SAXSdb — 2byt

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2byt
沉积日期 deposition_date	2005-08-04
结构标题 title	Thermus thermophilus Leucyl-tRNA synthetase complexed with a tRNAleu transcript in the post-editing conformation
关键词 keywords	;SYNTHETASE, AMINOACYL-TRNA SYNTHETASE, ATP + L-LEUCINE + TRNA (LEU) GIVES AMP + PPI L-LEUCYL-TRNA(LEU), CLASS I AMINOACYL-TRNA SYNTHETASE, EDITING ;; SYNTHETASE
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	46.99 Å
回转半径 Rg (电子) rg_electron	49.51 Å
零角强度 I(0) i0	1231080000.00
分子量 molecular_weight	254780.0 kDa
排除体积 excluded_volume	303020 Å³
包络体积 envelope_volume	449350 Å³
水化壳体积 shell_volume	77836 Å³
包络直径 envelope_diameter	175.3 Å
壳层 Rg shell_rg	51.28 Å
包络 Rg envelope_rg	47.90 Å
形状 Rg shape_rg	49.61 Å
总 Rg total_rg	49.29 Å
总原子数 total_atoms	17697
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	163.3 Å
Rg (实空间) rg_real	47.19 Å
Rg 误差 (实空间) rg_real_error	1.40 Å
I(0) (实空间) i0_real	1.2310e+09
I(0) 误差 (实空间) i0_real_error	2.2760e+07
Rg (倒空间) rg_reciprocal	46.99 Å
I(0) (倒空间) i0_reciprocal	1231000000.0000
解质量估计 total_estimate	0.8598
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	52.9 Å
偏度 Skewness skewness	0.469
峰度 Kurtosis kurtosis	-0.210
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	169400000.0000
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: 0.793; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.798

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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 (6)

Entity 1 polymer

描述 description	LEUCYL-TRNA SYNTHETASE
分子量 formula_weight	101170.1 kDa
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	17697

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

Entity 4 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 5 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 6 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	15

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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	2bytA01
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	2bytA02
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	2bytA03
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	2bytA04
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	2bytA05
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	2bytD01
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	2bytD02
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	2bytD03
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	2bytD04
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	2bytD05
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	203.869 Å
晶胞边长 b length_b	125.578 Å
晶胞边长 c length_c	172.979 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	118.44 °
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	3.300 Å
最低分辨率 resolution_low	24.450 Å
R 因子 r_factor	0.2430
R_work r_work	0.2430
R_free r_free	0.2820

fit	/app/data/saxs_computation/by/2byt/2byt.fit
pddf	/app/data/pr_computation/by/2byt/2byt.pr.out
profile	/app/data/saxs_computation/by/2byt/2byt.dat

Thermus thermophilus Leucyl-tRNA synthetase complexed with a tRNAleu transcript in the post-editing conformation

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 (6)

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

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)