SAXSdb — 1h3f

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1h3f
沉积日期 deposition_date	2002-08-28
结构标题 title	Tyrosyl-tRNA synthetase from Thermus thermophilus complexed with tyrosinol
关键词 keywords	LIGASE, AMINOACYL-TRNA SYNTHETASE, ATP + L-TYROSINE + TRNA(TYR)->AMP + PPI + L-TYROSYL-TRNA(TY CLASS I AMINOACYL-TRNA SYNTHETASE; 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	45.16 Å
回转半径 Rg (电子) rg_electron	45.89 Å
零角强度 I(0) i0	127519000.00
分子量 molecular_weight	92670.0 kDa
排除体积 excluded_volume	116730 Å³
包络体积 envelope_volume	171850 Å³
水化壳体积 shell_volume	36407 Å³
包络直径 envelope_diameter	174.8 Å
壳层 Rg shell_rg	41.28 Å
包络 Rg envelope_rg	46.78 Å
形状 Rg shape_rg	45.87 Å
总 Rg total_rg	45.69 Å
总原子数 total_atoms	6523
残基数 n_residues	809
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	166.2 Å
Rg (实空间) rg_real	46.05 Å
Rg 误差 (实空间) rg_real_error	2.29 Å
I(0) (实空间) i0_real	1.2750e+08
I(0) 误差 (实空间) i0_real_error	2.7330e+06
Rg (倒空间) rg_reciprocal	45.16 Å
I(0) (倒空间) i0_reciprocal	127400000.0000
解质量估计 total_estimate	0.6852
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	28.5 Å
偏度 Skewness skewness	0.642
峰度 Kurtosis kurtosis	-0.148
角度范围 angular_range	— – 0.1750 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	7981000.0000
实空间数据点数 n_real_points	36
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.404; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.160; Smooth: 0.533

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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 (4)

Entity 1 polymer

描述 description	TYROSYL-TRNA SYNTHETASE
分子量 formula_weight	48786.2 kDa
EC 编号 ec_number	6.1.1.1
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	6777

MAGTGHTPEEALALLKRGAEEIVPEEELLAKLKEGRPLTVKLGADPTRPDLHLGHAVVLRKMRQFQELGHKVVLIIGDFTGMIGDPSGRSKTRPPLTLEETRENAKTYVAQAGKILRQEPHLFELRYNSEWLEGLTFKEVVRLTSLMTVAQMLEREDFKKRYEAGIPISLHELLYPFAQAYDSVAIRADVEMGGTDQRFNLLVGREVQRAYGQSPQVCFLMPLLVGLDGREKMSKSLDNYIGLTEPPEAMFKKLMRVPDPLLPSYFRLLTDLEEEEIEALLKAGPVPAHRVLARLLTAAYALPQIPPRIDRAFYESLGYAWEAFGRDKEAGPEEVRRAEARYDEVAKGGIPEEIPEVTIPASELKEGRIWVARLFTLAGLTPSNAEARRLIQNRGLRLDGEVLTDPMLQVDLSRPRILQRGKDRFVRVRLSD

来源 Source

来源生物 organism	THERMUS THERMOPHILUS
NCBI 分类编号 ncbi_taxonomy_id	262724
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 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	5

Entity 3 non-polymer

描述 description	4-[(2S)-2-amino-3-hydroxypropyl]phenol
分子量 formula_weight	167.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 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	254

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6. 折叠分类 (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1h3fa1
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	d1h3fa2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.66 — Alpha-L RNA-binding motif
超家族 Superfamily superfamily	d.66.1 — Alpha-L RNA-binding motif
家族 Family family	d.66.1.4 — Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain

结构域编号 domain_id	d1h3fb1
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	d1h3fb2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.66 — Alpha-L RNA-binding motif
超家族 Superfamily superfamily	d.66.1 — Alpha-L RNA-binding motif
家族 Family family	d.66.1.4 — Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain

CATH v4.4 (6 domains)

结构域编号 domain_id	1h3fA01
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	1h3fA02
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	1h3fA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	290 — Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A
同源超家族 H-superfamily homologous superfamily	10 — RNA-binding S4 domain

结构域编号 domain_id	1h3fB01
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	1h3fB02
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	1h3fB03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	290 — Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A
同源超家族 H-superfamily homologous superfamily	10 — RNA-binding S4 domain

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7. 引用文献 (1)

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晶胞边长 a length_a	67.794 Å
晶胞边长 b length_b	111.050 Å
晶胞边长 c length_c	141.226 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	2.000 Å
最低分辨率 resolution_low	25.000 Å
R 因子 r_factor	0.2340
R_work r_work	0.2340
R_free r_free	0.2610

fit	/app/data/saxs_computation/h3/1h3f/1h3f.fit
pddf	/app/data/pr_computation/h3/1h3f/1h3f.pr.out
profile	/app/data/saxs_computation/h3/1h3f/1h3f.dat

Tyrosyl-tRNA synthetase from Thermus thermophilus complexed with tyrosinol

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