2iy5

PHENYLALANYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS complexed with tRNA and a phenylalanyl-adenylate analog

Method: X-RAY DIFFRACTION D_max: 176.5 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	2iy5
沉积日期 deposition_date	2006-07-12
结构标题 title	PHENYLALANYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS complexed with tRNA and a phenylalanyl-adenylate analog
关键词 keywords	;CLASS II AMINOACYL-TRNA SYNTHETASE, LIGASE, RBD DOMIN, MAGNESIUM, SH3 DOMAIN, PHENYLALANYL-TRNA SYNTHETASE, THERMUS THERMOPHILUS, PROTEIN BIOSYNTHESIS, METAL-BINDING, NUCLEOTIDE-BINDING, RNA-BINDING, ATP-BINDING, TRNA-BINDING, HELIX-TURN-HELIX MOTIF, AMINOACYL-TRNA SYNTHETASE ;; 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	49.68 Å
回转半径 Rg (电子) rg_electron	48.66 Å
零角强度 I(0) i0	396887000.00
分子量 molecular_weight	148890.0 kDa
排除体积 excluded_volume	180110 Å³
包络体积 envelope_volume	280110 Å³
水化壳体积 shell_volume	53515 Å³
包络直径 envelope_diameter	171.6 Å
壳层 Rg shell_rg	45.77 Å
包络 Rg envelope_rg	48.09 Å
形状 Rg shape_rg	48.47 Å
总 Rg total_rg	49.10 Å
总原子数 total_atoms	10418
残基数 n_residues	1193
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	176.5 Å
Rg (实空间) rg_real	50.44 Å
Rg 误差 (实空间) rg_real_error	2.19 Å
I(0) (实空间) i0_real	3.9690e+08
I(0) 误差 (实空间) i0_real_error	7.5810e+06
Rg (倒空间) rg_reciprocal	49.69 Å
I(0) (倒空间) i0_reciprocal	396500000.0000
解质量估计 total_estimate	0.7815
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	33.1 Å
偏度 Skewness skewness	0.478
峰度 Kurtosis kurtosis	-0.594
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	18210000.0000
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: 0.632; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.535; Smooth: 0.723

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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 (6)

Entity 1 polymer

描述 description	PHENYLALANYL-TRNA SYNTHETASE ALPHA CHAIN
分子量 formula_weight	39309.2 kDa
EC 编号 ec_number	6.1.1.20
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	10649

MLEEALAAIQNARDLEELKALKARYLGKKGLLTQEMKGLSALPLEERRKRGQELNAIKAALEAALEAREKALEEAALKEALERERVDVSLPGASLFSGGLHPITLMERELVEIFRALGYQAVEGPEVESEFFNFDALNIPEHHPARDMWDTFWLTGEGFRLEGPLGEEVEGRLLLRTHTSPMQVRYMVAHTPPFRIVVPGRVFRFEQTDATHEAVFHQLEGLVVGEGIAMAHLKGAIYELAQALFGPDSKVRFQPVYFPFVEPGAQFAVWWPEGGKWLELGGAGMVHPKVFQAVDAYRERLGLPPAYRGVTGFAFGLGVERLAMLRYGIPDIRYFFGGRLKFLEQFKGVL

Entity 2 polymer

描述 description	PHENYLALANYL-TRNA SYNTHETASE BETA CHAIN
分子量 formula_weight	86736.7 kDa
EC 编号 ec_number	6.1.1.20
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B

MRVPFSWLKAYVPELESPEVLEERLAGLGFETDRIERVFPIPRGVVFARVLEAHPIPGTRLKRLVLDAGRTVEVVSGAENARKGIGVALALPGTELPGLGQKVGERVIQGVRSFGMALSPRELGVGEYGGGLLEFPEDALPPGTPLSEAWPEEVVLDLEVTPNRPDALGLLGLARDLHALGYALVEPEAALKAEALPLPFALKVEDPEGAPHFTLGYAFGLRVAPSPLWMQRALFAAGMRPINNVVDVTNYVMLERAQPMHAFDLRFVGEGIAVRRAREGERLKTLDGVERTLHPEDLVIAGWRGEESFPLGLAGVMGGAESEVREDTEAIALEVACFDPVSIRKTARRHGLRTEASHRFERGVDPLGQVPAQRRALSLLQALAGARVAEALLEAGSPKPPEAIPFRPEYANRLLGTSYPEAEQIAILKRLGCRVEGEGPTYRVTPPSHRLDLRLEEDLVEEVARIEGYETIPLALPAFFPAPDNRAVEAPYRKEQRLREVLSGLGFQEVYTYSFMDPEDARRFRLDPPRLLLLNPLAPEKAALRTHLFPGLVRVLKENLDLDRPERALLFEVGRVFREREETHLAGLLFGEGVGLPWAKERLSGYFLLKGYLEALFARLGLAFRVEAEAFPFLHPGVSGRVLVEGEEVGFLGALHPEIAQELELPPVHLFELRLPLPDKPLAFQDPSRHPAAFRDLAVVVPAPTPYGEVEALVREAAGPYLESLALFDLYQGPPLPEGHKSLAFHLRFRHPKRTLRDEEVEEAVSRVAEALRARGFGLRGLDTP

