SAXSdb — 1gtr

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1gtr
沉积日期 deposition_date	1993-09-15
结构标题 title	STRUCTURAL BASIS OF ANTICODON LOOP RECOGNITION BY GLUTAMINYL-TRNA SYNTHETASE
关键词 keywords	COMPLEX (LIGASE-TRNA), COMPLEX (LIGASE-TRNA) complex; COMPLEX (LIGASE/TRNA)
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	30.78 Å
回转半径 Rg (电子) rg_electron	30.91 Å
零角强度 I(0) i0	169671000.00
分子量 molecular_weight	85105.0 kDa
排除体积 excluded_volume	98309 Å³
包络体积 envelope_volume	127250 Å³
水化壳体积 shell_volume	35750 Å³
包络直径 envelope_diameter	107.5 Å
壳层 Rg shell_rg	36.53 Å
包络 Rg envelope_rg	30.79 Å
形状 Rg shape_rg	30.91 Å
总 Rg total_rg	31.29 Å
总原子数 total_atoms	5883
残基数 n_residues	603
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	101.7 Å
Rg (实空间) rg_real	30.83 Å
Rg 误差 (实空间) rg_real_error	0.76 Å
I(0) (实空间) i0_real	1.6970e+08
I(0) 误差 (实空间) i0_real_error	2.5970e+06
Rg (倒空间) rg_reciprocal	30.81 Å
I(0) (倒空间) i0_reciprocal	169700000.0000
解质量估计 total_estimate	0.8916
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	33.9 Å
偏度 Skewness skewness	0.374
峰度 Kurtosis kurtosis	-0.371
角度范围 angular_range	— – 0.2550 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	15740000.0000
实空间数据点数 n_real_points	52
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.896; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.950; Smooth: 0.949

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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	RNA (74-MER)
分子量 formula_weight	23754.1 kDa
EC 编号 ec_number	6.1.1.18
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	B
原子数 atom_count	6114

GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA

Entity 2 polymer

描述 description	GLUTAMINYL-tRNA SYNTHETASE
分子量 formula_weight	63434.6 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A

SEAEARPTNFIRQIIDEDLASGKHTTVHTRFPPEPNGYLHIGHAKSICLNFGIAQDYKGQCNLRFDDTNPVKEDIEYVESIKNDVEWLGFHWSGNVRYSSDYFDQLHAYAIELINKGLAYVDELTPEQIREYRGTLTQPGKNSPYRDRSVEENLALFEKMRAGGFEEGKACLRAKIDMASPFIVMRDPVLYRIKFAEHHQTGNKWCIYPMYDFTHCISDALEGITHSLCTLEFQDNRRLYDWVLDNITIPVHPRQYEFSRLNLEYTVMSKRKLNLLVTDKHVEGWDDPRMPTISGLRRRGYTAASIREFCKRIGVTKQDNTIEMASLESCIREDLNENAPRAMAVIDPVKLVIENYQGEGEMVTMPNHPNKPEMGSRQVPFSGEIWIDRADFREEANKQYKRLVLGKEVRLRNAYVIKAERVEKDAEGNITTIFCTYDADTLSKDPADGRKVKGVIHWVSAAHALPVEIRLYDRLFSVPNPGAADDFLSVINPESLVIKQGFAEPSLKDAVAGKAFQFEREGYFCLDSRHSTAEKPVFNRTVGLRDTWAKVGE

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562

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	1

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	231

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6. 折叠分类 (SCOP + CATH) 7 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1gtra1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.53 — Ribosomal protein L25-like
超家族 Superfamily superfamily	b.53.1 — Ribosomal protein L25-like
家族 Family family	b.53.1.2 — Gln-tRNA synthetase (GlnRS), C-terminal (anticodon-binding) domain

结构域编号 domain_id	d1gtra2
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 (5 domains)

结构域编号 domain_id	1gtrA01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	240 — Ribosomal Protein L25; Chain P
同源超家族 H-superfamily homologous superfamily	10 — Ribosomal Protein L25; Chain P

结构域编号 domain_id	1gtrA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	240 — Ribosomal Protein L25; Chain P
同源超家族 H-superfamily homologous superfamily	10 — Ribosomal Protein L25; Chain P

结构域编号 domain_id	1gtrA03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1160 — Glutamyl-tRNA Synthetase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Glutamyl-trna Synthetase; Domain 2

结构域编号 domain_id	1gtrA04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	800 — Glutamyl-tRNA Synthetase; domain 3
同源超家族 H-superfamily homologous superfamily	10 — Glutamyl-tRNA Synthetase; Domain 3

结构域编号 domain_id	1gtrA05
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

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7. 引用文献 (1)

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晶胞边长 a length_a	242.800 Å
晶胞边长 b length_b	94.300 Å
晶胞边长 c length_c	115.800 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	C 2 2 21
空间群编号 int_tables_number	20
晶系 crystal_system	—

分辨率 resolution	2.500 Å
最低分辨率 resolution_low	6.000 Å
R 因子 r_factor	0.2100
R_work r_work	0.2100
R_free r_free	—

fit	/app/data/saxs_computation/gt/1gtr/1gtr.fit
pddf	/app/data/pr_computation/gt/1gtr/1gtr.pr.out
profile	/app/data/saxs_computation/gt/1gtr/1gtr.dat

STRUCTURAL BASIS OF ANTICODON LOOP RECOGNITION BY GLUTAMINYL-TRNA SYNTHETASE

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

5. 实体与聚合体信息 (4)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

Entity 4 water

6. 折叠分类 (SCOP + CATH) 7 domains

SCOP 2.08 (2 domains)

CATH v4.4 (5 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)