8h1c

;Cryo-EM structure of Oryza sativa plastid glycyl-tRNA synthetase in complex with two tRNAs (one in tRNA binding state and the other in tRNA locked state) ;

Method: ELECTRON MICROSCOPY D_max: 199.1 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

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8h1c
沉积日期 deposition_date	2022-10-02
结构标题 title	;Cryo-EM structure of Oryza sativa plastid glycyl-tRNA synthetase in complex with two tRNAs (one in tRNA binding state and the other in tRNA locked state) ;
关键词 keywords	GlyRS2, Glycine-tRNA ligase, tRNA selection, GlyRS tRNA complex, chloroplasts, LIGASE, LIGASE-RNA complex; LIGASE/RNA
实验方法 method	ELECTRON MICROSCOPY

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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	60.03 Å
回转半径 Rg (电子) rg_electron	59.06 Å
零角强度 I(0) i0	1265380000.00
分子量 molecular_weight	265260.0 kDa
排除体积 excluded_volume	318780 Å³
包络体积 envelope_volume	515530 Å³
水化壳体积 shell_volume	80057 Å³
包络直径 envelope_diameter	217.4 Å
壳层 Rg shell_rg	52.98 Å
包络 Rg envelope_rg	59.07 Å
形状 Rg shape_rg	58.97 Å
总 Rg total_rg	59.17 Å
总原子数 total_atoms	18472
残基数 n_residues	2107
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	199.1 Å
Rg (实空间) rg_real	60.85 Å
Rg 误差 (实空间) rg_real_error	2.20 Å
I(0) (实空间) i0_real	1.2650e+09
I(0) 误差 (实空间) i0_real_error	2.9460e+07
Rg (倒空间) rg_reciprocal	59.30 Å
I(0) (倒空间) i0_reciprocal	1262000000.0000
解质量估计 total_estimate	0.8007
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	53.6 Å
偏度 Skewness skewness	0.598
峰度 Kurtosis kurtosis	-0.319
角度范围 angular_range	— – 0.1300 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	68750000.0000
实空间数据点数 n_real_points	27
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.783; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.961; Smooth: 0.095

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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)

Entity 1 polymer

描述 description	Glycine--tRNA ligase
分子量 formula_weight	117050.5 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 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B,A
原子数 atom_count	18483

HHHHHHHHGSSLEVLFQGPAVASADGDAPSPVSVSASAATKGPSSSSVLTFQQAIQRLQDYWASVGCAVMQCSNTEVGAGTMNPLTFLRVLGPEPWNVAYVEPSIRPDDSRYGDNPNRLQRHTQFQVILKPDPGNSQDLFLHSLSALGINVREHDIRFVEDNWESPVLGAWGLGWEVWMDGMEITQFTYFQQSGSLPLLPVSVEITYGLERILMSLQGVDHFKNIQYTKGITYGELFLENEKEMSAYYLEHANVDNIQKHFDDFEEEARSLLSLWLPIPAYDHVLKASHAFNILDSRGFVGVTERARYFGRMRSLARQCAQLWVKTRENLGYPLGTYQESNLIYPHVSEKPSRKGVVGQPRAFVLEIGTEELPPHDVIEATKQLEKSLIQILEKRRLSHGKVRSYGTPRRLAVVVENLNMKQMEEEIELRGPPVAKAFDQEGRPTKAAEGFCRKNNVPIDSLYRRTDGKTEYIYARVKESARFADEVLTEDLPTIISGISFPKSMRWNSNIVFSRPIRWIFALHGDLIVPFCFAGISSGNQSCGLRNSSLANFKVEAAELYLHTLEKAGILIDMQERKQRILHDSSILAEGVGGDIIAPDSLVQEVINLVEAPMPIIGRYDVSFLALPKDVLITVMQKHQKYFPVTSKTMGNLLPCFITVANGAIKEEVVRKGNEAVLRARYEDAKFFYKMDTQKKLSEFRDQLSSILFHERLGTMLDKMKRVENTVAEVALLLGINEKMIPAIKDAAALAMSDLATNIVTEFTSLAGIMARHYALRDGLSEQIAEALFEITLPRFSGDVFPKTDPGIVLAVTDRLDSLVGLFGAGCQPSSTNDPFGLRRISYGLVQILVENKKNFDLTKALTLVAEEQPITIDSGVIDEVVQFVTRRLEQLLVDEGINCEIVRSVLIERANCPYLASQTAIEMEAFSRTEDFPKIVEAYSRPTRIIRGKEIGSALEVDASVFEKDEERALWSAYLEVADKIHPGVDIKAFADASLELLQPLEDFFTNVFVMAEDEKVRNNRLALLTKVASLPKGIADLSVLPGF

来源 Source

来源生物 organism	Oryza sativa Japonica Group
通用名 common_name	Japanese rice
NCBI 分类编号 ncbi_taxonomy_id	39947
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

描述 description	tRNA(gly) (74-MER)
分子量 formula_weight	23906.1 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	C,D

GCGAGCGUAGUUCAAUGGUAAAACAUCUCCUUGCCAAGGAGAAGAUACGGGUUCGAUUCCCGCCGCUCGCCCCA

来源 Source

来源生物 organism	Oryza sativa
NCBI 分类编号 ncbi_taxonomy_id	4530
宿主生物 host_organism	in vitro transcription vector pT7-TP(deltai)

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7. 引用文献 (1)

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晶胞边长 a length_a	1.000 Å
晶胞边长 b length_b	1.000 Å
晶胞边长 c length_c	1.000 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	—

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	triclinic

分辨率 resolution	4.50 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	24747

fit	/app/data/saxs_computation/h1/8h1c/8h1c.fit
pddf	/app/data/pr_computation/h1/8h1c/8h1c.pr.out
profile	/app/data/saxs_computation/h1/8h1c/8h1c.dat

;Cryo-EM structure of Oryza sativa plastid glycyl-tRNA synthetase in complex with two tRNAs (one in tRNA binding state and the other in tRNA locked state) ;

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

冷冻电镜 EM 3D

5. 实体与聚合体信息 (2)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)