Entity 3 polymer

描述 description	TRNAPHE
分子量 formula_weight	24484.6 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	T

GCCGAGGUAGCUCAGUUGGUAGAGCAUGCGACUGAAAAUCGCAGUGUCCGCGGUUCGAUUCCGCGCCUCGGCACCA

Entity 4 non-polymer

描述 description	ADENOSINE-5'-[PHENYLALANINOL-PHOSPHATE]
分子量 formula_weight	480.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 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	1

Entity 6 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	231

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6. 折叠分类 (SCOP + CATH) 15 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d2iy5a1
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.2.7.2 — Phenylalanyl-tRNA synthetase (PheRS)

结构域编号 domain_id	d2iy5a2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.104 — Class II aaRS and biotin synthetases
超家族 Superfamily superfamily	d.104.1 — Class II aaRS and biotin synthetases
家族 Family family	d.104.1.1 — Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain

结构域编号 domain_id	d2iy5b1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.6 — Putative DNA-binding domain
超家族 Superfamily superfamily	a.6.1 — Putative DNA-binding domain
家族 Family family	a.6.1.1 — Domains B1 and B5 of PheRS-beta, PheT

结构域编号 domain_id	d2iy5b2
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.6 — Putative DNA-binding domain
超家族 Superfamily superfamily	a.6.1 — Putative DNA-binding domain
家族 Family family	a.6.1.1 — Domains B1 and B5 of PheRS-beta, PheT

结构域编号 domain_id	d2iy5b3
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.40 — OB-fold
超家族 Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
家族 Family family	b.40.4.4 — Myf domain

结构域编号 domain_id	d2iy5b4
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.153 — PheT/TilS domain
超家族 Superfamily superfamily	b.153.1 — PheT/TilS domain
家族 Family family	b.153.1.1 — B3/B4 domain of PheRS, PheT

结构域编号 domain_id	d2iy5b5
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.58.13 — Anticodon-binding domain of PheRS
家族 Family family	d.58.13.1 — Anticodon-binding domain of PheRS

结构域编号 domain_id	d2iy5b6
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.104 — Class II aaRS and biotin synthetases
超家族 Superfamily superfamily	d.104.1 — Class II aaRS and biotin synthetases
家族 Family family	d.104.1.1 — Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain

CATH v4.4 (7 domains)

结构域编号 domain_id	2iy5A00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	930 — BirA Bifunctional Protein; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Bira Bifunctional Protein; Domain 2

结构域编号 domain_id	2iy5B01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	56 — Phenylalanyl-tRNA Synthetase; Chain B, domain 1
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	2iy5B02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	140 — Nucleic acid-binding proteins

结构域编号 domain_id	2iy5B03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	40 — Phenylalanyl-tRNA Synthetase; Chain B, domain 3
同源超家族 H-superfamily homologous superfamily	10 — Phenylalanyl-trna Synthetase, Chain B, domain 3

结构域编号 domain_id	2iy5B04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	56 — Phenylalanyl-tRNA Synthetase; Chain B, domain 1
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	2iy5B05
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	930 — BirA Bifunctional Protein; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Bira Bifunctional Protein; Domain 2

结构域编号 domain_id	2iy5B06
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	380 — Ferrodoxin-fold anticodon-binding domain

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7. 引用文献 (1)

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晶胞边长 a length_a	173.400 Å
晶胞边长 b length_b	173.400 Å
晶胞边长 c length_c	139.400 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	120.00 °
晶胞分子数 Z z_pdb	6

空间群 space_group	P 32 2 1
空间群编号 int_tables_number	154
晶系 crystal_system	—

分辨率 resolution	3.100 Å
最低分辨率 resolution_low	9.990 Å
R 因子 r_factor	0.2380
R_work r_work	0.2380
R_free r_free	0.2990

fit	/app/data/saxs_computation/iy/2iy5/2iy5.fit
pddf	/app/data/pr_computation/iy/2iy5/2iy5.pr.out
profile	/app/data/saxs_computation/iy/2iy5/2iy5.dat

PHENYLALANYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS complexed with tRNA and a phenylalanyl-adenylate analog

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 (6)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 water

6. 折叠分类 (SCOP + CATH) 15 domains

SCOP 2.08 (8 domains)

CATH v4.4 (7 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)