1ivs

CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS VALYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(VAL) AND VALYL-ADENYLATE ANALOGUE

Method: X-RAY DIFFRACTION D_max: 187.7 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	1ivs
沉积日期 deposition_date	2002-03-29
结构标题 title	CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS VALYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(VAL) AND VALYL-ADENYLATE ANALOGUE
关键词 keywords	;Rossmann fold, helix bundle, coiled coil, beta barrel, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Structural Genomics, 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	56.02 Å
回转半径 Rg (电子) rg_electron	58.85 Å
零角强度 I(0) i0	1137550000.00
分子量 molecular_weight	247040.0 kDa
排除体积 excluded_volume	294560 Å³
包络体积 envelope_volume	425790 Å³
水化壳体积 shell_volume	65533 Å³
包络直径 envelope_diameter	199.1 Å
壳层 Rg shell_rg	52.68 Å
包络 Rg envelope_rg	57.56 Å
形状 Rg shape_rg	58.97 Å
总 Rg total_rg	58.32 Å
总原子数 total_atoms	17206
残基数 n_residues	1874
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	187.7 Å
Rg (实空间) rg_real	56.65 Å
Rg 误差 (实空间) rg_real_error	2.33 Å
I(0) (实空间) i0_real	1.1380e+09
I(0) 误差 (实空间) i0_real_error	2.4790e+07
Rg (倒空间) rg_reciprocal	55.48 Å
I(0) (倒空间) i0_reciprocal	1136000000.0000
解质量估计 total_estimate	0.7682
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	40.2 Å
偏度 Skewness skewness	0.527
峰度 Kurtosis kurtosis	-0.475
角度范围 angular_range	— – 0.1400 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	55980000.0000
实空间数据点数 n_real_points	29
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.710; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.727; Smooth: 0.126

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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 (4)

Entity 1 polymer

描述 description	tRNA (Val)
分子量 formula_weight	24174.5 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	C,D
原子数 atom_count	17424

GGGCGGCUAGCUCAGCGGAAGAGCGCUCGCCUCACACGCGAGAGGUCGUAGGUUCAAGUCCUACGCCGCCCACCA

Entity 2 polymer

描述 description	Valyl-tRNA synthetase
分子量 formula_weight	98914.4 kDa
EC 编号 ec_number	6.1.1.9
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

MDLPKAYDPKSVEPKWAEKWAKNPFVANPKSGKPPFVIFMPPPNVTGSLHMGHALDNSLQDALIRYKRMRGFEAVWLPGTDHAGIATQVVVERLLLKEGKTRHDLGREKFLERVWQWKEESGGTILKQLKRLGASADWSREAFTMDEKRSRAVRYAFSRYYHEGLAYRAPRLVNWCPRCETTLSDLEVETEPTPGKLYTLRYEVEGGGFIEIATVRPETVFADQAIAVHPEDERYRHLLGKRARIPLTEVWIPILADPAVEKDFGTGALKVTPAHDPLDYEIGERHGLKPVSVINLEGRMEGERVPEALRGLDRFEARRKAVELFREAGHLVKEEDYTIALATCSRCGTPIEYAIFPQWWLRMRPLAEEVLKGLRRGDIAFVPERWKKVNMDWLENVKDWNISRQLWWGHQIPAWYCEDCQAVNVPRPERYLEDPTSCEACGSPRLKRDEDVFDTWFSSALWPLSTLGWPEETEDLKAFYPGDVLVTGYDILFLWVSRMEVSGYHFMGERPFKTVLLHGLVLDEKGQKMSKSKGNVIDPLEMVERYGADALRFALIYLATGGQDIRLDLRWLEMARNFANKLYNAARFVLLSREGFQAKEDTPTLADRFMRSRLSRGVEEITALYEALDLAQAAREVYELVWSEFCDWYLEAAKPALKAGNAHTLRTLEEVLAVLLKLLHPMMPFLTSELYQALTGKEELALEAWPEPGGRDEEAERAFEALKQAVTAVRALKAEAGLPPAQEVRVYLEGETAPVEENLEVFRFLSRADLLPERPAKALVKAMPRVTARMPLEGLLDVEEWRRRQEKRLKELLALAERSQRKLASPGFREKAPKEVVEAEEARLKENLEQAERIREALSQIG

来源 Source

来源生物 organism	Thermus thermophilus
NCBI 分类编号 ncbi_taxonomy_id	274
宿主生物 host_organism	Escherichia coli

