8ooq

Glutamine synthetase from Methanothermococcus thermolithotrophicus in complex with 2-oxoglutarate and Mg at 2.91 A resolution

Method: X-RAY DIFFRACTION D_max: 281.8 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	8ooq
沉积日期 deposition_date	2023-04-05
结构标题 title	Glutamine synthetase from Methanothermococcus thermolithotrophicus in complex with 2-oxoglutarate and Mg at 2.91 A resolution
关键词 keywords	;Nitrogen-assimilation, methanogenic archaea, allosteric activation, hydrogenotrophic, thermophile, marine, 2-oxoglutarate, glutamate, ATP, allosteric binding site, 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	79.09 Å
回转半径 Rg (电子) rg_electron	78.89 Å
零角强度 I(0) i0	19408200000.00
分子量 molecular_weight	1207400.0 kDa
排除体积 excluded_volume	1517100 Å³
包络体积 envelope_volume	2296300 Å³
水化壳体积 shell_volume	237450 Å³
包络直径 envelope_diameter	262.1 Å
壳层 Rg shell_rg	81.61 Å
包络 Rg envelope_rg	75.94 Å
形状 Rg shape_rg	78.88 Å
总 Rg total_rg	78.98 Å
总原子数 total_atoms	85163
残基数 n_residues	10724
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	281.8 Å
Rg (实空间) rg_real	82.40 Å
Rg 误差 (实空间) rg_real_error	1.81 Å
I(0) (实空间) i0_real	1.9410e+10
I(0) 误差 (实空间) i0_real_error	4.0420e+08
Rg (倒空间) rg_reciprocal	79.07 Å
I(0) (倒空间) i0_reciprocal	19410000000.0000
解质量估计 total_estimate	0.8730
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	84.5 Å
偏度 Skewness skewness	0.496
峰度 Kurtosis kurtosis	-0.105
角度范围 angular_range	— – 0.1000 Å⁻¹
当前正则化参数 α current_alpha	1.1470
最高正则化参数 α highest_alpha	2245000000.0000
实空间数据点数 n_real_points	21
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.705; Stabil: 0.883; Sysdev: 1.000; Positv: 1.000; Valcen: 0.973; Smooth: 0.632

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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 (5)

Entity 1 polymer

描述 description	Glutamine synthetase from Methanothermococcus thermolithotrophicus
分子量 formula_weight	50296.0 kDa
EC 编号 ec_number	6.3.1.2
来源方法 src_method	nat
拷贝数 entity_count	24

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H,I,J,K,L,P,Q,S,T,U,V,X,Y,Z,a,b,c
原子数 atom_count	85163

MSTVEQVLEYVKSNNVKFMRFQFVDILGVPKNVAFPIKAGEKGIEELRDVLENGLYFDGSSIEGFVGINESDMMLKPDLSTFSVLPWRPSEKSVARVICDVYTTKGKPFEGDPRGCLKRVMEEFKKEFNGEYFVGPEPEFFLLKKDPHNPHKYIPADDGGYFDLEPMDEAPDIRRDIVFALENLGFHVEASHHEVAPGQHEVDFKFDDALKTADSVITFKTTIKTIAEQHGLKATFMPKPFFGMNGSGMHCHQSIWLNGEPSFYDENAPYQLSETCMNYVAGILKHAKAIVAITNPTVNSYKRLVPGYEAPVNIAWANSNRSAIIRVPAARGKGTRIEFRAPDPSCNPYLAFTVMLAAGLDGVKNKLDAPEPVERNIFAMSEAEKKELGIESVPANLKAALDELENNDVLKNALGKHIFESFLEIKNAEWDSFRTSVTDWETTAYLKI

Entity 2 non-polymer

描述 description	1,2-ETHANEDIOL
分子量 formula_weight	62.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	25

Entity 3 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	17

Entity 4 non-polymer

描述 description	2-OXOGLUTARIC ACID
分子量 formula_weight	146.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	24

Entity 5 non-polymer

描述 description	DI(HYDROXYETHYL)ETHER
分子量 formula_weight	106.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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7. 引用文献 (1)

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晶胞边长 a length_a	131.808 Å
晶胞边长 b length_b	131.927 Å
晶胞边长 c length_c	203.544 Å
晶胞夹角 α angle_alpha	89.95 °
晶胞夹角 β angle_beta	89.86 °
晶胞夹角 γ angle_gamma	60.05 °
晶胞分子数 Z z_pdb	24

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

分辨率 resolution	2.910 Å
最低分辨率 resolution_low	43.740 Å
R 因子 r_factor	0.2553
R_work r_work	0.2541
R_free r_free	0.2780

fit	/app/data/saxs_computation/oo/8ooq/8ooq.fit
pddf	/app/data/pr_computation/oo/8ooq/8ooq.pr.out
profile	/app/data/saxs_computation/oo/8ooq/8ooq.dat

Glutamine synthetase from Methanothermococcus thermolithotrophicus in complex with 2-oxoglutarate and Mg at 2.91 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