SAXSdb — 1p42

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1p42
沉积日期 deposition_date	2003-04-21
结构标题 title	Crystal structure of Aquifex aeolicus LpxC Deacetylase (Zinc-Inhibited Form)
关键词 keywords	alpha+beta fold, hydrophobic tunnel, 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	29.53 Å
回转半径 Rg (电子) rg_electron	29.17 Å
零角强度 I(0) i0	56354400.00
分子量 molecular_weight	61752.0 kDa
排除体积 excluded_volume	78423 Å³
包络体积 envelope_volume	93171 Å³
水化壳体积 shell_volume	27698 Å³
包络直径 envelope_diameter	97.8 Å
壳层 Rg shell_rg	35.15 Å
包络 Rg envelope_rg	29.12 Å
形状 Rg shape_rg	29.16 Å
总 Rg total_rg	29.79 Å
总原子数 total_atoms	4353
残基数 n_residues	534
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	98.1 Å
Rg (实空间) rg_real	29.74 Å
Rg 误差 (实空间) rg_real_error	0.99 Å
I(0) (实空间) i0_real	5.6350e+07
I(0) 误差 (实空间) i0_real_error	8.8760e+05
Rg (倒空间) rg_reciprocal	29.66 Å
I(0) (倒空间) i0_reciprocal	56350000.0000
解质量估计 total_estimate	0.8203
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	25.4 Å
偏度 Skewness skewness	0.470
峰度 Kurtosis kurtosis	-0.553
角度范围 angular_range	— – 0.2700 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	35810000.0000
实空间数据点数 n_real_points	55
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.702; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.817; Smooth: 0.738

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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	UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
分子量 formula_weight	30858.3 kDa
EC 编号 ec_number	3.5.1.-
突变 mutation	C193A
来源方法 src_method	man
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	4750

GLEKTVKEKLSFEGVGIHTGEYSKLIIHPEKEGTGIRFFKNGVYIPARHEFVVHTNHSTDLGFKGQRIKTVEHILSVLHLLEITNVTIEVIGNEIPILDGSGWEFYEAIRKNILNQNREIDYFVVEEPIIVEDEGRLIKAEPSDTLEVTYEGEFKNFLGRQKFTFVEGNEEEIVLARTFAFDWEIEHIKKVGLGKGGSLKNTLVLGKDKVYNPEGLRYENEPVRHKVFDLIGDLYLLGSPVKGKFYSFRGGHSLNVKLVKELAKKQKLTR

来源 Source

来源生物 organism	Aquifex aeolicus
NCBI 分类编号 ncbi_taxonomy_id	63363
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	7

Entity 3 non-polymer

描述 description	MYRISTIC ACID
分子量 formula_weight	228.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	309

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1p42a1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.14 — Ribosomal protein S5 domain 2-like
超家族 Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
家族 Family family	d.14.1.7 — UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase LpxC

结构域编号 domain_id	d1p42a2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.14 — Ribosomal protein S5 domain 2-like
超家族 Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
家族 Family family	d.14.1.7 — UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase LpxC

结构域编号 domain_id	d1p42b1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.14 — Ribosomal protein S5 domain 2-like
超家族 Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
家族 Family family	d.14.1.7 — UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase LpxC

结构域编号 domain_id	d1p42b2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.14 — Ribosomal protein S5 domain 2-like
超家族 Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
家族 Family family	d.14.1.7 — UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase LpxC

CATH v4.4 (4 domains)

结构域编号 domain_id	1p42A01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	230 — Ribosomal Protein S5; domain 2
同源超家族 H-superfamily homologous superfamily	20 — lpxc deacetylase, domain 1

结构域编号 domain_id	1p42A02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1700 — lpxc deacetylase, domain 1
同源超家族 H-superfamily homologous superfamily	10 — lpxc deacetylase, domain 2

结构域编号 domain_id	1p42B01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	230 — Ribosomal Protein S5; domain 2
同源超家族 H-superfamily homologous superfamily	20 — lpxc deacetylase, domain 1

结构域编号 domain_id	1p42B02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1700 — lpxc deacetylase, domain 1
同源超家族 H-superfamily homologous superfamily	10 — lpxc deacetylase, domain 2

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7. 引用文献 (1)

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晶胞边长 a length_a	101.660 Å
晶胞边长 b length_b	101.660 Å
晶胞边长 c length_c	125.100 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	120.00 °
晶胞分子数 Z z_pdb	12

空间群 space_group	P 61
空间群编号 int_tables_number	169
晶系 crystal_system	—

分辨率 resolution	2.000 Å
最低分辨率 resolution_low	29.470 Å
R 因子 r_factor	0.1990
R_work r_work	0.1990
R_free r_free	0.2110

fit	/app/data/saxs_computation/p4/1p42/1p42.fit
pddf	/app/data/pr_computation/p4/1p42/1p42.pr.out
profile	/app/data/saxs_computation/p4/1p42/1p42.dat

Crystal structure of Aquifex aeolicus LpxC Deacetylase (Zinc-Inhibited Form)

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