Entity 3 non-polymer

描述 description	N-[VALINYL]-N'-[ADENOSYL]-DIAMINOSUFONE
分子量 formula_weight	444.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 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	218

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6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1ivsa1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.2 — Long alpha-hairpin
超家族 Superfamily superfamily	a.2.7 — tRNA-binding arm
家族 Family family	a.2.7.3 — Valyl-tRNA synthetase (ValRS) C-terminal domain

结构域编号 domain_id	d1ivsa2
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.27 — Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
超家族 Superfamily superfamily	a.27.1 — Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
家族 Family family	a.27.1.1 — Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases

结构域编号 domain_id	d1ivsa3
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.51 — ValRS/IleRS/LeuRS editing domain
超家族 Superfamily superfamily	b.51.1 — ValRS/IleRS/LeuRS editing domain
家族 Family family	b.51.1.1 — ValRS/IleRS/LeuRS editing domain

结构域编号 domain_id	d1ivsa4
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
超家族 Superfamily superfamily	c.26.1 — Nucleotidylyl transferase
家族 Family family	c.26.1.1 — Class I aminoacyl-tRNA synthetases (RS), catalytic domain

结构域编号 domain_id	d1ivsb1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.2 — Long alpha-hairpin
超家族 Superfamily superfamily	a.2.7 — tRNA-binding arm
家族 Family family	a.2.7.3 — Valyl-tRNA synthetase (ValRS) C-terminal domain

结构域编号 domain_id	d1ivsb2
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.27 — Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
超家族 Superfamily superfamily	a.27.1 — Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
家族 Family family	a.27.1.1 — Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases

结构域编号 domain_id	d1ivsb3
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.51 — ValRS/IleRS/LeuRS editing domain
超家族 Superfamily superfamily	b.51.1 — ValRS/IleRS/LeuRS editing domain
家族 Family family	b.51.1.1 — ValRS/IleRS/LeuRS editing domain

结构域编号 domain_id	d1ivsb4
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
超家族 Superfamily superfamily	c.26.1 — Nucleotidylyl transferase
家族 Family family	c.26.1.1 — Class I aminoacyl-tRNA synthetases (RS), catalytic domain

CATH v4.4 (10 domains)

结构域编号 domain_id	1ivsA01
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	620 — HUPs

结构域编号 domain_id	1ivsA02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	730 — Isoleucyl-tRNA Synthetase; Domain 1
同源超家族 H-superfamily homologous superfamily	10 — Isoleucyl-tRNA Synthetase; Domain 1

结构域编号 domain_id	1ivsA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	740 — Isoleucyl-tRNA Synthetase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain

结构域编号 domain_id	1ivsA04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1170 — Valyl-trna Synthetase; Chain: A, domain 4
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1ivsA05
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	380 — Valyl-tRNA synthetase, C-terminal domain

结构域编号 domain_id	1ivsB01
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	620 — HUPs

结构域编号 domain_id	1ivsB02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	730 — Isoleucyl-tRNA Synthetase; Domain 1
同源超家族 H-superfamily homologous superfamily	10 — Isoleucyl-tRNA Synthetase; Domain 1

结构域编号 domain_id	1ivsB03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	740 — Isoleucyl-tRNA Synthetase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain

结构域编号 domain_id	1ivsB04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1170 — Valyl-trna Synthetase; Chain: A, domain 4
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1ivsB05
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	380 — Valyl-tRNA synthetase, C-terminal domain

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7. 引用文献 (2)

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晶胞边长 a length_a	411.810 Å
晶胞边长 b length_b	411.810 Å
晶胞边长 c length_c	81.970 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	16

空间群 space_group	P 42 21 2
空间群编号 int_tables_number	94
晶系 crystal_system	—

分辨率 resolution	2.900 Å
最低分辨率 resolution_low	40.000 Å
R 因子 r_factor	0.2480
R_work r_work	0.2480
R_free r_free	0.2820

fit	/app/data/saxs_computation/iv/1ivs/1ivs.fit
pddf	/app/data/pr_computation/iv/1ivs/1ivs.pr.out
profile	/app/data/saxs_computation/iv/1ivs/1ivs.dat

CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS VALYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(VAL) AND VALYL-ADENYLATE ANALOGUE

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 (4)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

Entity 4 water

6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (8 domains)

CATH v4.4 (10 domains)

7. 引用文献 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)