1pdw

Crystal structure of human DJ-1, P 1 21 1 space group

Method: X-RAY DIFFRACTION D_max: 151.4 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	1pdw
沉积日期 deposition_date	2003-05-20
结构标题 title	Crystal structure of human DJ-1, P 1 21 1 space group
关键词 keywords	DJ-1, PROTEIN BINDING; PROTEIN BINDING
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	46.73 Å
回转半径 Rg (电子) rg_electron	46.37 Å
零角强度 I(0) i0	371832000.00
分子量 molecular_weight	159280.0 kDa
排除体积 excluded_volume	199340 Å³
包络体积 envelope_volume	272670 Å³
水化壳体积 shell_volume	49611 Å³
包络直径 envelope_diameter	145.0 Å
壳层 Rg shell_rg	50.36 Å
包络 Rg envelope_rg	45.05 Å
形状 Rg shape_rg	46.37 Å
总 Rg total_rg	46.50 Å
总原子数 total_atoms	11051
残基数 n_residues	1470
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	151.4 Å
Rg (实空间) rg_real	46.62 Å
Rg 误差 (实空间) rg_real_error	1.40 Å
I(0) (实空间) i0_real	3.7180e+08
I(0) 误差 (实空间) i0_real_error	6.8510e+06
Rg (倒空间) rg_reciprocal	46.73 Å
I(0) (倒空间) i0_reciprocal	371900000.0000
解质量估计 total_estimate	0.7952
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	71.3 Å
偏度 Skewness skewness	0.026
峰度 Kurtosis kurtosis	-0.785
角度范围 angular_range	— – 0.1700 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	19130000.0000
实空间数据点数 n_real_points	35
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.786; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; 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) 18 domains

SCOP 2.08 (10 domains)

结构域编号 domain_id	d1pdwa_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.23 — Flavodoxin-like
超家族 Superfamily superfamily	c.23.16 — Class I glutamine amidotransferase-like
家族 Family family	c.23.16.2 — DJ-1/PfpI

结构域编号 domain_id	d1pdwb_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.23 — Flavodoxin-like
超家族 Superfamily superfamily	c.23.16 — Class I glutamine amidotransferase-like
家族 Family family	c.23.16.2 — DJ-1/PfpI

结构域编号 domain_id	d1pdwc_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.23 — Flavodoxin-like
超家族 Superfamily superfamily	c.23.16 — Class I glutamine amidotransferase-like
家族 Family family	c.23.16.2 — DJ-1/PfpI

结构域编号 domain_id	d1pdwd_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.23 — Flavodoxin-like
超家族 Superfamily superfamily	c.23.16 — Class I glutamine amidotransferase-like
家族 Family family	c.23.16.2 — DJ-1/PfpI

结构域编号 domain_id	d1pdwe1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.23 — Flavodoxin-like
超家族 Superfamily superfamily	c.23.16 — Class I glutamine amidotransferase-like
家族 Family family	c.23.16.2 — DJ-1/PfpI

结构域编号 domain_id	d1pdwe2
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	d1pdwf_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.23 — Flavodoxin-like
超家族 Superfamily superfamily	c.23.16 — Class I glutamine amidotransferase-like
家族 Family family	c.23.16.2 — DJ-1/PfpI

结构域编号 domain_id	d1pdwg1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.23 — Flavodoxin-like
超家族 Superfamily superfamily	c.23.16 — Class I glutamine amidotransferase-like
家族 Family family	c.23.16.2 — DJ-1/PfpI

结构域编号 domain_id	d1pdwg2
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	d1pdwh_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.23 — Flavodoxin-like
超家族 Superfamily superfamily	c.23.16 — Class I glutamine amidotransferase-like
家族 Family family	c.23.16.2 — DJ-1/PfpI

CATH v4.4 (8 domains)

结构域编号 domain_id	1pdwA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	880 — Class I glutamine amidotransferase (GATase) domain

结构域编号 domain_id	1pdwB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	880 — Class I glutamine amidotransferase (GATase) domain

结构域编号 domain_id	1pdwC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	880 — Class I glutamine amidotransferase (GATase) domain

结构域编号 domain_id	1pdwD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	880 — Class I glutamine amidotransferase (GATase) domain

结构域编号 domain_id	1pdwE00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	880 — Class I glutamine amidotransferase (GATase) domain

结构域编号 domain_id	1pdwF00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	880 — Class I glutamine amidotransferase (GATase) domain

结构域编号 domain_id	1pdwG00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	880 — Class I glutamine amidotransferase (GATase) domain

结构域编号 domain_id	1pdwH00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	880 — Class I glutamine amidotransferase (GATase) domain

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7. 引用文献 (1)

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晶胞边长 a length_a	71.256 Å
晶胞边长 b length_b	83.664 Å
晶胞边长 c length_c	114.159 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	100.56 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	16

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	2.200 Å
最低分辨率 resolution_low	19.910 Å
R 因子 r_factor	—
R_work r_work	0.1800
R_free r_free	0.2430

描述 description	DJ-1
分子量 formula_weight	21175.8 kDa
来源方法 src_method	man
拷贝数 entity_count	8

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H
原子数 atom_count	12021

Crystal structure of human DJ-1, P 1 21 1 space group

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) 18 domains

SCOP 2.08 (10 domains)

CATH v4.4 (8 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	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	970

fit	/app/data/saxs_computation/pd/1pdw/1pdw.fit
pddf	/app/data/pr_computation/pd/1pdw/1pdw.pr.out
profile	/app/data/saxs_computation/pd/1pdw/1pdw.dat