
水化壳体积 shell_volume	35410 Å³
包络直径 envelope_diameter	105.5 Å
壳层 Rg shell_rg	36.82 Å
包络 Rg envelope_rg	30.15 Å
形状 Rg shape_rg	30.64 Å
总 Rg total_rg	31.17 Å
总原子数 total_atoms	5538
残基数 n_residues	681
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	99.7 Å
Rg (实空间) rg_real	30.93 Å
Rg 误差 (实空间) rg_real_error	0.75 Å
I(0) (实空间) i0_real	1.0390e+08
I(0) 误差 (实空间) i0_real_error	1.4990e+06
Rg (倒空间) rg_reciprocal	30.92 Å
I(0) (倒空间) i0_reciprocal	103900000.0000
解质量估计 total_estimate	0.8929
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	35.2 Å
偏度 Skewness skewness	0.347
峰度 Kurtosis kurtosis	-0.419
角度范围 angular_range	— – 0.2550 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	7776000.0000
实空间数据点数 n_real_points	52
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.919; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.871

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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	HEPATOCYTE GROWTH FACTOR
分子量 formula_weight	20329.2 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	5694

EAEAYVHEFKKSAKTTLIKIDPALKIKTKKVNTADQCANRCTRNKGLPFTCKAFVFDKARKQCLWFPFNSMSSGVKKEFGHEFDLYENKDYIRNCIIGKGRSYKGTVSITKSGIKCQPWSSMIPHEHSFLPSSYRGKDLQENYCRNPRGEEGGPWCFTSNPEVRYEVCDIPQCSEVE

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	Komagataella pastoris

Entity 2 non-polymer

描述 description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
分子量 formula_weight	238.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	5

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	156

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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	d1gp9a1
类 Class class	g — Small proteins
折叠类型 Fold fold	g.10 — Hairpin loop containing domain-like
超家族 Superfamily superfamily	g.10.1 — Hairpin loop containing domain-like
家族 Family family	g.10.1.1 — Hairpin loop containing domain

结构域编号 domain_id	d1gp9a2
类 Class class	g — Small proteins
折叠类型 Fold fold	g.14 — Kringle-like
超家族 Superfamily superfamily	g.14.1 — Kringle-like
家族 Family family	g.14.1.1 — Kringle modules

结构域编号 domain_id	d1gp9b1
类 Class class	g — Small proteins
折叠类型 Fold fold	g.10 — Hairpin loop containing domain-like
超家族 Superfamily superfamily	g.10.1 — Hairpin loop containing domain-like
家族 Family family	g.10.1.1 — Hairpin loop containing domain

结构域编号 domain_id	d1gp9b2
类 Class class	g — Small proteins
折叠类型 Fold fold	g.14 — Kringle-like
超家族 Superfamily superfamily	g.14.1 — Kringle-like
家族 Family family	g.14.1.1 — Kringle modules

结构域编号 domain_id	d1gp9c1
类 Class class	g — Small proteins
折叠类型 Fold fold	g.10 — Hairpin loop containing domain-like
超家族 Superfamily superfamily	g.10.1 — Hairpin loop containing domain-like
家族 Family family	g.10.1.1 — Hairpin loop containing domain

结构域编号 domain_id	d1gp9c2
类 Class class	g — Small proteins
折叠类型 Fold fold	g.14 — Kringle-like
超家族 Superfamily superfamily	g.14.1 — Kringle-like
家族 Family family	g.14.1.1 — Kringle modules

结构域编号 domain_id	d1gp9d1
类 Class class	g — Small proteins
折叠类型 Fold fold	g.10 — Hairpin loop containing domain-like
超家族 Superfamily superfamily	g.10.1 — Hairpin loop containing domain-like
家族 Family family	g.10.1.1 — Hairpin loop containing domain

结构域编号 domain_id	d1gp9d2
类 Class class	g — Small proteins
折叠类型 Fold fold	g.14 — Kringle-like
超家族 Superfamily superfamily	g.14.1 — Kringle-like
家族 Family family	g.14.1.1 — Kringle modules

CATH v4.4 (8 domains)

结构域编号 domain_id	1gp9A01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	4 — Hepatocyte Growth Factor
同源超家族 H-superfamily homologous superfamily	10 — Hepatocyte Growth Factor

结构域编号 domain_id	1gp9A02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	20 — Plasminogen Kringle 4
同源超家族 H-superfamily homologous superfamily	10 — Plasminogen Kringle 4

结构域编号 domain_id	1gp9B01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	4 — Hepatocyte Growth Factor
同源超家族 H-superfamily homologous superfamily	10 — Hepatocyte Growth Factor

结构域编号 domain_id	1gp9B02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	20 — Plasminogen Kringle 4
同源超家族 H-superfamily homologous superfamily	10 — Plasminogen Kringle 4

结构域编号 domain_id	1gp9C01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	4 — Hepatocyte Growth Factor
同源超家族 H-superfamily homologous superfamily	10 — Hepatocyte Growth Factor

结构域编号 domain_id	1gp9C02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	20 — Plasminogen Kringle 4
同源超家族 H-superfamily homologous superfamily	10 — Plasminogen Kringle 4

结构域编号 domain_id	1gp9D01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	4 — Hepatocyte Growth Factor
同源超家族 H-superfamily homologous superfamily	10 — Hepatocyte Growth Factor

结构域编号 domain_id	1gp9D02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	20 — Plasminogen Kringle 4
同源超家族 H-superfamily homologous superfamily	10 — Plasminogen Kringle 4

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7. 引用文献 (1)

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晶胞边长 a length_a	73.480 Å
晶胞边长 b length_b	78.260 Å
晶胞边长 c length_c	304.460 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	90.00 °
晶胞分子数 Z z_pdb	32

空间群 space_group	C 2 2 21
空间群编号 int_tables_number	20
晶系 crystal_system	—

分辨率 resolution	2.500 Å
最低分辨率 resolution_low	19.920 Å
R 因子 r_factor	0.2370
R_work r_work	0.2370
R_free r_free	0.2880

fit	/app/data/saxs_computation/gp/1gp9/1gp9.fit
pddf	/app/data/pr_computation/gp/1gp9/1gp9.pr.out
profile	/app/data/saxs_computation/gp/1gp9/1gp9.dat