1j5w

Crystal structure of Glycyl-tRNA synthetase alpha chain (TM0216) from Thermotoga maritima at 1.95 A resolution

Method: X-RAY DIFFRACTION D_max: 71.9 Å Quality: EXCELLENT

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	1j5w
沉积日期 deposition_date	2002-07-05
结构标题 title	Crystal structure of Glycyl-tRNA synthetase alpha chain (TM0216) from Thermotoga maritima at 1.95 A resolution
关键词 keywords	;structural genomics, TM0216, JCSG, Glycyl-tRNA synthetase alpha chain, PSI, Protein Structure Initiative, Joint Center for Structural Genomics, LIGASE ;; 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	23.88 Å
回转半径 Rg (电子) rg_electron	22.64 Å
零角强度 I(0) i0	67080600.00
分子量 molecular_weight	65113.0 kDa
排除体积 excluded_volume	81416 Å³
包络体积 envelope_volume	92760 Å³
水化壳体积 shell_volume	32316 Å³
包络直径 envelope_diameter	73.1 Å
壳层 Rg shell_rg	31.14 Å
包络 Rg envelope_rg	22.82 Å
形状 Rg shape_rg	22.63 Å
总 Rg total_rg	23.58 Å
总原子数 total_atoms	4574
残基数 n_residues	542
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	71.9 Å
Rg (实空间) rg_real	23.67 Å
Rg 误差 (实空间) rg_real_error	0.24 Å
I(0) (实空间) i0_real	6.7080e+07
I(0) 误差 (实空间) i0_real_error	8.0070e+05
Rg (倒空间) rg_reciprocal	23.72 Å
I(0) (倒空间) i0_reciprocal	67080000.0000
解质量估计 total_estimate	0.9011
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	70.7 Å
偏度 Skewness skewness	0.057
峰度 Kurtosis kurtosis	-0.510
角度范围 angular_range	— – 0.3350 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	25430000.0000
实空间数据点数 n_real_points	65
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.915; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.997

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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 (2)

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6. 折叠分类 (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1j5wa_
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	d1j5wb_
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 (4 domains)

结构域编号 domain_id	1j5wA01
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	1j5wA02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
同源超家族 H-superfamily homologous superfamily	180 — Class II aaRS and biotin synthetases; domain 2

结构域编号 domain_id	1j5wB01
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	1j5wB02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
同源超家族 H-superfamily homologous superfamily	180 — Class II aaRS and biotin synthetases; domain 2

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7. 引用文献 (1)

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晶胞边长 a length_a	65.400 Å
晶胞边长 b length_b	66.200 Å
晶胞边长 c length_c	142.100 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	1.950 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.1970
R_work r_work	0.1970
R_free r_free	0.2540

描述 description	Glycyl-tRNA synthetase alpha chain
分子量 formula_weight	35362.7 kDa
EC 编号 ec_number	6.1.1.14
来源方法 src_method	man
拷贝数 entity_count	2

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	4829

Crystal structure of Glycyl-tRNA synthetase alpha chain (TM0216) from Thermotoga maritima at 1.95 A resolution

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 water

6. 折叠分类 (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)

来源生物 organism	Thermotoga maritima
NCBI 分类编号 ncbi_taxonomy_id	2336
宿主生物 host_organism	Escherichia coli

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	255

fit	/app/data/saxs_computation/j5/1j5w/1j5w.fit
pddf	/app/data/pr_computation/j5/1j5w/1j5w.pr.out
profile	/app/data/saxs_computation/j5/1j5w/1j5w.dat