1nap

THE CRYSTAL STRUCTURE OF RECOMBINANT HUMAN NEUTROPHIL-ACTIVATING PEPTIDE-2 (M6L) AT 1.9-ANGSTROMS RESOLUTION

Method: X-RAY DIFFRACTION D_max: 61.0 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	1nap
沉积日期 deposition_date	1994-12-19
结构标题 title	THE CRYSTAL STRUCTURE OF RECOMBINANT HUMAN NEUTROPHIL-ACTIVATING PEPTIDE-2 (M6L) AT 1.9-ANGSTROMS RESOLUTION
关键词 keywords	CYTOKINE; CYTOKINE
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	18.75 Å
回转半径 Rg (电子) rg_electron	17.66 Å
零角强度 I(0) i0	14261900.00
分子量 molecular_weight	28470.0 kDa
排除体积 excluded_volume	35982 Å³
包络体积 envelope_volume	42494 Å³
水化壳体积 shell_volume	19775 Å³
包络直径 envelope_diameter	57.5 Å
壳层 Rg shell_rg	24.23 Å
包络 Rg envelope_rg	17.63 Å
形状 Rg shape_rg	17.67 Å
总 Rg total_rg	18.66 Å
总原子数 total_atoms	1982
残基数 n_residues	261
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	61.0 Å
Rg (实空间) rg_real	18.58 Å
Rg 误差 (实空间) rg_real_error	0.36 Å
I(0) (实空间) i0_real	1.4260e+07
I(0) 误差 (实空间) i0_real_error	1.6640e+05
Rg (倒空间) rg_reciprocal	18.61 Å
I(0) (倒空间) i0_reciprocal	14260000.0000
解质量估计 total_estimate	0.7845
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	25.9 Å
偏度 Skewness skewness	0.027
峰度 Kurtosis kurtosis	-0.455
角度范围 angular_range	— – 0.4250 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	7086000.0000
实空间数据点数 n_real_points	74
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.737; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.000

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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	d1napa_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.9 — IL8-like
超家族 Superfamily superfamily	d.9.1 — Interleukin 8-like chemokines
家族 Family family	d.9.1.1 — Interleukin 8-like chemokines

结构域编号 domain_id	d1napb_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.9 — IL8-like
超家族 Superfamily superfamily	d.9.1 — Interleukin 8-like chemokines
家族 Family family	d.9.1.1 — Interleukin 8-like chemokines

结构域编号 domain_id	d1napc_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.9 — IL8-like
超家族 Superfamily superfamily	d.9.1 — Interleukin 8-like chemokines
家族 Family family	d.9.1.1 — Interleukin 8-like chemokines

结构域编号 domain_id	d1napd_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.9 — IL8-like
超家族 Superfamily superfamily	d.9.1 — Interleukin 8-like chemokines
家族 Family family	d.9.1.1 — Interleukin 8-like chemokines

CATH v4.4 (4 domains)

结构域编号 domain_id	1napA00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	40 —

结构域编号 domain_id	1napB00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	40 —

结构域编号 domain_id	1napC00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	40 —

结构域编号 domain_id	1napD00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	40 —

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7. 引用文献 (4)

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晶胞边长 a length_a	40.770 Å
晶胞边长 b length_b	43.810 Å
晶胞边长 c length_c	44.650 Å
晶胞夹角 α angle_alpha	98.37 °
晶胞夹角 β angle_beta	120.28 °
晶胞夹角 γ angle_gamma	92.78 °
晶胞分子数 Z z_pdb	4

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

分辨率 resolution	1.900 Å
最低分辨率 resolution_low	7.000 Å
R 因子 r_factor	0.2020
R_work r_work	0.2020
R_free r_free	0.2300

描述 description	NEUTROPHIL ACTIVATING PEPTIDE-2
分子量 formula_weight	7623.9 kDa
突变 mutation	M26L
来源方法 src_method	man
拷贝数 entity_count	4

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	2254

THE CRYSTAL STRUCTURE OF RECOMBINANT HUMAN NEUTROPHIL-ACTIVATING PEPTIDE-2 (M6L) AT 1.9-ANGSTROMS 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

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 (4)

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	Escherichia coli

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	265

fit	/app/data/saxs_computation/na/1nap/1nap.fit
pddf	/app/data/pr_computation/na/1nap/1nap.pr.out
profile	/app/data/saxs_computation/na/1nap/1nap.dat