1nyr

Structure of Staphylococcus aureus threonyl-tRNA synthetase complexed with ATP

Method: X-RAY DIFFRACTION D_max: 145.8 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

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1nyr
沉积日期 deposition_date	2003-02-13
结构标题 title	Structure of Staphylococcus aureus threonyl-tRNA synthetase complexed with ATP
关键词 keywords	threonyl-tRNA synthetase, ATP, threonine, LIGASE; LIGASE
实验方法 method	X-RAY DIFFRACTION

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	39.14 Å
回转半径 Rg (电子) rg_electron	39.28 Å
零角强度 I(0) i0	349359000.00
分子量 molecular_weight	148930.0 kDa
排除体积 excluded_volume	185170 Å³
包络体积 envelope_volume	256180 Å³
水化壳体积 shell_volume	56346 Å³
包络直径 envelope_diameter	156.4 Å
壳层 Rg shell_rg	43.10 Å
包络 Rg envelope_rg	39.61 Å
形状 Rg shape_rg	39.27 Å
总 Rg total_rg	39.53 Å
总原子数 total_atoms	10468
残基数 n_residues	1279
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

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	145.8 Å
Rg (实空间) rg_real	39.36 Å
Rg 误差 (实空间) rg_real_error	1.41 Å
I(0) (实空间) i0_real	3.4940e+08
I(0) 误差 (实空间) i0_real_error	5.9190e+06
Rg (倒空间) rg_reciprocal	39.22 Å
I(0) (倒空间) i0_reciprocal	349300000.0000
解质量估计 total_estimate	0.8277
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	43.8 Å
偏度 Skewness skewness	0.544
峰度 Kurtosis kurtosis	0.114
角度范围 angular_range	— – 0.2000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	41470000.0000
实空间数据点数 n_real_points	41
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.633; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.896; Smooth: 0.961

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (5)

Entity 1 polymer

描述 description	threonyl-tRNA synthetase 1
分子量 formula_weight	74562.2 kDa
EC 编号 ec_number	6.1.1.3
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
原子数 atom_count	10684

MEQINIQFPDGNKKAFDKGTTTEDIAQSISPGLRKKAVAGKFNGQLVDLTKPLETDGSIEIVTPGSEEALEVLRHSTAHLMAHAIKRLYGNVKFGVGPVIEGGFYYDFDIDQNISSDDFEQIEKTMKQIVNENMKIERKVVSRDEAKELFSNDEYKLELIDAIPEDENVTLYSQGDFTDLCRGVHVPSTAKIKEFKLLSTAGAYWRGDSNNKMLQRIYGTAFFDKKELKAHLQMLEERKERDHRKIGKELELFTNSQLVGAGLPLWLPNGATIRREIERYIVDKEVSMGYDHVYTPVLANVDLYKTSGHWDHYQEDMFPPMQLDETESMVLRPMNCPHHMMIYANKPHSYRELPIRIAELGTMHRYEASGAVSGLQRVRGMTLNDSHIFVRPDQIKEEFKRVVNMIIDVYKDFGFEDYSFRLSYRDPEDKEKYFDDDDMWNKAENMLKEAADELGLSYEEAIGEAAFYGPKLDVQVKTAMGKEETLSTAQLDFLLPERFDLTYIGQDGEHHRPVVIHRGVVSTMERFVAFLTEETKGAFPTWLAPKQVQIIPVNVDLHYDYARQLQDELKSQGVRVSIDDRNEKMGYKIREAQMQKIPYQIVVGDKEVENNQVNVRQYGSQDQETVEKDEFIWNLVDEIRLKKHR

来源 Source

来源生物 organism	Staphylococcus aureus
NCBI 分类编号 ncbi_taxonomy_id	1280
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 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	3

Entity 3 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 4 non-polymer

描述 description	THREONINE
分子量 formula_weight	119.1 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	216

▼

6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1nyra1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.51 — Anticodon-binding domain-like
超家族 Superfamily superfamily	c.51.1 — Class II aaRS ABD-related
家族 Family family	c.51.1.1 — Anticodon-binding domain of Class II aaRS

结构域编号 domain_id	d1nyra2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.15 — beta-Grasp (ubiquitin-like)
超家族 Superfamily superfamily	d.15.10 — TGS-like
家族 Family family	d.15.10.1 — TGS domain

结构域编号 domain_id	d1nyra3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.67 — RRF/tRNA synthetase additional domain-like
超家族 Superfamily superfamily	d.67.1 — ThrRS/AlaRS common domain
家族 Family family	d.67.1.1 — Threonyl-tRNA synthetase (ThrRS), second 'additional' domain

结构域编号 domain_id	d1nyra4
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.104 — Class II aaRS and biotin synthetases
超家族 Superfamily superfamily	d.104.1 — Class II aaRS and biotin synthetases
家族 Family family	d.104.1.1 — Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain

结构域编号 domain_id	d1nyrb1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.51 — Anticodon-binding domain-like
超家族 Superfamily superfamily	c.51.1 — Class II aaRS ABD-related
家族 Family family	c.51.1.1 — Anticodon-binding domain of Class II aaRS

结构域编号 domain_id	d1nyrb2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.15 — beta-Grasp (ubiquitin-like)
超家族 Superfamily superfamily	d.15.10 — TGS-like
家族 Family family	d.15.10.1 — TGS domain

结构域编号 domain_id	d1nyrb3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.67 — RRF/tRNA synthetase additional domain-like
超家族 Superfamily superfamily	d.67.1 — ThrRS/AlaRS common domain
家族 Family family	d.67.1.1 — Threonyl-tRNA synthetase (ThrRS), second 'additional' domain

结构域编号 domain_id	d1nyrb4
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.104 — Class II aaRS and biotin synthetases
超家族 Superfamily superfamily	d.104.1 — Class II aaRS and biotin synthetases
家族 Family family	d.104.1.1 — Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain

CATH v4.4 (8 domains)

结构域编号 domain_id	1nyrA01
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	30 — Beta-grasp domain

结构域编号 domain_id	1nyrA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	980 — Threonyl-tRNA Synthetase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Threonyl-trna Synthetase; Chain A, domain 2

结构域编号 domain_id	1nyrA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	930 — BirA Bifunctional Protein; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Bira Bifunctional Protein; Domain 2

结构域编号 domain_id	1nyrA04
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	800 — Anticodon-binding domain

结构域编号 domain_id	1nyrB01
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	30 — Beta-grasp domain

结构域编号 domain_id	1nyrB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	980 — Threonyl-tRNA Synthetase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Threonyl-trna Synthetase; Chain A, domain 2

结构域编号 domain_id	1nyrB03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	930 — BirA Bifunctional Protein; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Bira Bifunctional Protein; Domain 2

结构域编号 domain_id	1nyrB04
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	800 — Anticodon-binding domain

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	104.130 Å
晶胞边长 b length_b	122.521 Å
晶胞边长 c length_c	148.661 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	8

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	2.800 Å
最低分辨率 resolution_low	15.000 Å
R 因子 r_factor	0.2390
R_work r_work	0.2390
R_free r_free	0.3130

fit	/app/data/saxs_computation/ny/1nyr/1nyr.fit
pddf	/app/data/pr_computation/ny/1nyr/1nyr.pr.out
profile	/app/data/saxs_computation/ny/1nyr/1nyr.dat