1mb2

Crystal Structure of Tryptophanyl-tRNA Synthetase Complexed with Tryptophan in an Open Conformation

Method: X-RAY DIFFRACTION D_max: 182.6 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	1mb2
沉积日期 deposition_date	2002-08-02
结构标题 title	Crystal Structure of Tryptophanyl-tRNA Synthetase Complexed with Tryptophan in an Open Conformation
关键词 keywords	Aminoacyl-tRNA Synthetase, Rossmann fold, amino acid binding site, 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	50.89 Å
回转半径 Rg (电子) rg_electron	50.95 Å
零角强度 I(0) i0	692890000.00
分子量 molecular_weight	219880.0 kDa
排除体积 excluded_volume	275910 Å³
包络体积 envelope_volume	387710 Å³
水化壳体积 shell_volume	65909 Å³
包络直径 envelope_diameter	191.8 Å
壳层 Rg shell_rg	51.61 Å
包络 Rg envelope_rg	50.12 Å
形状 Rg shape_rg	50.95 Å
总 Rg total_rg	50.97 Å
总原子数 total_atoms	15468
残基数 n_residues	1956
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	182.6 Å
Rg (实空间) rg_real	50.95 Å
Rg 误差 (实空间) rg_real_error	2.56 Å
I(0) (实空间) i0_real	6.9290e+08
I(0) 误差 (实空间) i0_real_error	1.4810e+07
Rg (倒空间) rg_reciprocal	50.84 Å
I(0) (倒空间) i0_reciprocal	692800000.0000
解质量估计 total_estimate	0.8601
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	70.7 Å
偏度 Skewness skewness	0.306
峰度 Kurtosis kurtosis	-0.287
角度范围 angular_range	— – 0.1550 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	45600000.0000
实空间数据点数 n_real_points	32
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.779; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.918; Smooth: 0.922

▶

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

▶

5. 实体与聚合体信息 (2)

▼

6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d1mb2a_
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	d1mb2b_
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	d1mb2c_
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	d1mb2d_
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	d1mb2e_
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	d1mb2f_
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 (12 domains)

结构域编号 domain_id	1mb2A01
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	1mb2A02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	240 — Tyrosyl-Transfer RNA Synthetase
同源超家族 H-superfamily homologous superfamily	10 — Tyrosyl-Transfer RNA Synthetase

结构域编号 domain_id	1mb2B01
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	1mb2B02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	240 — Tyrosyl-Transfer RNA Synthetase
同源超家族 H-superfamily homologous superfamily	10 — Tyrosyl-Transfer RNA Synthetase

结构域编号 domain_id	1mb2C01
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	1mb2C02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	240 — Tyrosyl-Transfer RNA Synthetase
同源超家族 H-superfamily homologous superfamily	10 — Tyrosyl-Transfer RNA Synthetase

结构域编号 domain_id	1mb2D01
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	1mb2D02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	240 — Tyrosyl-Transfer RNA Synthetase
同源超家族 H-superfamily homologous superfamily	10 — Tyrosyl-Transfer RNA Synthetase

结构域编号 domain_id	1mb2E01
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	1mb2E02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	240 — Tyrosyl-Transfer RNA Synthetase
同源超家族 H-superfamily homologous superfamily	10 — Tyrosyl-Transfer RNA Synthetase

结构域编号 domain_id	1mb2F01
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	1mb2F02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	240 — Tyrosyl-Transfer RNA Synthetase
同源超家族 H-superfamily homologous superfamily	10 — Tyrosyl-Transfer RNA Synthetase

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	228.730 Å
晶胞边长 b length_b	92.240 Å
晶胞边长 c length_c	157.590 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	132.71 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	24

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	2.700 Å
最低分辨率 resolution_low	14.980 Å
R 因子 r_factor	—
R_work r_work	0.2200
R_free r_free	0.2540

描述 description	TRYPTOPHAN-TRNA LIGASE
分子量 formula_weight	37225.7 kDa
EC 编号 ec_number	6.1.1.2
来源方法 src_method	man
拷贝数 entity_count	6

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F
原子数 atom_count	15468

Crystal Structure of Tryptophanyl-tRNA Synthetase Complexed with Tryptophan in an Open 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 (2)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 non-polymer

6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

CATH v4.4 (12 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)

来源生物 organism	Geobacillus stearothermophilus
NCBI 分类编号 ncbi_taxonomy_id	1422
宿主生物 host_organism	Escherichia coli

描述 description	TRYPTOPHAN
分子量 formula_weight	204.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

fit	/app/data/saxs_computation/mb/1mb2/1mb2.fit
pddf	/app/data/pr_computation/mb/1mb2/1mb2.pr.out
profile	/app/data/saxs_computation/mb/1mb2/1mb2.dat