1n1i

The structure of MSP-1(19) from Plasmodium knowlesi

Method: X-RAY DIFFRACTION D_max: 84.0 Å Quality: EXCELLENT

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	1n1i
沉积日期 deposition_date	2002-10-17
结构标题 title	The structure of MSP-1(19) from Plasmodium knowlesi
关键词 keywords	MSP1, malaria, surface protein, surface antigen, glycoprotein, EGF domain, CELL ADHESION; CELL ADHESION
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	26.29 Å
回转半径 Rg (电子) rg_electron	25.66 Å
零角强度 I(0) i0	32181900.00
分子量 molecular_weight	39504.0 kDa
排除体积 excluded_volume	47668 Å³
包络体积 envelope_volume	70728 Å³
水化壳体积 shell_volume	23754 Å³
包络直径 envelope_diameter	88.7 Å
壳层 Rg shell_rg	32.08 Å
包络 Rg envelope_rg	25.12 Å
形状 Rg shape_rg	25.64 Å
总 Rg total_rg	26.46 Å
总原子数 total_atoms	2736
残基数 n_residues	364
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	84.0 Å
Rg (实空间) rg_real	26.25 Å
Rg 误差 (实空间) rg_real_error	0.69 Å
I(0) (实空间) i0_real	3.2180e+07
I(0) 误差 (实空间) i0_real_error	4.9600e+05
Rg (倒空间) rg_reciprocal	26.27 Å
I(0) (倒空间) i0_reciprocal	32180000.0000
解质量估计 total_estimate	0.9079
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	35.0 Å
偏度 Skewness skewness	0.210
峰度 Kurtosis kurtosis	-0.460
角度范围 angular_range	— – 0.3000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	2427000.0000
实空间数据点数 n_real_points	61
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.943; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.984

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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 (4)

Entity 1 polymer

描述 description	Merozoite surface protein-1
分子量 formula_weight	11450.6 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	3042

EAEASNMSSAHKCIDTNVPENAACYRYLDGTEEWRCLLGFKEVGGKCVPASITCEENNGGCAPEAECTMDDKKEVECKCTKEGSEPLFEGVFCSSSSGPHHHHHH

来源 Source

来源生物 organism	Plasmodium knowlesi strain H
NCBI 分类编号 ncbi_taxonomy_id	5851
宿主生物 host_organism	Saccharomyces cerevisiae

Entity 2 non-polymer

描述 description	IMIDAZOLE
分子量 formula_weight	69.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 non-polymer

描述 description	HISTIDINE
分子量 formula_weight	156.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 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	306

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6. 折叠分类 (SCOP + CATH) 19 domains

SCOP 2.08 (11 domains)

结构域编号 domain_id	d1n1ia1
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.3.11.4 — Merozoite surface protein 1 (MSP-1)

结构域编号 domain_id	d1n1ia2
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.3.11.4 — Merozoite surface protein 1 (MSP-1)

结构域编号 domain_id	d1n1ia3
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	d1n1ib1
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.3.11.4 — Merozoite surface protein 1 (MSP-1)

结构域编号 domain_id	d1n1ib2
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.3.11.4 — Merozoite surface protein 1 (MSP-1)

结构域编号 domain_id	d1n1ib3
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	d1n1ic1
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.3.11.4 — Merozoite surface protein 1 (MSP-1)

结构域编号 domain_id	d1n1ic2
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.3.11.4 — Merozoite surface protein 1 (MSP-1)

结构域编号 domain_id	d1n1ic3
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	d1n1id1
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.3.11.4 — Merozoite surface protein 1 (MSP-1)

结构域编号 domain_id	d1n1id2
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.3.11.4 — Merozoite surface protein 1 (MSP-1)

CATH v4.4 (8 domains)

结构域编号 domain_id	1n1iA01
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	1n1iA02
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	1n1iB01
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	1n1iB02
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	1n1iC01
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	1n1iC02
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	1n1iD01
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	1n1iD02
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	33.880 Å
晶胞边长 b length_b	106.460 Å
晶胞边长 c length_c	62.690 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	102.05 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

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	2.400 Å
最低分辨率 resolution_low	20.590 Å
R 因子 r_factor	0.2340
R_work r_work	0.2340
R_free r_free	0.2640

fit	/app/data/saxs_computation/n1/1n1i/1n1i.fit
pddf	/app/data/pr_computation/n1/1n1i/1n1i.pr.out
profile	/app/data/saxs_computation/n1/1n1i/1n1i.dat