SAXSdb — 1tc5

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1tc5
沉积日期 deposition_date	2004-05-20
结构标题 title	Structural Analysis of a probable eukaryotic D-amino acid tRNA deacylase
关键词 keywords	;SGPP, STRUCTURAL GENOMICS, PSI, Protein Structure Initiative, Structural Genomics of Pathogenic Protozoa Consortium, UNKNOWN FUNCTION ;; STRUCTURAL GENOMICS, UNKNOWN FUNCTION
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	34.77 Å
回转半径 Rg (电子) rg_electron	34.57 Å
零角强度 I(0) i0	110864000.00
分子量 molecular_weight	82350.0 kDa
排除体积 excluded_volume	102500 Å³
包络体积 envelope_volume	140440 Å³
水化壳体积 shell_volume	35728 Å³
包络直径 envelope_diameter	126.4 Å
壳层 Rg shell_rg	38.64 Å
包络 Rg envelope_rg	34.64 Å
形状 Rg shape_rg	34.56 Å
总 Rg total_rg	34.95 Å
总原子数 total_atoms	5790
残基数 n_residues	746
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	119.8 Å
Rg (实空间) rg_real	34.88 Å
Rg 误差 (实空间) rg_real_error	0.94 Å
I(0) (实空间) i0_real	1.1090e+08
I(0) 误差 (实空间) i0_real_error	1.8250e+06
Rg (倒空间) rg_reciprocal	34.81 Å
I(0) (倒空间) i0_reciprocal	110900000.0000
解质量估计 total_estimate	0.8663
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	31.3 Å
偏度 Skewness skewness	0.332
峰度 Kurtosis kurtosis	-0.599
角度范围 angular_range	— – 0.2300 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	28540000.0000
实空间数据点数 n_real_points	47
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.797; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.876; Smooth: 0.992

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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) 12 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1tc5a1
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	d1tc5a2
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	d1tc5b1
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	d1tc5b2
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	d1tc5c1
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	d1tc5c2
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	d1tc5d1
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	d1tc5d2
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

CATH v4.4 (4 domains)

结构域编号 domain_id	1tc5A00
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	1tc5B00
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	1tc5C00
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	1tc5D00
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	67.479 Å
晶胞边长 b length_b	67.465 Å
晶胞边长 c length_c	174.410 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	16

空间群 space_group	P 2 2 21
空间群编号 int_tables_number	17
晶系 crystal_system	—

分辨率 resolution	1.930 Å
最低分辨率 resolution_low	46.130 Å
R 因子 r_factor	0.2005
R_work r_work	0.1987
R_free r_free	0.2343

描述 description	Probable eukaryotic D-amino acid tRNA deacylase, LMAJ005534AAA
分子量 formula_weight	21774.9 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	6204

Structural Analysis of a probable eukaryotic D-amino acid tRNA deacylase

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) 12 domains

SCOP 2.08 (8 domains)

CATH v4.4 (4 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)

来源生物 organism	Leishmania major
NCBI 分类编号 ncbi_taxonomy_id	5664
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	382

fit	/app/data/saxs_computation/tc/1tc5/1tc5.fit
pddf	/app/data/pr_computation/tc/1tc5/1tc5.pr.out
profile	/app/data/saxs_computation/tc/1tc5/1tc5.dat