SAXSdb — 2ash

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2ash
沉积日期 deposition_date	2005-08-23
结构标题 title	;Crystal structure of Queuine tRNA-ribosyltransferase (EC 2.4.2.29) (tRNA-guanine (tm1561) from THERMOTOGA MARITIMA at 1.90 A resolution ;
关键词 keywords	;tm1561, Queuine tRNA-ribosyltransferase, tRNA-guanine, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI, transferase ;; TRANSFERASE
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	39.80 Å
回转半径 Rg (电子) rg_electron	39.36 Å
零角强度 I(0) i0	349386000.00
分子量 molecular_weight	158160.0 kDa
排除体积 excluded_volume	200000 Å³
包络体积 envelope_volume	250520 Å³
水化壳体积 shell_volume	52520 Å³
包络直径 envelope_diameter	116.5 Å
壳层 Rg shell_rg	45.40 Å
包络 Rg envelope_rg	38.81 Å
形状 Rg shape_rg	39.40 Å
总 Rg total_rg	39.56 Å
总原子数 total_atoms	11119
残基数 n_residues	1443
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	116.9 Å
Rg (实空间) rg_real	39.57 Å
Rg 误差 (实空间) rg_real_error	0.62 Å
I(0) (实空间) i0_real	3.4940e+08
I(0) 误差 (实空间) i0_real_error	4.9280e+06
Rg (倒空间) rg_reciprocal	39.72 Å
I(0) (倒空间) i0_reciprocal	349400000.0000
解质量估计 total_estimate	0.8811
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	58.4 Å
偏度 Skewness skewness	0.011
峰度 Kurtosis kurtosis	-0.781
角度范围 angular_range	— – 0.2000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	43680000.0000
实空间数据点数 n_real_points	41
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.978; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.516

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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	Queuine tRNA-ribosyltransferase
分子量 formula_weight	42945.4 kDa
EC 编号 ec_number	2.4.2.29
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	11856

MGSDKIHHHHHHMEFEVKKTFGKARLGVMKLHHGAVETPVFMPVGTNASVKLLTPRDLEEAGAEIILSNTFHLMLKPGVEIIKLHRGLHNFMGWKRPILTDSGGFQVFSLPKIRIDDEGVVFRSPIDGSKVFLNPEISMEVQIALGSDICMVFDHCPVPDADYEEVKEATERTYRWALRSKKAFKTENQALFGIVQGGIYPDLRRESALQLTSIGFDGYAIGGLSIGEERSLTLEMTEVTVEFLPEDKPRYFMGGGSPELILELVDRGVDMFDSVFPTRIARHGTALTWNGKLNLKASYNKRSLEPVDERCGCYTCKNFTRSYIHHLFDRGEVLGQILLTIHNINFMISLMKEVRRSIESGTFKELKSKVVEVYSSGGVNV

来源 Source

来源生物 organism	Thermotoga maritima
NCBI 分类编号 ncbi_taxonomy_id	2336
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	4

Entity 3 non-polymer

描述 description	CHLORIDE ION
分子量 formula_weight	35.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	5

Entity 4 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	10

Entity 5 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	655

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d2asha_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.20 — tRNA-guanine transglycosylase
家族 Family family	c.1.20.1 — tRNA-guanine transglycosylase

结构域编号 domain_id	d2ashb_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.20 — tRNA-guanine transglycosylase
家族 Family family	c.1.20.1 — tRNA-guanine transglycosylase

结构域编号 domain_id	d2ashc_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.20 — tRNA-guanine transglycosylase
家族 Family family	c.1.20.1 — tRNA-guanine transglycosylase

结构域编号 domain_id	d2ashd_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.20 — tRNA-guanine transglycosylase
家族 Family family	c.1.20.1 — tRNA-guanine transglycosylase

CATH v4.4 (4 domains)

结构域编号 domain_id	2ashA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	105 — Queuine tRNA-ribosyltransferase-like

结构域编号 domain_id	2ashB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	105 — Queuine tRNA-ribosyltransferase-like

结构域编号 domain_id	2ashC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	105 — Queuine tRNA-ribosyltransferase-like

结构域编号 domain_id	2ashD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	105 — Queuine tRNA-ribosyltransferase-like

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7. 引用文献 (1)

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晶胞边长 a length_a	169.467 Å
晶胞边长 b length_b	99.422 Å
晶胞边长 c length_c	124.163 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	123.80 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	16

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	1.900 Å
最低分辨率 resolution_low	51.700 Å
R 因子 r_factor	—
R_work r_work	0.1930
R_free r_free	0.2290

fit	/app/data/saxs_computation/as/2ash/2ash.fit
pddf	/app/data/pr_computation/as/2ash/2ash.pr.out
profile	/app/data/saxs_computation/as/2ash/2ash.dat

;Crystal structure of Queuine tRNA-ribosyltransferase (EC 2.4.2.29) (tRNA-guanine (tm1561) from THERMOTOGA MARITIMA at 1.90 A resolution ;

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution