1tfy

;How CCA is added to the 3' end of immature tRNA without the use of an oligonucleotide template ;

Method: X-RAY DIFFRACTION D_max: 180.5 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	1tfy
沉积日期 deposition_date	2004-05-27
结构标题 title	;How CCA is added to the 3' end of immature tRNA without the use of an oligonucleotide template ;
关键词 keywords	CCA-adding Complex, CTP, TRANSFERASE-RNA COMPLEX; TRANSFERASE/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	48.83 Å
回转半径 Rg (电子) rg_electron	50.03 Å
零角强度 I(0) i0	876808000.00
分子量 molecular_weight	230820.0 kDa
排除体积 excluded_volume	283000 Å³
包络体积 envelope_volume	405750 Å³
水化壳体积 shell_volume	72754 Å³
包络直径 envelope_diameter	191.2 Å
壳层 Rg shell_rg	48.97 Å
包络 Rg envelope_rg	49.06 Å
形状 Rg shape_rg	50.03 Å
总 Rg total_rg	49.99 Å
总原子数 total_atoms	16180
残基数 n_residues	1821
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	180.5 Å
Rg (实空间) rg_real	49.51 Å
Rg 误差 (实空间) rg_real_error	2.14 Å
I(0) (实空间) i0_real	8.7680e+08
I(0) 误差 (实空间) i0_real_error	1.7890e+07
Rg (倒空间) rg_reciprocal	48.84 Å
I(0) (倒空间) i0_reciprocal	876000000.0000
解质量估计 total_estimate	0.7989
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	45.1 Å
偏度 Skewness skewness	0.665
峰度 Kurtosis kurtosis	0.059
角度范围 angular_range	— – 0.1600 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	92000000.0000
实空间数据点数 n_real_points	33
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.602; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.812; Smooth: 0.763

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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 (7)

Entity 1 polymer

描述 description	5'-R(GPCPGPGPAPUPAPUPCPCPGPCP*G)-3'
分子量 formula_weight	4172.5 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	16180

GCGGAUAUCCGCG

Entity 2 polymer

描述 description	5'-R(GPCPGPGPAPUPAPUPCPCPGPCPAPC)-3'
分子量 formula_weight	4461.7 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	H,I

GCGGAUAUCCGCAC

Entity 3 polymer

描述 description	5'-R(CPGPGPAPUPCPCPGPCPAP*C)-3'
分子量 formula_weight	3481.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	G

CGGAUCCGCAC

Entity 4 polymer

描述 description	5'-R(CPGPCPGPGPAPUPC)-3'
分子量 formula_weight	2541.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	J

CGCGGAUC

Entity 5 polymer

描述 description	tRNA nucleotidyltransferase
分子量 formula_weight	51469.1 kDa
EC 编号 ec_number	2.7.7.25
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

MKVEEILEKALELVIPDEEEVRKGREAEEELRRRLDELGVEYVFVGSYARNTWLKGSLEIDVFLLFPEEFSKEELRERGLEIGKAVLDSYEIRYAEHPYVHGVVKGVEVDVVPCYKLKEPKNIKSAVDRTPFHHKWLEGRIKGKENEVRLLKGFLKANGIYGAEYKVRGFSGYLCELLIVFYGSFLETVKNARRWTRRTVIDVAKGEVRKGEEFFVVDPVDEKRNVAANLSLDNLARFVHLCREFMEAPSLGFFKPKHPLEIEPERLRKIVEERGTAVFAVKFRKPDIVDDNLYPQLERASRKIFEFLERENFMPLRSAFKASEEFCYLLFECQIKEISRVFRRMGPQFEDERNVKKFLSRNRAFRPFIENGRWWAFEMRKFTTPEEGVRSYASTHWHTLGKNVGESIREYFEIISGEKLFKEPVTAELCEMMGVKD

来源 Source

来源生物 organism	Archaeoglobus fulgidus
NCBI 分类编号 ncbi_taxonomy_id	2234
宿主生物 host_organism	Escherichia coli BL21

Entity 6 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	4

Entity 7 non-polymer

描述 description	CYTIDINE-5'-TRIPHOSPHATE
分子量 formula_weight	483.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

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6. 折叠分类 (SCOP + CATH) 28 domains

SCOP 2.08 (12 domains)

结构域编号 domain_id	d1tfya1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.160 — PAP/OAS1 substrate-binding domain
超家族 Superfamily superfamily	a.160.1 — PAP/OAS1 substrate-binding domain
家族 Family family	a.160.1.3 — Archaeal tRNA CCA-adding enzyme substrate-binding domain

结构域编号 domain_id	d1tfya2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.218 — Nucleotidyltransferase
超家族 Superfamily superfamily	d.218.1 — Nucleotidyltransferase
家族 Family family	d.218.1.7 — Archaeal tRNA CCA-adding enzyme catalytic domain

结构域编号 domain_id	d1tfya3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.16 — PAP/Archaeal CCA-adding enzyme, C-terminal domain
家族 Family family	d.58.16.2 — Archaeal tRNA CCA-adding enzyme

结构域编号 domain_id	d1tfyb1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.160 — PAP/OAS1 substrate-binding domain
超家族 Superfamily superfamily	a.160.1 — PAP/OAS1 substrate-binding domain
家族 Family family	a.160.1.3 — Archaeal tRNA CCA-adding enzyme substrate-binding domain

