1n77

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

Method: X-RAY DIFFRACTION D_max: 149.3 Å Quality: REASONABLE

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	1n77
沉积日期 deposition_date	2002-11-13
结构标题 title	Crystal structure of Thermus thermophilus glutamyl-tRNA synthetase complexed with tRNA(Glu) and ATP.
关键词 keywords	ERS/tRNA/ATP, 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	52.37 Å
回转半径 Rg (电子) rg_electron	52.45 Å
零角强度 I(0) i0	529932000.00
分子量 molecular_weight	157360.0 kDa
排除体积 excluded_volume	182040 Å³
包络体积 envelope_volume	293330 Å³
水化壳体积 shell_volume	45905 Å³
包络直径 envelope_diameter	162.3 Å
壳层 Rg shell_rg	59.94 Å
包络 Rg envelope_rg	49.02 Å
形状 Rg shape_rg	52.44 Å
总 Rg total_rg	52.67 Å
总原子数 total_atoms	10886
残基数 n_residues	1084
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	149.3 Å
Rg (实空间) rg_real	52.41 Å
Rg 误差 (实空间) rg_real_error	1.39 Å
I(0) (实空间) i0_real	5.2990e+08
I(0) 误差 (实空间) i0_real_error	8.8160e+06
Rg (倒空间) rg_reciprocal	52.31 Å
I(0) (倒空间) i0_reciprocal	529800000.0000
解质量估计 total_estimate	0.7407
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	89.6 Å
偏度 Skewness skewness	0.024
峰度 Kurtosis kurtosis	-1.092
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	12410000.0000
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: 0.651; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.673; 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 (5)

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	C,D
原子数 atom_count	11391

GGCCCCAUCGUCUAGCGGUUAGGACGCGGCCCUCUCAAGGCCGAAACGGGGGUUCGAUUCCCCCUGGGGUCACCA

Entity 2 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	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B

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 3 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	2

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	2

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	505

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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	d1n77a1
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	d1n77a2
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	d1n77b1
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	d1n77b2
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	1n77A01
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	1n77A02
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	1n77A03
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	1n77A04
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	1n77A05
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	1n77B01
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	1n77B02
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	1n77B03
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	1n77B04
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	1n77B05
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	110.689 Å
晶胞边长 b length_b	219.124 Å
晶胞边长 c length_c	135.215 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	49.400 Å
R 因子 r_factor	0.2130
R_work r_work	0.2130
R_free r_free	0.2570

fit	/app/data/saxs_computation/n7/1n77/1n77.fit
pddf	/app/data/pr_computation/n7/1n77/1n77.pr.out
profile	/app/data/saxs_computation/n7/1n77/1n77.dat

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

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 (5)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 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 (3)

8. 文件与曲线 (10)

Files (7)

Curves (3)