2dg0

Crystal structure of Drp35, a 35kDa drug responsive protein from Staphylococcus aureus

Method: X-RAY DIFFRACTION D_max: 185.3 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	2dg0
沉积日期 deposition_date	2006-03-07
结构标题 title	Crystal structure of Drp35, a 35kDa drug responsive protein from Staphylococcus aureus
关键词 keywords	BETA PROPELLER, HYDROLASE; HYDROLASE
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	55.96 Å
回转半径 Rg (电子) rg_electron	55.91 Å
零角强度 I(0) i0	2608250000.00
分子量 molecular_weight	429200.0 kDa
排除体积 excluded_volume	535140 Å³
包络体积 envelope_volume	719250 Å³
水化壳体积 shell_volume	106460 Å³
包络直径 envelope_diameter	188.6 Å
壳层 Rg shell_rg	59.48 Å
包络 Rg envelope_rg	54.29 Å
形状 Rg shape_rg	55.92 Å
总 Rg total_rg	55.96 Å
总原子数 total_atoms	30096
残基数 n_residues	3787
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	185.3 Å
Rg (实空间) rg_real	55.97 Å
Rg 误差 (实空间) rg_real_error	1.68 Å
I(0) (实空间) i0_real	2.6080e+09
I(0) 误差 (实空间) i0_real_error	5.2910e+07
Rg (倒空间) rg_reciprocal	55.93 Å
I(0) (倒空间) i0_reciprocal	2608000000.0000
解质量估计 total_estimate	0.8243
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	59.6 Å
偏度 Skewness skewness	0.300
峰度 Kurtosis kurtosis	-0.515
角度范围 angular_range	— – 0.1400 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	123500000.0000
实空间数据点数 n_real_points	29
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.904; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; 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) 27 domains

SCOP 2.08 (15 domains)

结构域编号 domain_id	d2dg0a1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.68 — 6-bladed beta-propeller
超家族 Superfamily superfamily	b.68.6 — Calcium-dependent phosphotriesterase
家族 Family family	b.68.6.1 — SGL-like

结构域编号 domain_id	d2dg0a2
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	d2dg0b_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.68 — 6-bladed beta-propeller
超家族 Superfamily superfamily	b.68.6 — Calcium-dependent phosphotriesterase
家族 Family family	b.68.6.1 — SGL-like

结构域编号 domain_id	d2dg0c_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.68 — 6-bladed beta-propeller
超家族 Superfamily superfamily	b.68.6 — Calcium-dependent phosphotriesterase
家族 Family family	b.68.6.1 — SGL-like

结构域编号 domain_id	d2dg0d_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.68 — 6-bladed beta-propeller
超家族 Superfamily superfamily	b.68.6 — Calcium-dependent phosphotriesterase
家族 Family family	b.68.6.1 — SGL-like

结构域编号 domain_id	d2dg0e2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.68 — 6-bladed beta-propeller
超家族 Superfamily superfamily	b.68.6 — Calcium-dependent phosphotriesterase
家族 Family family	b.68.6.1 — SGL-like

结构域编号 domain_id	d2dg0e3
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	d2dg0f_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.68 — 6-bladed beta-propeller
超家族 Superfamily superfamily	b.68.6 — Calcium-dependent phosphotriesterase
家族 Family family	b.68.6.1 — SGL-like

结构域编号 domain_id	d2dg0g_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.68 — 6-bladed beta-propeller
超家族 Superfamily superfamily	b.68.6 — Calcium-dependent phosphotriesterase
家族 Family family	b.68.6.1 — SGL-like

结构域编号 domain_id	d2dg0h_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.68 — 6-bladed beta-propeller
超家族 Superfamily superfamily	b.68.6 — Calcium-dependent phosphotriesterase
家族 Family family	b.68.6.1 — SGL-like

结构域编号 domain_id	d2dg0i_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.68 — 6-bladed beta-propeller
超家族 Superfamily superfamily	b.68.6 — Calcium-dependent phosphotriesterase
家族 Family family	b.68.6.1 — SGL-like

结构域编号 domain_id	d2dg0j2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.68 — 6-bladed beta-propeller
超家族 Superfamily superfamily	b.68.6 — Calcium-dependent phosphotriesterase
家族 Family family	b.68.6.1 — SGL-like

