1nk1

NK1 FRAGMENT OF HUMAN HEPATOCYTE GROWTH FACTOR/SCATTER FACTOR (HGF/SF) AT 2.5 ANGSTROM RESOLUTION

Method: X-RAY DIFFRACTION D_max: 69.6 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	1nk1
沉积日期 deposition_date	1998-08-20
结构标题 title	NK1 FRAGMENT OF HUMAN HEPATOCYTE GROWTH FACTOR/SCATTER FACTOR (HGF/SF) AT 2.5 ANGSTROM RESOLUTION
关键词 keywords	HGF/SF, 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	21.67 Å
回转半径 Rg (电子) rg_electron	20.99 Å
零角强度 I(0) i0	27377400.00
分子量 molecular_weight	39425.0 kDa
排除体积 excluded_volume	49144 Å³
包络体积 envelope_volume	58578 Å³
水化壳体积 shell_volume	23154 Å³
包络直径 envelope_diameter	71.8 Å
壳层 Rg shell_rg	27.59 Å
包络 Rg envelope_rg	21.07 Å
形状 Rg shape_rg	21.00 Å
总 Rg total_rg	21.80 Å
总原子数 total_atoms	2764
残基数 n_residues	344
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	69.6 Å
Rg (实空间) rg_real	21.54 Å
Rg 误差 (实空间) rg_real_error	0.33 Å
I(0) (实空间) i0_real	2.7380e+07
I(0) 误差 (实空间) i0_real_error	2.6400e+05
Rg (倒空间) rg_reciprocal	21.56 Å
I(0) (倒空间) i0_reciprocal	27380000.0000
解质量估计 total_estimate	0.8961
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	29.1 Å
偏度 Skewness skewness	0.141
峰度 Kurtosis kurtosis	-0.465
角度范围 angular_range	— – 0.3650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	6646000.0000
实空间数据点数 n_real_points	68
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.887; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.985

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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 (2)

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1nk1a1
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	d1nk1a2
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	d1nk1b1
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	d1nk1b2
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 (4 domains)

结构域编号 domain_id	1nk1A01
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	1nk1A02
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	1nk1B01
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	1nk1B02
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	53.420 Å
晶胞边长 b length_b	63.560 Å
晶胞边长 c length_c	56.810 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	96.04 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	2.500 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.2450
R_work r_work	0.2450
R_free r_free	0.3190

描述 description	PROTEIN (HEPATOCYTE GROWTH FACTOR PRECURSOR)
分子量 formula_weight	21172.3 kDa
突变 mutation	A29V
来源方法 src_method	man
拷贝数 entity_count	2

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	2823

NK1 FRAGMENT OF HUMAN HEPATOCYTE GROWTH FACTOR/SCATTER FACTOR (HGF/SF) AT 2.5 ANGSTROM RESOLUTION

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 (2)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 water

6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)

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	Pichia pastoris

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	59

fit	/app/data/saxs_computation/nk/1nk1/1nk1.fit
pddf	/app/data/pr_computation/nk/1nk1/1nk1.pr.out
profile	/app/data/saxs_computation/nk/1nk1/1nk1.dat