SAXSdb — 1j09

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1j09
沉积日期 deposition_date	2002-11-12
结构标题 title	Crystal structure of Thermus thermophilus glutamyl-tRNA synthetase complexed with ATP and Glu
关键词 keywords	GluRS-ATP-Glu complex, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Structural Genomics, ligase; LIGASE
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	30.85 Å
回转半径 Rg (电子) rg_electron	31.10 Å
零角强度 I(0) i0	47391200.00
分子量 molecular_weight	54586.0 kDa
排除体积 excluded_volume	68559 Å³
包络体积 envelope_volume	87061 Å³
水化壳体积 shell_volume	26194 Å³
包络直径 envelope_diameter	113.9 Å
壳层 Rg shell_rg	34.01 Å
包络 Rg envelope_rg	31.48 Å
形状 Rg shape_rg	31.09 Å
总 Rg total_rg	31.40 Å
总原子数 total_atoms	3856
残基数 n_residues	468
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	109.6 Å
Rg (实空间) rg_real	31.34 Å
Rg 误差 (实空间) rg_real_error	1.23 Å
I(0) (实空间) i0_real	4.7390e+07
I(0) 误差 (实空间) i0_real_error	8.8040e+05
Rg (倒空间) rg_reciprocal	31.13 Å
I(0) (倒空间) i0_reciprocal	47380000.0000
解质量估计 total_estimate	0.7555
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	25.8 Å
偏度 Skewness skewness	0.652
峰度 Kurtosis kurtosis	-0.238
角度范围 angular_range	— – 0.2550 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	8238000.0000
实空间数据点数 n_real_points	52
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.544; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.360; Smooth: 0.824

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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 (5)

Entity 1 polymer

描述 description	Glutamyl-tRNA synthetase
分子量 formula_weight	53988.7 kDa
EC 编号 ec_number	6.1.1.17
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	4211

MVVTRIAPSPTGDPHVGTAYIALFNYAWARRNGGRFIVRIEDTDRARYVPGAEERILAALKWLGLSYDEGPDVGGPHGPYRQSERLPLYQKYAEELLKRGWAYRAFETPEELEQIRKEKGGYDGRARNIPPEEAEERARRGEPHVIRLKVPRPGTTEVKDELRGVVVYDNQEIPDVVLLKSDGYPTYHLANVVDDHLMGVTDVIRAEEWLVSTPIHVLLYRAFGWEAPRFYHMPLLRNPDKTKISKRKSHTSLDWYKAEGFLPEALRNYLCLMGFSMPDGREIFTLEEFIQAFTWERVSLGGPVFDLEKLRWMNGKYIREVLSLEEVAERVKPFLREAGLSWESEAYLRRAVELMRPRFDTLKEFPEKARYLFTEDYPVSEKAQRKLEEGLPLLKELYPRLRAQEEWTEAALEALLRGFAAEKGVKLGQVAQPLRAALTGSLETPGLFEILALLGKERALRRLERALA

来源 Source

来源生物 organism	Thermus thermophilus
NCBI 分类编号 ncbi_taxonomy_id	274
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	GLUTAMIC ACID
分子量 formula_weight	147.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	ADENOSINE-5'-TRIPHOSPHATE
分子量 formula_weight	507.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 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	355

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6. 折叠分类 (SCOP + CATH) 7 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1j09a1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.97 — An anticodon-binding domain of class I aminoacyl-tRNA synthetases
超家族 Superfamily superfamily	a.97.1 — An anticodon-binding domain of class I aminoacyl-tRNA synthetases
家族 Family family	a.97.1.1 — C-terminal domain of glutamyl-tRNA synthetase (GluRS)

结构域编号 domain_id	d1j09a2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
超家族 Superfamily superfamily	c.26.1 — Nucleotidylyl transferase
家族 Family family	c.26.1.1 — Class I aminoacyl-tRNA synthetases (RS), catalytic domain

CATH v4.4 (5 domains)

结构域编号 domain_id	1j09A01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	620 — HUPs

结构域编号 domain_id	1j09A02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1160 — Glutamyl-tRNA Synthetase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Glutamyl-trna Synthetase; Domain 2

结构域编号 domain_id	1j09A03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	800 — Glutamyl-tRNA Synthetase; domain 3
同源超家族 H-superfamily homologous superfamily	10 — Glutamyl-tRNA Synthetase; Domain 3

结构域编号 domain_id	1j09A04
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily	70 — Glutamate-tRNA synthetase, class I, anticodon-binding domain 1

结构域编号 domain_id	1j09A05
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	10 — Arc Repressor Mutant, subunit A
同源超家族 H-superfamily homologous superfamily	350 —

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7. 引用文献 (3)

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晶胞边长 a length_a	81.920 Å
晶胞边长 b length_b	82.620 Å
晶胞边长 c length_c	83.110 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	4

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	1.800 Å
最低分辨率 resolution_low	37.120 Å
R 因子 r_factor	0.1990
R_work r_work	0.1990
R_free r_free	0.2270

fit	/app/data/saxs_computation/j0/1j09/1j09.fit
pddf	/app/data/pr_computation/j0/1j09/1j09.pr.out
profile	/app/data/saxs_computation/j0/1j09/1j09.dat

Crystal structure of Thermus thermophilus glutamyl-tRNA synthetase complexed with ATP and Glu

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