SAXSdb — 1r5t

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1r5t
沉积日期 deposition_date	2003-10-13
结构标题 title	The Crystal Structure of Cytidine Deaminase CDD1, an Orphan C to U editase from Yeast
关键词 keywords	Zinc Dependent Deaminase, RNA editing, APOBEC-1 related protein, 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	24.05 Å
回转半径 Rg (电子) rg_electron	23.05 Å
零角强度 I(0) i0	65760700.00
分子量 molecular_weight	60748.0 kDa
排除体积 excluded_volume	74899 Å³
包络体积 envelope_volume	86584 Å³
水化壳体积 shell_volume	30246 Å³
包络直径 envelope_diameter	87.2 Å
壳层 Rg shell_rg	31.24 Å
包络 Rg envelope_rg	23.55 Å
形状 Rg shape_rg	23.07 Å
总 Rg total_rg	23.82 Å
总原子数 total_atoms	4199
残基数 n_residues	554
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	84.5 Å
Rg (实空间) rg_real	23.91 Å
Rg 误差 (实空间) rg_real_error	0.54 Å
I(0) (实空间) i0_real	6.5760e+07
I(0) 误差 (实空间) i0_real_error	9.2500e+05
Rg (倒空间) rg_reciprocal	23.95 Å
I(0) (倒空间) i0_reciprocal	65760000.0000
解质量估计 total_estimate	0.8565
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	83.2 Å
偏度 Skewness skewness	0.213
峰度 Kurtosis kurtosis	-0.344
角度范围 angular_range	— – 0.3300 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	30220000.0000
实空间数据点数 n_real_points	65
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.714; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.999

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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	Cytidine deaminase
分子量 formula_weight	15552.0 kDa
EC 编号 ec_number	3.5.4.5
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	4517

MKVGGIEDRQLEALKRAALKACELSYSPYSHFRVGCSILTNNDVIFTGANVENASYSNCICAERSAMIQVLMAGHRSGWKCMVICGDSEDQCVSPCGVCRQFINEFVVKDFPIVMLNSTGSRSKVMTMGELLPMAFGPSHLN

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI 分类编号 ncbi_taxonomy_id	4932
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	4

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	318

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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	d1r5ta_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.97 — Cytidine deaminase-like
超家族 Superfamily superfamily	c.97.1 — Cytidine deaminase-like
家族 Family family	c.97.1.1 — Cytidine deaminase

结构域编号 domain_id	d1r5tb_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.97 — Cytidine deaminase-like
超家族 Superfamily superfamily	c.97.1 — Cytidine deaminase-like
家族 Family family	c.97.1.1 — Cytidine deaminase

结构域编号 domain_id	d1r5tc_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.97 — Cytidine deaminase-like
超家族 Superfamily superfamily	c.97.1 — Cytidine deaminase-like
家族 Family family	c.97.1.1 — Cytidine deaminase

结构域编号 domain_id	d1r5td_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.97 — Cytidine deaminase-like
超家族 Superfamily superfamily	c.97.1 — Cytidine deaminase-like
家族 Family family	c.97.1.1 — Cytidine deaminase

CATH v4.4 (4 domains)

结构域编号 domain_id	1r5tA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	140 — Cytidine Deaminase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Cytidine Deaminase, domain 2

结构域编号 domain_id	1r5tB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	140 — Cytidine Deaminase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Cytidine Deaminase, domain 2

结构域编号 domain_id	1r5tC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	140 — Cytidine Deaminase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Cytidine Deaminase, domain 2

结构域编号 domain_id	1r5tD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	140 — Cytidine Deaminase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Cytidine Deaminase, domain 2

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7. 引用文献 (5)

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晶胞边长 a length_a	78.520 Å
晶胞边长 b length_b	86.370 Å
晶胞边长 c length_c	156.260 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	32

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	2.000 Å
最低分辨率 resolution_low	29.050 Å
R 因子 r_factor	0.1880
R_work r_work	0.1880
R_free r_free	0.2220

fit	/app/data/saxs_computation/r5/1r5t/1r5t.fit
pddf	/app/data/pr_computation/r5/1r5t/1r5t.pr.out
profile	/app/data/saxs_computation/r5/1r5t/1r5t.dat

The Crystal Structure of Cytidine Deaminase CDD1, an Orphan C to U editase from Yeast

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

5. 实体与聚合体信息 (3)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 non-polymer

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 (5)

8. 文件与曲线 (10)

Files (7)

Curves (3)