1jq9

;Crystal structure of a complex formed between phospholipase A2 from Daboia russelli pulchella and a designed pentapeptide Phe-Leu-Ser-Tyr-Lys at 1.8 resolution ;

Method: X-RAY DIFFRACTION D_max: 59.6 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

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1jq9
沉积日期 deposition_date	2001-08-04
结构标题 title	;Crystal structure of a complex formed between phospholipase A2 from Daboia russelli pulchella and a designed pentapeptide Phe-Leu-Ser-Tyr-Lys at 1.8 resolution ;
关键词 keywords	phospholipase A2, Daboia russelli pulchella, neurotoxic, designed peptide, HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX; HYDROLASE/HYDROLASE INHIBITOR
实验方法 method	X-RAY DIFFRACTION

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	18.80 Å
回转半径 Rg (电子) rg_electron	18.09 Å
零角强度 I(0) i0	15004700.00
分子量 molecular_weight	28128.0 kDa
排除体积 excluded_volume	34768 Å³
包络体积 envelope_volume	40472 Å³
水化壳体积 shell_volume	18637 Å³
包络直径 envelope_diameter	62.5 Å
壳层 Rg shell_rg	24.36 Å
包络 Rg envelope_rg	18.28 Å
形状 Rg shape_rg	18.06 Å
总 Rg total_rg	19.07 Å
总原子数 total_atoms	1951
残基数 n_residues	247
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

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	59.6 Å
Rg (实空间) rg_real	18.68 Å
Rg 误差 (实空间) rg_real_error	0.32 Å
I(0) (实空间) i0_real	1.5000e+07
I(0) 误差 (实空间) i0_real_error	1.8900e+05
Rg (倒空间) rg_reciprocal	18.70 Å
I(0) (倒空间) i0_reciprocal	15000000.0000
解质量估计 total_estimate	0.8962
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	25.3 Å
偏度 Skewness skewness	0.124
峰度 Kurtosis kurtosis	-0.457
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	5479000.0000
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: 0.885; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.996

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (4)

Entity 1 polymer

描述 description	Phospholipase A2
分子量 formula_weight	13629.8 kDa
EC 编号 ec_number	3.1.1.4
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	2230

SLLEFGKMILEETGKLAIPSYSSYGCYCGWGGKGTPKDATDRCCFVHDCCYGNLPDCNPKSDRYKYKRVNGAIVCEKGTSCENRICECDKAAAICFRQNLNTYSKKYMLYPDFLCKGELKC

Entity 2 polymer

描述 description	Peptide inhibitor
分子量 formula_weight	657.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	P

FLSYK

Entity 3 non-polymer

描述 description	ACETIC ACID
分子量 formula_weight	60.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

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	279

▼

6. 折叠分类 (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1jq9a_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.133 — Phospholipase A2, PLA2
超家族 Superfamily superfamily	a.133.1 — Phospholipase A2, PLA2
家族 Family family	a.133.1.2 — Vertebrate phospholipase A2

结构域编号 domain_id	d1jq9b_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.133 — Phospholipase A2, PLA2
超家族 Superfamily superfamily	a.133.1 — Phospholipase A2, PLA2
家族 Family family	a.133.1.2 — Vertebrate phospholipase A2

CATH v4.4 (2 domains)

结构域编号 domain_id	1jq9A00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	90 — Phospholipase A2
同源超家族 H-superfamily homologous superfamily	10 — Phospholipase A2 domain

结构域编号 domain_id	1jq9B00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	90 — Phospholipase A2
同源超家族 H-superfamily homologous superfamily	10 — Phospholipase A2 domain

▶

7. 引用文献 (6)

;Crystal Structure of a Complex Formed between a Snake Venom Phospholipase A2 and a Potent Peptide Inhibitor Phe-Leu-Ser-Tyr-Lys at 1.8 A Resolution ;

J.BIOL.CHEM. (2002)

PMID: 12186870 · DOI: 10.1074/jbc.M206130200 PRIMARY

;First structural evidence of a specific inhibition of phospholipase A2 by alpha-tocopherol (vitamin E) and its implications in inflammation: crystal structure of the complex formed between phospholipase A2 and alpha-tocopherol at 1.8 A resolution ;

J.MOL.BIOL. (2002)

DOI: 10.1016/S0022-2836(02)00473-4

;Structural basis of phospholipase A2 inhibition for the synthesis of prostaglandins by the plant alkaloid aristolochic acid from a 1.7 A crystal structure ;

Biochemistry (2002)

DOI: 10.1021/bi0258593

;Design of specific peptide inhibitors of phospholipase A2: structure of a complex formed between Russell's viper phospholipase A2 and a designed peptide Leu-Ala-Ile-Tyr-Ser (LAIYS) ;

Acta Crystallogr.,Sect.D (2002)

DOI: 10.1107/S0907444902013720

;Regulation of catalytic function by molecular association: structure of phospholipase A2 from Daboia russelli pulchella (DPLA2) at 1.9 A resolution ;

Acta Crystallogr.,Sect.D (2001)

DOI: 10.1107/S0907444901014524

Three-dimensional structure of a presynaptic neurotoxic phospholipase A2 from Daboia russelli pulchella at 2.4 resolution

J.Mol.Biol. (2000)

DOI: 10.1006/jmbi.2000.3537

▶

晶胞边长 a length_a	76.130 Å
晶胞边长 b length_b	89.161 Å
晶胞边长 c length_c	77.548 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	16

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	1.800 Å
最低分辨率 resolution_low	11.950 Å
R 因子 r_factor	0.2050
R_work r_work	0.2050
R_free r_free	0.2250

fit	/app/data/saxs_computation/jq/1jq9/1jq9.fit
pddf	/app/data/pr_computation/jq/1jq9/1jq9.pr.out
profile	/app/data/saxs_computation/jq/1jq9/1jq9.dat

;Crystal structure of a complex formed between phospholipase A2 from Daboia russelli pulchella and a designed pentapeptide Phe-Leu-Ser-Tyr-Lys at 1.8 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 (4)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 non-polymer

Entity 4 water

6. 折叠分类 (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. 引用文献 (6)

8. 文件与曲线 (10)

Files (7)

Curves (3)