8wo2

Crystal structure of H. pylori isoleucyl-tRNA synthetase (HpIleRS) in complex with Val-AMP

Method: X-RAY DIFFRACTION D_max: 130.0 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	8wo2
沉积日期 deposition_date	2023-10-06
结构标题 title	Crystal structure of H. pylori isoleucyl-tRNA synthetase (HpIleRS) in complex with Val-AMP
关键词 keywords	isoleucyl-tRNA synthetase, Helicobacter pylori, HpIleRS, IleRS, aminoacylation, 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	37.73 Å
回转半径 Rg (电子) rg_electron	37.98 Å
零角强度 I(0) i0	165468000.00
分子量 molecular_weight	106240.0 kDa
排除体积 excluded_volume	133870 Å³
包络体积 envelope_volume	176130 Å³
水化壳体积 shell_volume	41500 Å³
包络直径 envelope_diameter	139.1 Å
壳层 Rg shell_rg	40.64 Å
包络 Rg envelope_rg	38.16 Å
形状 Rg shape_rg	37.92 Å
总 Rg total_rg	38.35 Å
总原子数 total_atoms	7489
残基数 n_residues	918
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	130.0 Å
Rg (实空间) rg_real	38.15 Å
Rg 误差 (实空间) rg_real_error	1.14 Å
I(0) (实空间) i0_real	1.6550e+08
I(0) 误差 (实空间) i0_real_error	3.1140e+06
Rg (倒空间) rg_reciprocal	37.90 Å
I(0) (倒空间) i0_reciprocal	165400000.0000
解质量估计 total_estimate	0.8274
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	34.1 Å
偏度 Skewness skewness	0.532
峰度 Kurtosis kurtosis	-0.432
角度范围 angular_range	— – 0.2100 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	33130000.0000
实空间数据点数 n_real_points	43
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.716; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.795; Smooth: 0.808

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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 (6)

Entity 1 polymer

描述 description	Isoleucine--tRNA ligase
分子量 formula_weight	106233.5 kDa
EC 编号 ec_number	6.1.1.5
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
原子数 atom_count	7806

MEEYKDTLNLNTTTFSMKGNLSVNEPKTYAKWQEQQAFKRMQARKDNHGDFTLHDGPPYANGHLHLGHALNKILKDIVVKREYFKGKKIYYTPGWDCHGLPIEQQILERLEKEKTSLENPTLFREKCRDHAKKFLEIQKNEFLQLGVLGDFEDPYKTMDFKFEASIYRALVEVAKKGLLKERHKPIYWSYACESALAEAEVEYKMKKSPSIFVAFGLKKESLEKLKVKKASLVIWTTTPWTLYANVAIALKKDAVYALTQKGYLVAKALHEKLAALGVVDNEITHEFNSNDLEYLVATNPLNQRDSLVALGEHVGLEDGTGAVHTAPGHGEEDYYLGLRYNLEVLMSVDEKGCYDEGIIHNQLLDESYLGEHVFKAQKRIIEQLGDSLLLEQEIEHSYPHCWRTHKPVIYRATTQWFILMDEPFIQNDGSQKTLREVALDAIEKVEFVPSSGKNRLKTMIENRPDWCLSRQRKWGVPLAFFIDKRTNKPCFESEVLEHVANLFEKKGCDVWWEYSVKDLLPPSYQEDAKHYEKIMHILDVWFDSGSTFKAVLEDYHGEKGQSPSDVILEGSDQHRGWFQSSLLIGCVLNNQAPFKKVITHGFIVDEKGEKMSKSKGNVVSLDKLLKTHGSDVVRLWVAFNDYQNDLRVSQTFFTQTEQHYKKFRNTLKFLLANFSDMDLKNLERPHNFSPLDHFMLETLETISAGVNSAFEEHDFVKGLNILMAFVTNELSGIYLDACKDSLYCDSKNNEKRQAIQMVLLATASKLCYFLAPILTHTIEEVLEHSQALRIFLQAKDVFDLKDISVSEKLHLKEFKKPENFEAVLALRSAFNEELDRLKKEGVIKNSLECAIEVKEKALDENLVEELLMVSFVGIAKEKLSETPAFTLFKAPFYKCPRCWRFKSELENTPCKRCEQVLKER

来源 Source

来源生物 organism	Helicobacter pylori
通用名 common_name	Campylobacter pylori
NCBI 分类编号 ncbi_taxonomy_id	210
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] (2S)-2-azanyl-3-methyl-butanoate
分子量 formula_weight	446.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 non-polymer

描述 description	ACETATE ION
分子量 formula_weight	59.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 6 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	317

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7. 引用文献 (1)

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晶胞边长 a length_a	52.972 Å
晶胞边长 b length_b	53.084 Å
晶胞边长 c length_c	102.947 Å
晶胞夹角 α angle_alpha	97.15 °
晶胞夹角 β angle_beta	92.61 °
晶胞夹角 γ angle_gamma	105.11 °
晶胞分子数 Z z_pdb	1

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

分辨率 resolution	2.340 Å
最低分辨率 resolution_low	50.970 Å
R 因子 r_factor	0.2114
R_work r_work	0.2097
R_free r_free	0.2450

fit	/app/data/saxs_computation/wo/8wo2/8wo2.fit
pddf	/app/data/pr_computation/wo/8wo2/8wo2.pr.out
profile	/app/data/saxs_computation/wo/8wo2/8wo2.dat