SAXSdb — 1uug

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1uug
沉积日期 deposition_date	1998-10-31
结构标题 title	ESCHERICHIA COLI URACIL-DNA GLYCOSYLASE:INHIBITOR COMPLEX WITH WILD-TYPE UDG AND WILD-TYPE UGI
关键词 keywords	DNA BASE EXCISION REPAIR, PROTEIN MIMICRY OF DNA, PROTEIN INHIBITOR, REPLICATION, HYDROLASE; REPLICATION, 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	40.30 Å
回转半径 Rg (电子) rg_electron	39.88 Å
零角强度 I(0) i0	67680600.00
分子量 molecular_weight	68165.0 kDa
排除体积 excluded_volume	85761 Å³
包络体积 envelope_volume	124660 Å³
水化壳体积 shell_volume	25632 Å³
包络直径 envelope_diameter	122.6 Å
壳层 Rg shell_rg	47.36 Å
包络 Rg envelope_rg	37.79 Å
形状 Rg shape_rg	39.85 Å
总 Rg total_rg	40.45 Å
总原子数 total_atoms	5848
残基数 n_residues	607
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	123.6 Å
Rg (实空间) rg_real	40.51 Å
Rg 误差 (实空间) rg_real_error	1.30 Å
I(0) (实空间) i0_real	6.7680e+07
I(0) 误差 (实空间) i0_real_error	1.1930e+06
Rg (倒空间) rg_reciprocal	40.31 Å
I(0) (倒空间) i0_reciprocal	67670000.0000
解质量估计 total_estimate	0.6237
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	25.4 Å
偏度 Skewness skewness	0.152
峰度 Kurtosis kurtosis	-1.304
角度范围 angular_range	— – 0.1950 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	15840000.0000
实空间数据点数 n_real_points	40
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.060; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.299; Smooth: 0.625

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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	URACIL-DNA GLYCOSYLASE
分子量 formula_weight	25725.2 kDa
EC 编号 ec_number	3.2.2.3
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,C
原子数 atom_count	6412

MANELTWHDVLAEEKQQPYFLNTLQTVASERQSGVTIYPPQKDVFNAFRFTELGDVKVVILGQDPYHGPGQAHGLAFSVRPGIAIPPSLLNMYKELENTIPGFTRPNHGYLESWARQGVLLLNTVLTVRAGQAHSHASLGWETFTDKVISLINQHREGVVFLLWGSHAQKKGAIIDKQRHHVLKAPHPSPLSAHRGFFGCNHFVLANQWLEQRGETPIDWMPVLPAESE

来源 Source

来源生物 organism	Escherichia coli K12
NCBI 分类编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	URACIL-DNA GLYCOSYLASE INHIBITOR
分子量 formula_weight	9482.7 kDa
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	B,D

MTNLSDIIEKETGKQLVIQESILMLPEEVEEVIGNKPESDILVHTAYDESTDENVMLLTSDAPEYKPWALVIQDSNGENKIKML

来源 Source

来源生物 organism	Bacillus phage PBS2
NCBI 分类编号 ncbi_taxonomy_id	10684
宿主生物 host_organism	Escherichia coli

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	188

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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	d1uuga_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.18 — Uracil-DNA glycosylase-like
超家族 Superfamily superfamily	c.18.1 — Uracil-DNA glycosylase-like
家族 Family family	c.18.1.1 — Uracil-DNA glycosylase

结构域编号 domain_id	d1uugb_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.17 — Cystatin-like
超家族 Superfamily superfamily	d.17.5 — Uracil-DNA glycosylase inhibitor protein
家族 Family family	d.17.5.1 — Uracil-DNA glycosylase inhibitor protein

结构域编号 domain_id	d1uugc_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.18 — Uracil-DNA glycosylase-like
超家族 Superfamily superfamily	c.18.1 — Uracil-DNA glycosylase-like
家族 Family family	c.18.1.1 — Uracil-DNA glycosylase

结构域编号 domain_id	d1uugd_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.17 — Cystatin-like
超家族 Superfamily superfamily	d.17.5 — Uracil-DNA glycosylase inhibitor protein
家族 Family family	d.17.5.1 — Uracil-DNA glycosylase inhibitor protein

CATH v4.4 (4 domains)

结构域编号 domain_id	1uugA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	470 — Uracil-DNA Glycosylase, subunit E
同源超家族 H-superfamily homologous superfamily	10 — Uracil-DNA glycosylase-like domain

结构域编号 domain_id	1uugB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
同源超家族 H-superfamily homologous superfamily	20 — Bacteriophage PBS2, uracil-glycosylase inhibitor

结构域编号 domain_id	1uugC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	470 — Uracil-DNA Glycosylase, subunit E
同源超家族 H-superfamily homologous superfamily	10 — Uracil-DNA glycosylase-like domain

结构域编号 domain_id	1uugD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
同源超家族 H-superfamily homologous superfamily	20 — Bacteriophage PBS2, uracil-glycosylase inhibitor

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7. 引用文献 (1)

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晶胞边长 a length_a	79.986 Å
晶胞边长 b length_b	86.713 Å
晶胞边长 c length_c	108.641 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	8

空间群 space_group	P 21 21 2
空间群编号 int_tables_number	18
晶系 crystal_system	—

分辨率 resolution	2.400 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	—
R_work r_work	0.1900
R_free r_free	0.2320

fit	/app/data/saxs_computation/uu/1uug/1uug.fit
pddf	/app/data/pr_computation/uu/1uug/1uug.pr.out
profile	/app/data/saxs_computation/uu/1uug/1uug.dat

ESCHERICHIA COLI URACIL-DNA GLYCOSYLASE:INHIBITOR COMPLEX WITH WILD-TYPE UDG AND WILD-TYPE UGI

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 (3)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 water

6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)