SAXSdb — 1jke

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1jke
沉积日期 deposition_date	2001-07-12
结构标题 title	D-Tyr tRNATyr deacylase from Escherichia coli
关键词 keywords	beta-alpha-barrel, 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	28.94 Å
回转半径 Rg (电子) rg_electron	28.16 Å
零角强度 I(0) i0	73873600.00
分子量 molecular_weight	63906.0 kDa
排除体积 excluded_volume	78461 Å³
包络体积 envelope_volume	95935 Å³
水化壳体积 shell_volume	29497 Å³
包络直径 envelope_diameter	101.1 Å
壳层 Rg shell_rg	33.97 Å
包络 Rg envelope_rg	28.19 Å
形状 Rg shape_rg	28.13 Å
总 Rg total_rg	28.81 Å
总原子数 total_atoms	4435
残基数 n_residues	580
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	95.6 Å
Rg (实空间) rg_real	29.09 Å
Rg 误差 (实空间) rg_real_error	0.71 Å
I(0) (实空间) i0_real	7.3870e+07
I(0) 误差 (实空间) i0_real_error	1.0930e+06
Rg (倒空间) rg_reciprocal	29.03 Å
I(0) (倒空间) i0_reciprocal	73870000.0000
解质量估计 total_estimate	0.8547
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	29.6 Å
偏度 Skewness skewness	0.512
峰度 Kurtosis kurtosis	-0.307
角度范围 angular_range	— – 0.2750 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	15740000.0000
实空间数据点数 n_real_points	56
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.787; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.894; Smooth: 0.851

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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	D-Tyr-tRNATyr deacylase
分子量 formula_weight	15965.0 kDa
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	4890

MIALIQRVTRASVTVEGEVTGEIGAGLLVLLGVEKDDDEQKANRLCERVLGYRIFSDAEGKMNLNVQQAGGSVLVVSQFTLAADTERGMRPSFSKGASPDRAEALYDYFVERCRQQEMNTQTGRFAADMQVSLVNDGPVTFWLQV

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562
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	12

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	419

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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	d1jkea_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.110 — DTD-like
超家族 Superfamily superfamily	c.110.1 — DTD-like
家族 Family family	c.110.1.1 — DTD-like

结构域编号 domain_id	d1jkeb_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.110 — DTD-like
超家族 Superfamily superfamily	c.110.1 — DTD-like
家族 Family family	c.110.1.1 — DTD-like

结构域编号 domain_id	d1jkec_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.110 — DTD-like
超家族 Superfamily superfamily	c.110.1 — DTD-like
家族 Family family	c.110.1.1 — DTD-like

结构域编号 domain_id	d1jked_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.110 — DTD-like
超家族 Superfamily superfamily	c.110.1 — DTD-like
家族 Family family	c.110.1.1 — DTD-like

CATH v4.4 (4 domains)

结构域编号 domain_id	1jkeA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	80 — D-tyrosyl-trna(Tyr) Deacylase; Chain: A;
同源超家族 H-superfamily homologous superfamily	10 — D-tyrosyl-tRNA(Tyr) deacylase

结构域编号 domain_id	1jkeB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	80 — D-tyrosyl-trna(Tyr) Deacylase; Chain: A;
同源超家族 H-superfamily homologous superfamily	10 — D-tyrosyl-tRNA(Tyr) deacylase

结构域编号 domain_id	1jkeC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	80 — D-tyrosyl-trna(Tyr) Deacylase; Chain: A;
同源超家族 H-superfamily homologous superfamily	10 — D-tyrosyl-tRNA(Tyr) deacylase

结构域编号 domain_id	1jkeD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	80 — D-tyrosyl-trna(Tyr) Deacylase; Chain: A;
同源超家族 H-superfamily homologous superfamily	10 — D-tyrosyl-tRNA(Tyr) deacylase

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7. 引用文献 (1)

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晶胞边长 a length_a	118.300 Å
晶胞边长 b length_b	82.930 Å
晶胞边长 c length_c	83.510 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	128.29 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	16

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	1.550 Å
最低分辨率 resolution_low	500.000 Å
R 因子 r_factor	0.2090
R_work r_work	0.2090
R_free r_free	0.2280

fit	/app/data/saxs_computation/jk/1jke/1jke.fit
pddf	/app/data/pr_computation/jk/1jke/1jke.pr.out
profile	/app/data/saxs_computation/jk/1jke/1jke.dat

D-Tyr tRNATyr deacylase from Escherichia coli

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 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 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)