结构域编号 domain_id	d1tfyb2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.218 — Nucleotidyltransferase
超家族 Superfamily superfamily	d.218.1 — Nucleotidyltransferase
家族 Family family	d.218.1.7 — Archaeal tRNA CCA-adding enzyme catalytic domain

结构域编号 domain_id	d1tfyb3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.16 — PAP/Archaeal CCA-adding enzyme, C-terminal domain
家族 Family family	d.58.16.2 — Archaeal tRNA CCA-adding enzyme

结构域编号 domain_id	d1tfyc1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.160 — PAP/OAS1 substrate-binding domain
超家族 Superfamily superfamily	a.160.1 — PAP/OAS1 substrate-binding domain
家族 Family family	a.160.1.3 — Archaeal tRNA CCA-adding enzyme substrate-binding domain

结构域编号 domain_id	d1tfyc2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.218 — Nucleotidyltransferase
超家族 Superfamily superfamily	d.218.1 — Nucleotidyltransferase
家族 Family family	d.218.1.7 — Archaeal tRNA CCA-adding enzyme catalytic domain

结构域编号 domain_id	d1tfyc3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.16 — PAP/Archaeal CCA-adding enzyme, C-terminal domain
家族 Family family	d.58.16.2 — Archaeal tRNA CCA-adding enzyme

结构域编号 domain_id	d1tfyd1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.160 — PAP/OAS1 substrate-binding domain
超家族 Superfamily superfamily	a.160.1 — PAP/OAS1 substrate-binding domain
家族 Family family	a.160.1.3 — Archaeal tRNA CCA-adding enzyme substrate-binding domain

结构域编号 domain_id	d1tfyd2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.218 — Nucleotidyltransferase
超家族 Superfamily superfamily	d.218.1 — Nucleotidyltransferase
家族 Family family	d.218.1.7 — Archaeal tRNA CCA-adding enzyme catalytic domain

结构域编号 domain_id	d1tfyd3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.16 — PAP/Archaeal CCA-adding enzyme, C-terminal domain
家族 Family family	d.58.16.2 — Archaeal tRNA CCA-adding enzyme

CATH v4.4 (16 domains)

结构域编号 domain_id	1tfyA01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1410 — Poly(a)-polymerase, middle domain
同源超家族 H-superfamily homologous superfamily	30 — CCA tRNA nucleotidyltransferase, domain 2

结构域编号 domain_id	1tfyA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	460 — Beta Polymerase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Beta Polymerase, domain 2

结构域编号 domain_id	1tfyA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	590 — Poly(A) polymerase predicted RNA binding domain

结构域编号 domain_id	1tfyA04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	1550 — Archaeal tRNA CCA-adding enzyme catalytic domain

结构域编号 domain_id	1tfyB01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1410 — Poly(a)-polymerase, middle domain
同源超家族 H-superfamily homologous superfamily	30 — CCA tRNA nucleotidyltransferase, domain 2

结构域编号 domain_id	1tfyB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	460 — Beta Polymerase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Beta Polymerase, domain 2

结构域编号 domain_id	1tfyB03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	590 — Poly(A) polymerase predicted RNA binding domain

结构域编号 domain_id	1tfyB04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	1550 — Archaeal tRNA CCA-adding enzyme catalytic domain

结构域编号 domain_id	1tfyC01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1410 — Poly(a)-polymerase, middle domain
同源超家族 H-superfamily homologous superfamily	30 — CCA tRNA nucleotidyltransferase, domain 2

结构域编号 domain_id	1tfyC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	460 — Beta Polymerase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Beta Polymerase, domain 2

结构域编号 domain_id	1tfyC03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	590 — Poly(A) polymerase predicted RNA binding domain

结构域编号 domain_id	1tfyC04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	1550 — Archaeal tRNA CCA-adding enzyme catalytic domain

结构域编号 domain_id	1tfyD01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1410 — Poly(a)-polymerase, middle domain
同源超家族 H-superfamily homologous superfamily	30 — CCA tRNA nucleotidyltransferase, domain 2

结构域编号 domain_id	1tfyD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	460 — Beta Polymerase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Beta Polymerase, domain 2

结构域编号 domain_id	1tfyD03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	590 — Poly(A) polymerase predicted RNA binding domain

结构域编号 domain_id	1tfyD04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	1550 — Archaeal tRNA CCA-adding enzyme catalytic domain

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7. 引用文献 (1)

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晶胞边长 a length_a	114.092 Å
晶胞边长 b length_b	84.023 Å
晶胞边长 c length_c	134.561 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	102.38 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	3.200 Å
最低分辨率 resolution_low	44.280 Å
R 因子 r_factor	0.2380
R_work r_work	0.2352
R_free r_free	0.2904

fit	/app/data/saxs_computation/tf/1tfy/1tfy.fit
pddf	/app/data/pr_computation/tf/1tfy/1tfy.pr.out
profile	/app/data/saxs_computation/tf/1tfy/1tfy.dat

;How CCA is added to the 3' end of immature tRNA without the use of an oligonucleotide template ;

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 (7)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

Entity 4 polymer

聚合体 Polymer

Entity 5 polymer

聚合体 Polymer

来源 Source

Entity 6 non-polymer

Entity 7 non-polymer

6. 折叠分类 (SCOP + CATH) 28 domains

SCOP 2.08 (12 domains)

CATH v4.4 (16 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)