SAXSdb — 1pfz

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1pfz
沉积日期 deposition_date	1998-07-07
结构标题 title	PROPLASMEPSIN II FROM PLASMODIUM FALCIPARUM
关键词 keywords	ASPARTIC PROTEINASE ZYMOGEN, HEMOGLOBINASE, MALARIA, HYDROLASE, ASPARTYL PROTEASE, GLYCOPROTEIN, ASPARTIC PROTEASE ZYMOGEN; ASPARTIC PROTEASE ZYMOGEN
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	42.61 Å
回转半径 Rg (电子) rg_electron	42.17 Å
零角强度 I(0) i0	369394000.00
分子量 molecular_weight	165400.0 kDa
排除体积 excluded_volume	209830 Å³
包络体积 envelope_volume	274510 Å³
水化壳体积 shell_volume	55475 Å³
包络直径 envelope_diameter	145.3 Å
壳层 Rg shell_rg	46.17 Å
包络 Rg envelope_rg	41.39 Å
形状 Rg shape_rg	42.18 Å
总 Rg total_rg	42.32 Å
总原子数 total_atoms	11684
残基数 n_residues	1464
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	142.2 Å
Rg (实空间) rg_real	42.65 Å
Rg 误差 (实空间) rg_real_error	1.24 Å
I(0) (实空间) i0_real	3.6940e+08
I(0) 误差 (实空间) i0_real_error	6.1100e+06
Rg (倒空间) rg_reciprocal	42.61 Å
I(0) (倒空间) i0_reciprocal	369400000.0000
解质量估计 total_estimate	0.8879
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	50.0 Å
偏度 Skewness skewness	0.296
峰度 Kurtosis kurtosis	-0.507
角度范围 angular_range	— – 0.1850 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	35340000.0000
实空间数据点数 n_real_points	38
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.912; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.814

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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	PROPLASMEPSIN II
分子量 formula_weight	42733.3 kDa
EC 编号 ec_number	3.4.23.39
突变 mutation	;76 RESIDUES AT THE N-TERMINUS OF THE PROSEGMENT (1P - 76P) HAVE BEEN TRUNCATED, 3 RESIDUES (GLY-ARG-GLY) HAVE BEEN ADDED AT THE N-TERMINUS AS AN ARTIFACT OF THE EXPRESSION SYSTEM ;
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	12503

GRGSEHLTIGFKVENAHDRILKTIKTHKLKNYIKESVNFLNSGLTKTNYLGSSNDNIELVDFQNIMFYGDAEVGDNQQPFTFILDTGSANLWVPSVKCTTAGCLTKHLYDSSKSRTYEKDGTKVEMNYVSGTVSGFFSKDLVTVGNLSLPYKFIEVIDTNGFEPTYTASTFDGILGLGWKDLSIGSVDPIVVELKNQNKIENALFTFYLPVHDKHTGFLTIGGIEERFYEGPLTYEKLNHDLYWQITLDAHVGNIMLEKANCIVDSGTSAITVPTDFLNKMLQNLDVIKVPFLPFYVTLCNNSKLPTFEFTSENGKYTLEPEYYLQHIEDVGPGLCMLNIIGLDFPVPTFILGDPFMRKYFTVFDYDNHSVGIALAKKNL

来源 Source

来源生物 organism	Plasmodium falciparum
通用名 common_name	malaria parasite P. falciparum
NCBI 分类编号 ncbi_taxonomy_id	5833
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

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	731

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6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1pfza_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.50 — Acid proteases
超家族 Superfamily superfamily	b.50.1 — Acid proteases
家族 Family family	b.50.1.2 — Pepsin-like

结构域编号 domain_id	d1pfzb_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.50 — Acid proteases
超家族 Superfamily superfamily	b.50.1 — Acid proteases
家族 Family family	b.50.1.2 — Pepsin-like

结构域编号 domain_id	d1pfzc_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.50 — Acid proteases
超家族 Superfamily superfamily	b.50.1 — Acid proteases
家族 Family family	b.50.1.2 — Pepsin-like

结构域编号 domain_id	d1pfzd_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.50 — Acid proteases
超家族 Superfamily superfamily	b.50.1 — Acid proteases
家族 Family family	b.50.1.2 — Pepsin-like

CATH v4.4 (8 domains)

结构域编号 domain_id	1pfzA01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	70 — Cathepsin D, subunit A; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Acid Proteases

结构域编号 domain_id	1pfzA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	70 — Cathepsin D, subunit A; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Acid Proteases

结构域编号 domain_id	1pfzB01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	70 — Cathepsin D, subunit A; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Acid Proteases

结构域编号 domain_id	1pfzB02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	70 — Cathepsin D, subunit A; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Acid Proteases

结构域编号 domain_id	1pfzC01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	70 — Cathepsin D, subunit A; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Acid Proteases

结构域编号 domain_id	1pfzC02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	70 — Cathepsin D, subunit A; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Acid Proteases

结构域编号 domain_id	1pfzD01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	70 — Cathepsin D, subunit A; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Acid Proteases

结构域编号 domain_id	1pfzD02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	70 — Cathepsin D, subunit A; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Acid Proteases

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7. 引用文献 (2)

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晶胞边长 a length_a	52.007 Å
晶胞边长 b length_b	133.223 Å
晶胞边长 c length_c	114.234 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	98.45 °
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	1.850 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.2140
R_work r_work	0.2140
R_free r_free	0.2370

fit	/app/data/saxs_computation/pf/1pfz/1pfz.fit
pddf	/app/data/pr_computation/pf/1pfz/1pfz.pr.out
profile	/app/data/saxs_computation/pf/1pfz/1pfz.dat

PROPLASMEPSIN II FROM PLASMODIUM FALCIPARUM

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