结构域编号 domain_id	d2dg0j3
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	d2dg0k_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.68 — 6-bladed beta-propeller
超家族 Superfamily superfamily	b.68.6 — Calcium-dependent phosphotriesterase
家族 Family family	b.68.6.1 — SGL-like

结构域编号 domain_id	d2dg0l_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.68 — 6-bladed beta-propeller
超家族 Superfamily superfamily	b.68.6 — Calcium-dependent phosphotriesterase
家族 Family family	b.68.6.1 — SGL-like

CATH v4.4 (12 domains)

结构域编号 domain_id	2dg0A00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	120 — 6 Propeller
拓扑 Topology topology	10 — Neuraminidase
同源超家族 H-superfamily homologous superfamily	30 — TolB, C-terminal domain

结构域编号 domain_id	2dg0B00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	120 — 6 Propeller
拓扑 Topology topology	10 — Neuraminidase
同源超家族 H-superfamily homologous superfamily	30 — TolB, C-terminal domain

结构域编号 domain_id	2dg0C00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	120 — 6 Propeller
拓扑 Topology topology	10 — Neuraminidase
同源超家族 H-superfamily homologous superfamily	30 — TolB, C-terminal domain

结构域编号 domain_id	2dg0D00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	120 — 6 Propeller
拓扑 Topology topology	10 — Neuraminidase
同源超家族 H-superfamily homologous superfamily	30 — TolB, C-terminal domain

结构域编号 domain_id	2dg0E00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	120 — 6 Propeller
拓扑 Topology topology	10 — Neuraminidase
同源超家族 H-superfamily homologous superfamily	30 — TolB, C-terminal domain

结构域编号 domain_id	2dg0F00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	120 — 6 Propeller
拓扑 Topology topology	10 — Neuraminidase
同源超家族 H-superfamily homologous superfamily	30 — TolB, C-terminal domain

结构域编号 domain_id	2dg0G00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	120 — 6 Propeller
拓扑 Topology topology	10 — Neuraminidase
同源超家族 H-superfamily homologous superfamily	30 — TolB, C-terminal domain

结构域编号 domain_id	2dg0H00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	120 — 6 Propeller
拓扑 Topology topology	10 — Neuraminidase
同源超家族 H-superfamily homologous superfamily	30 — TolB, C-terminal domain

结构域编号 domain_id	2dg0I00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	120 — 6 Propeller
拓扑 Topology topology	10 — Neuraminidase
同源超家族 H-superfamily homologous superfamily	30 — TolB, C-terminal domain

结构域编号 domain_id	2dg0J00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	120 — 6 Propeller
拓扑 Topology topology	10 — Neuraminidase
同源超家族 H-superfamily homologous superfamily	30 — TolB, C-terminal domain

结构域编号 domain_id	2dg0K00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	120 — 6 Propeller
拓扑 Topology topology	10 — Neuraminidase
同源超家族 H-superfamily homologous superfamily	30 — TolB, C-terminal domain

结构域编号 domain_id	2dg0L00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	120 — 6 Propeller
拓扑 Topology topology	10 — Neuraminidase
同源超家族 H-superfamily homologous superfamily	30 — TolB, C-terminal domain

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7. 引用文献 (1)

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晶胞边长 a length_a	86.089 Å
晶胞边长 b length_b	146.062 Å
晶胞边长 c length_c	151.947 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	93.39 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	24

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	15.000 Å
R 因子 r_factor	0.2000
R_work r_work	0.2000
R_free r_free	0.2220

描述 description	DrP35
分子量 formula_weight	37466.0 kDa
EC 编号 ec_number	3.1.1.25
来源方法 src_method	man
拷贝数 entity_count	12

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H,I,J,K,L
原子数 atom_count	31391

Crystal structure of Drp35, a 35kDa drug responsive protein from Staphylococcus aureus

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) 27 domains

SCOP 2.08 (15 domains)

CATH v4.4 (12 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)

来源生物 organism	Staphylococcus aureus
NCBI 分类编号 ncbi_taxonomy_id	1280
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	1295

fit	/app/data/saxs_computation/dg/2dg0/2dg0.fit
pddf	/app/data/pr_computation/dg/2dg0/2dg0.pr.out
profile	/app/data/saxs_computation/dg/2dg0/2dg0.dat