2d6f

Crystal structure of Glu-tRNA(Gln) amidotransferase in the complex with tRNA(Gln)

Method: X-RAY DIFFRACTION D_max: 167.3 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	2d6f
沉积日期 deposition_date	2005-11-13
结构标题 title	Crystal structure of Glu-tRNA(Gln) amidotransferase in the complex with tRNA(Gln)
关键词 keywords	ligase, RNA, ligase-RNA COMPLEX; ligase/RNA
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	53.14 Å
回转半径 Rg (电子) rg_electron	50.57 Å
零角强度 I(0) i0	1270090000.00
分子量 molecular_weight	254450.0 kDa
排除体积 excluded_volume	301000 Å³
包络体积 envelope_volume	464640 Å³
水化壳体积 shell_volume	76079 Å³
包络直径 envelope_diameter	169.5 Å
壳层 Rg shell_rg	54.60 Å
包络 Rg envelope_rg	50.12 Å
形状 Rg shape_rg	50.45 Å
总 Rg total_rg	51.03 Å
总原子数 total_atoms	17636
残基数 n_residues	2001
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	167.3 Å
Rg (实空间) rg_real	53.11 Å
Rg 误差 (实空间) rg_real_error	1.76 Å
I(0) (实空间) i0_real	1.2700e+09
I(0) 误差 (实空间) i0_real_error	2.7520e+07
Rg (倒空间) rg_reciprocal	53.14 Å
I(0) (倒空间) i0_reciprocal	1270000000.0000
解质量估计 total_estimate	0.8803
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	55.8 Å
偏度 Skewness skewness	0.156
峰度 Kurtosis kurtosis	-0.799
角度范围 angular_range	— – 0.1500 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	40070000.0000
实空间数据点数 n_real_points	31
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.969; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.537

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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	tRNA
分子量 formula_weight	23835.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	E,F
原子数 atom_count	17816

AGUCCCGUGGGGUAGUGGUAAUCCUGCUGGGCUUUGGACCCGGCGACAGCGGUUCGACUCCGCUCGGGACUACC

Entity 2 polymer

描述 description	Glutamyl-tRNA(Gln) amidotransferase subunit D
分子量 formula_weight	48053.4 kDa
EC 编号 ec_number	6.3.5.-
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	A,B

MSYQGRARKFLESASIDVGDMVLVEKPDVTYEGMVLDRADDADDRHIVLKLENGYNIGVEISDARIELLEKGSEPRIELPPVEAAEDPELPDVSIISTGGTVASIIDYRTGAVHPAFTADDLLRANPELLDIANIRGRAVFNILSENMKPEYWVETARAVYGEIKDGADGVVVAHGTDTMHYTSAALSFMLRTPVPVVFTGAQRSSDRPSSDASLNIQCSVRAATSEIAEVTVCMHATMDDLSCHLHRGVKVRKMHTSRRDTFRSMNALPLAEVTPDGIKILEENYRKRGSDELELSDRVEERVAFIKSYPGISPDIIKWHLDEGYRGIVIEGTGLGHCPDTLIPVIGEAHDMGVPVAMTSQCLNGRVNMNVYSTGRRLLQAGVIPCDDMLPEVAYVKMCWVLGQTDDPEMAREMMRENIAGEINERTSIAYFRG

来源 Source

来源生物 organism	Methanothermobacter thermautotrophicus
NCBI 分类编号 ncbi_taxonomy_id	145262
宿主生物 host_organism	Escherichia coli

Entity 3 polymer

描述 description	Glutamyl-tRNA(Gln) amidotransferase subunit E
分子量 formula_weight	69626.2 kDa
EC 编号 ec_number	6.3.5.-
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	C,D

MDWEKVGLKMGLEIHQQLDTESKLFCPCRTELTDSEPDHDIVRNLRPTQSELGKFDRAAFEEAMRKLHFHYENYHEETCLVEADEEPPHPLNPEALEIAVTIALLLNMRVVDEFHTMRKQVIDGSNTGGFQRTGLVATDGHLETPQGTVKIENLCLEEDAARRIRETGDGVVFRLDRLGIPLVEITTDPSMSDPQQLREVAYQIGQILRSTRVKRGLGTIRQDLNISIRDGARVEVKGVQDLDLIPEIVEREVKRQLSLVEIRDTLQERGAVVEDKIFDVSEVFADTESRIISSAESVLAVKLRGFDGLIGVEIQPGRRLGTEMADYAKKRGVSGIFHTDELPAYGITEEEVRGLRDAVGASQGDAVVMVAHERVTAENALREVIRRAEMAIQGVPEETRKALPDGNTQYLRPLPTSSRMYLETDIPLFRIEDDLLEGIRRNLPELPSEKKERIMRDYGLSEDLASQLVKRNLVDEFEALTEFRVDTTVIASLLAYTLRELRREGHDVDGLGLDELRDAIKLLEVGKISKDALRDIVACMADEGLAAEDAARKLNLLLLAEDEIESIIQEIVEGNLDMISERGMGAMGPLMGQAMGRLRGRADGKVVNRILREKIQERL

