2bte

;Thermus thermophilus Leucyl-tRNA synthetase complexed with a tRNAleu transcript in the post-editing conformation and a post- transfer editing substrate analogue ;

Method: X-RAY DIFFRACTION D_max: 162.1 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	2bte
沉积日期 deposition_date	2005-05-31
结构标题 title	;Thermus thermophilus Leucyl-tRNA synthetase complexed with a tRNAleu transcript in the post-editing conformation and a post- transfer editing substrate analogue ;
关键词 keywords	LIGASE, CLASS I AMINOACYL-TRNA SYNTHETASE EDITING; 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	47.02 Å
回转半径 Rg (电子) rg_electron	49.55 Å
零角强度 I(0) i0	1259270000.00
分子量 molecular_weight	256440.0 kDa
排除体积 excluded_volume	304410 Å³
包络体积 envelope_volume	443350 Å³
水化壳体积 shell_volume	77291 Å³
包络直径 envelope_diameter	175.0 Å
壳层 Rg shell_rg	50.80 Å
包络 Rg envelope_rg	47.73 Å
形状 Rg shape_rg	49.64 Å
总 Rg total_rg	49.32 Å
总原子数 total_atoms	17797
残基数 n_residues	1894
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	162.1 Å
Rg (实空间) rg_real	47.23 Å
Rg 误差 (实空间) rg_real_error	1.54 Å
I(0) (实空间) i0_real	1.2590e+09
I(0) 误差 (实空间) i0_real_error	2.4540e+07
Rg (倒空间) rg_reciprocal	47.02 Å
I(0) (倒空间) i0_reciprocal	1259000000.0000
解质量估计 total_estimate	0.8587
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	52.4 Å
偏度 Skewness skewness	0.475
峰度 Kurtosis kurtosis	-0.200
角度范围 angular_range	— – 0.1700 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	151900000.0000
实空间数据点数 n_real_points	35
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.807; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.742

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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 (9)

Entity 1 polymer

描述 description	AMINOACYL-TRNA SYNTHETASE
分子量 formula_weight	101170.1 kDa
EC 编号 ec_number	6.1.1.4
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,D
原子数 atom_count	17815

MEKYNPHAIEAKWQRFWEEKGFMKAKDLPGGRGKQYVLVMFPYPSGDLHMGHLKNYTMGDVLARFRRMQGYEVLHPMGWDAFGLPAENAALKFGVHPKDWTYANIRQAKESLRLMGILYDWDREVTTCEPEYYRWNQWIFLKMWEKGLAYRAKGLVNWCPKCQTVLANEQVVEGRCWRHEDTPVEKRELEQWYLRITAYAERLLKDLEGLNWPEKVKAMQRAWIGRSEGAEILFPVEGKEVRIPVFTTRPDTLFGATFLVLAPEHPLTLELAAPEKREEVLAYVEAAKRKTEIERQAEGREKTGVFLGAYALNPATGERIPIWTADYVLFGYGTGAIMAVPAHDQRDYEFARKFGLPIKKVIERPGEPLPEPLERAYEEPGIMVNSGPFDGTESEEGKRKVIAWLEEKGLGKGRVTYRLRDWLISRQRYWGTPIPMVHCEACGVVPVPEEELPVLLPDLKDVEDIRPKGKSPLEAHPEFYETTCPKCGGPAKRDTDTMDTFFDSSWYYLRYTDPHNDRLPFDPEKANAWMPVDQYIGGVEHAVLHLLYSRFFTKFLHDLGMVKVEEPFQGLFTQGMVLAWTDFGPVEVEGSVVRLPEPTRIRLEIPESALSLEDVRKMGAELRPHEDGTLHLWKPAVMSKSKGNGVMVGPFVKEQGADIARITILFAAPPENEMVWTEEGVQGAWRFLNRIYRRVAEDREALLETSGVFQAEALEGKDRELYGKLHETLKKVTEDLEALRFNTAIAALMEFLNALYEYRKDRPVTPVYRTAIRYYLQMLFPFAPHLAEELWHWFWPDSLFEAGWPELDEKALEKDVVEVAVQVNGRVRGTIHIPKDAPLEVARAEALKVRNVRAHLEGKEVVKEIYVPGKILNLVVRG

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 2 polymer

描述 description	TRNALEU TRANSCRIPT WITH ANTICODON CAG
分子量 formula_weight	26898.0 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,E

GCCGGGGUGGCGGAAUGGGUAGACGCGCAUGACUCAGGAUCAUGUGCGCAAGCGUGCGGGUUCAAGUCCCGCCCCCGGCACCA

Entity 3 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	4

Entity 4 non-polymer

描述 description	MERCURY (II) ION
分子量 formula_weight	200.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 5 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	25

Entity 6 non-polymer

描述 description	NORVALINE
分子量 formula_weight	117.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 7 non-polymer

描述 description	2'-AMINO-2'-DEOXYADENOSINE
分子量 formula_weight	266.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 8 non-polymer

描述 description	LEUCINE
分子量 formula_weight	131.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 9 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	18

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6. 折叠分类 (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

结构域编号 domain_id	2bteA01
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	2bteA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	740 — Isoleucyl-tRNA Synthetase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain

结构域编号 domain_id	2bteA03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	210 — Leucyl-tRNA synthetase, domain 3
同源超家族 H-superfamily homologous superfamily	10 — Leucyl-tRNA synthetase, domain 3

结构域编号 domain_id	2bteA04
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	730 — Isoleucyl-tRNA Synthetase; Domain 1
同源超家族 H-superfamily homologous superfamily	10 — Isoleucyl-tRNA Synthetase; Domain 1

结构域编号 domain_id	2bteA05
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	20 — Ubiquitin-like (UB roll)
同源超家族 H-superfamily homologous superfamily	590 —

结构域编号 domain_id	2bteD01
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	2bteD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	740 — Isoleucyl-tRNA Synthetase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain

结构域编号 domain_id	2bteD03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	210 — Leucyl-tRNA synthetase, domain 3
同源超家族 H-superfamily homologous superfamily	10 — Leucyl-tRNA synthetase, domain 3

结构域编号 domain_id	2bteD04
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	730 — Isoleucyl-tRNA Synthetase; Domain 1
同源超家族 H-superfamily homologous superfamily	10 — Isoleucyl-tRNA Synthetase; Domain 1

结构域编号 domain_id	2bteD05
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	20 — Ubiquitin-like (UB roll)
同源超家族 H-superfamily homologous superfamily	590 —

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7. 引用文献 (1)

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晶胞边长 a length_a	204.121 Å
晶胞边长 b length_b	125.705 Å
晶胞边长 c length_c	175.432 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	120.86 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

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	2.900 Å
最低分辨率 resolution_low	24.890 Å
R 因子 r_factor	0.2170
R_work r_work	0.2170
R_free r_free	0.2530

fit	/app/data/saxs_computation/bt/2bte/2bte.fit
pddf	/app/data/pr_computation/bt/2bte/2bte.pr.out
profile	/app/data/saxs_computation/bt/2bte/2bte.dat

;Thermus thermophilus Leucyl-tRNA synthetase complexed with a tRNAleu transcript in the post-editing conformation and a post- transfer editing substrate analogue ;

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 (9)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 water

6. 折叠分类 (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)