1g59

GLUTAMYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(GLU).

Method: X-RAY DIFFRACTION D_max: 149.5 Å Quality: GOOD

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1g59
沉积日期 deposition_date	2000-10-31
结构标题 title	GLUTAMYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(GLU).
关键词 keywords	;aminoacyl-tRNA synthetase, protein-RNA complex, transfer RNA, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Structural Genomics, LIGASE-RNA COMPLEX ;; LIGASE/RNA
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	52.20 Å
回转半径 Rg (电子) rg_electron	52.25 Å
零角强度 I(0) i0	517008000.00
分子量 molecular_weight	156290.0 kDa
排除体积 excluded_volume	181260 Å³
包络体积 envelope_volume	289870 Å³
水化壳体积 shell_volume	45648 Å³
包络直径 envelope_diameter	161.0 Å
壳层 Rg shell_rg	59.52 Å
包络 Rg envelope_rg	48.81 Å
形状 Rg shape_rg	52.24 Å
总 Rg total_rg	52.47 Å
总原子数 total_atoms	10820
残基数 n_residues	1086
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	149.5 Å
Rg (实空间) rg_real	52.24 Å
Rg 误差 (实空间) rg_real_error	1.40 Å
I(0) (实空间) i0_real	5.1700e+08
I(0) 误差 (实空间) i0_real_error	8.5840e+06
Rg (倒空间) rg_reciprocal	52.14 Å
I(0) (倒空间) i0_reciprocal	516900000.0000
解质量估计 total_estimate	0.7562
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	89.7 Å
偏度 Skewness skewness	0.030
峰度 Kurtosis kurtosis	-1.071
角度范围 angular_range	— – 0.1500 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	12060000.0000
实空间数据点数 n_real_points	31
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.707; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.704; Smooth: 0.000

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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	TRNA(GLU)
分子量 formula_weight	24105.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	B,D
原子数 atom_count	11092

GGCCCCAUCGUCUAGCGGUUAGGACGCGGCCCUCUCAAGGCCGAAACGGGGGUUCGAUUCCCCCUGGGGUCACCA

Entity 2 polymer

描述 description	GLUTAMYL-TRNA SYNTHETASE
分子量 formula_weight	53979.7 kDa
EC 编号 ec_number	6.1.1.17
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

MVVTRIAPSPTGDPHVGTAYIALFNYAWARRNGGRFIVRIEDTDRARYVPGAEERILAALKWLGLSYDEGPDVAAPTGPYRQSERLPLYQKYAEELLKRGWAYRAFETPEELEQIRKEKGGYDGRARNIPPEEAEERARRGEPHVIRLKVPRPGTTEVKDELRGVVVYDNQEIPDVVLLKSDGYPTYHLANVVDDHLMGVTDVIRAEEWLVSTPIHVLLYRAFGWEAPRFYHMPLLRNPDKTKISKRKSHTSLDWYKAEGFLPEALRNYLCLMGFSMPDGREIFTLEEFIQAFTWERVSLGGPVFDLEKLRWMNGKYIREVLSLEEVAERVKPFLREAGLSWESEAYLRRAVELMRPRFDTLKEFPEKARYLFTEDYPVSEKAQRKLEEGLPLLKELYPRLRAQEEWTEAALEALLRGFAAEKGVKLGQVAQPLRAALTGSLETPGLFEILALLGKERALRRLERALA

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

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	272

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6. 折叠分类 (SCOP + CATH) 14 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1g59a1
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	d1g59a2
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

结构域编号 domain_id	d1g59c1
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	d1g59c2
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 (10 domains)

结构域编号 domain_id	1g59A01
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	1g59A02
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	1g59A03
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	1g59A04
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	1g59A05
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 —

结构域编号 domain_id	1g59C01
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	1g59C02
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	1g59C03
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	1g59C04
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	1g59C05
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 (1)

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晶胞边长 a length_a	109.980 Å
晶胞边长 b length_b	218.670 Å
晶胞边长 c length_c	134.670 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	C 2 2 21
空间群编号 int_tables_number	20
晶系 crystal_system	—

分辨率 resolution	2.400 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	0.2190
R_work r_work	0.2180
R_free r_free	0.2980

fit	/app/data/saxs_computation/g5/1g59/1g59.fit
pddf	/app/data/pr_computation/g5/1g59/1g59.pr.out
profile	/app/data/saxs_computation/g5/1g59/1g59.dat

GLUTAMYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(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

5. 实体与聚合体信息 (3)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 water

6. 折叠分类 (SCOP + CATH) 14 domains

SCOP 2.08 (4 domains)

CATH v4.4 (10 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)