来源 Source

来源生物 organism	Methanothermobacter thermautotrophicus
NCBI 分类编号 ncbi_taxonomy_id	145262
宿主生物 host_organism	Escherichia coli

Entity 4 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	2

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	180

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6. 折叠分类 (SCOP + CATH) 19 domains

SCOP 2.08 (10 domains)

结构域编号 domain_id	d2d6fa1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.38 — Sm-like fold
超家族 Superfamily superfamily	b.38.3 — GatD N-terminal domain-like
家族 Family family	b.38.3.1 — GatD N-terminal domain-like

结构域编号 domain_id	d2d6fa2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.88 — Glutaminase/Asparaginase
超家族 Superfamily superfamily	c.88.1 — Glutaminase/Asparaginase
家族 Family family	c.88.1.1 — Glutaminase/Asparaginase

结构域编号 domain_id	d2d6fb1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.38 — Sm-like fold
超家族 Superfamily superfamily	b.38.3 — GatD N-terminal domain-like
家族 Family family	b.38.3.0 — automated matches

结构域编号 domain_id	d2d6fb2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.88 — Glutaminase/Asparaginase
超家族 Superfamily superfamily	c.88.1 — Glutaminase/Asparaginase
家族 Family family	c.88.1.1 — Glutaminase/Asparaginase

结构域编号 domain_id	d2d6fc1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.182 — GatB/YqeY motif
超家族 Superfamily superfamily	a.182.1 — GatB/YqeY motif
家族 Family family	a.182.1.2 — GatB/GatE C-terminal domain-like

结构域编号 domain_id	d2d6fc2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.74 — DCoH-like
超家族 Superfamily superfamily	d.74.4 — GAD domain-like
家族 Family family	d.74.4.1 — GAD domain

结构域编号 domain_id	d2d6fc3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.128 — Glutamine synthetase/guanido kinase
超家族 Superfamily superfamily	d.128.1 — Glutamine synthetase/guanido kinase
家族 Family family	d.128.1.5 — GatB/GatE catalytic domain-like

结构域编号 domain_id	d2d6fd1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.182 — GatB/YqeY motif
超家族 Superfamily superfamily	a.182.1 — GatB/YqeY motif
家族 Family family	a.182.1.2 — GatB/GatE C-terminal domain-like

结构域编号 domain_id	d2d6fd2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.74 — DCoH-like
超家族 Superfamily superfamily	d.74.4 — GAD domain-like
家族 Family family	d.74.4.1 — GAD domain

结构域编号 domain_id	d2d6fd3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.128 — Glutamine synthetase/guanido kinase
超家族 Superfamily superfamily	d.128.1 — Glutamine synthetase/guanido kinase
家族 Family family	d.128.1.5 — GatB/GatE catalytic domain-like

CATH v4.4 (9 domains)

结构域编号 domain_id	2d6fA01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	520 —

结构域编号 domain_id	2d6fA02
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	1170 — L-asparaginase, N-terminal domain

结构域编号 domain_id	2d6fA03
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	40 —

结构域编号 domain_id	2d6fB01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	520 —

结构域编号 domain_id	2d6fB02
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	1170 — L-asparaginase, N-terminal domain

结构域编号 domain_id	2d6fB03
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	40 —

结构域编号 domain_id	2d6fC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1360 — Gyrase A; domain 2
同源超家族 H-superfamily homologous superfamily	30 — GAD-like domain

结构域编号 domain_id	2d6fC03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	150 — DNA polymerase; domain 1
同源超家族 H-superfamily homologous superfamily	380 — GatB domain, N-terminal subdomain

结构域编号 domain_id	2d6fD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1360 — Gyrase A; domain 2
同源超家族 H-superfamily homologous superfamily	30 — GAD-like domain

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7. 引用文献 (1)

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晶胞边长 a length_a	118.812 Å
晶胞边长 b length_b	140.706 Å
晶胞边长 c length_c	186.044 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	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	3.150 Å
最低分辨率 resolution_low	46.520 Å
R 因子 r_factor	0.2300
R_work r_work	0.2300
R_free r_free	0.2920

fit	/app/data/saxs_computation/d6/2d6f/2d6f.fit
pddf	/app/data/pr_computation/d6/2d6f/2d6f.pr.out
profile	/app/data/saxs_computation/d6/2d6f/2d6f.dat

Crystal structure of Glu-tRNA(Gln) amidotransferase in the complex with tRNA(Gln)

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

5. 实体与聚合体信息 (5)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 polymer

聚合体 Polymer

来源 Source

Entity 4 non-polymer

Entity 5 water

6. 折叠分类 (SCOP + CATH) 19 domains

SCOP 2.08 (10 domains)

CATH v4.4 (9 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)