SAXSdb — 1h4q

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1h4q
沉积日期 deposition_date	2001-05-13
结构标题 title	Prolyl-tRNA synthetase from Thermus thermophilus complexed with tRNApro(CGG), ATP and prolinol
关键词 keywords	AMINOACYL-TRNA SYNTHETASE, ATP + L-PROLINE + TRNA(PRO) AMP + PPI + L-PROLYL-TRNA(PRO), CLASS II AMINOACYL-TRNA SYNTHETASE; AMINOACYL-TRNA SYNTHETASE
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	34.65 Å
回转半径 Rg (电子) rg_electron	33.01 Å
零角强度 I(0) i0	324039000.00
分子量 molecular_weight	129010.0 kDa
排除体积 excluded_volume	154360 Å³
包络体积 envelope_volume	199120 Å³
水化壳体积 shell_volume	49759 Å³
包络直径 envelope_diameter	120.6 Å
壳层 Rg shell_rg	40.39 Å
包络 Rg envelope_rg	32.89 Å
形状 Rg shape_rg	32.90 Å
总 Rg total_rg	33.78 Å
总原子数 total_atoms	9003
残基数 n_residues	994
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	112.6 Å
Rg (实空间) rg_real	34.51 Å
Rg 误差 (实空间) rg_real_error	0.92 Å
I(0) (实空间) i0_real	3.2400e+08
I(0) 误差 (实空间) i0_real_error	5.5590e+06
Rg (倒空间) rg_reciprocal	34.60 Å
I(0) (倒空间) i0_reciprocal	324100000.0000
解质量估计 total_estimate	0.8967
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	44.1 Å
偏度 Skewness skewness	0.172
峰度 Kurtosis kurtosis	-0.416
角度范围 angular_range	— – 0.2300 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	22880000.0000
实空间数据点数 n_real_points	47
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.893; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.978

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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	PROLYL-TRNA SYNTHETASE
分子量 formula_weight	54563.0 kDa
EC 编号 ec_number	6.1.1.15
来源方法 src_method	nat
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
原子数 atom_count	9027

MAKEKGLTPQSQDFSEWYLEVIQKAELADYGPVRGTIVVRPYGYAIWENIQQVLDRMFKETGHQNAYFPLFIPMSFLRKEAEHVEGFSPELAVVTHAGGEELEEPLAVRPTSETVIGYMWSKWIRSWRDLPQLLNQWGNVVRWEMRTRPFLRTSEFLWQEGHTAHATREEAEEEVRRMLSIYARLAREYAAIPVIEGLKTEKEKFAGAVYTTTIEALMKDGKALQAGTSHYLGENFARAFDIKFQDRDLQVKYVHTTSWGLSWRFIGAIIMTHGDDRGLVLPPRLAPIQVVIVPIYKDESRERVLEAAQGLRQALLAQGLRVHLDDRDQHTPGYKFHEWELKGVPFRVELGPKDLEGGQAVLASRLGGKETLPLAALPEALPGKLDAFHEELYRRALAFREDHTRKVDTYEAFKEAVQEGFALAFHCGDKACERLIQEETTATTRCVPFEAEPEEGFCVRCGRPSAYGKRVVFAKAY

Entity 2 polymer

描述 description	TRNAPRO(CGG)
分子量 formula_weight	24927.9 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

CGGGGAGUAGCGCAGCCCGGUAGCGCACCUCGUUCGGGACGAGGGGGGCGCUGGUUCAGAUCCAGUCUCCCCGACCA

Entity 3 non-polymer

描述 description	ADENOSINE-5'-TRIPHOSPHATE
分子量 formula_weight	507.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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 non-polymer

描述 description	PYRROLIDINE-2-CARBALDEHYDE
分子量 formula_weight	99.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 6 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 7 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	24

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6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d1h4qa1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.51 — Anticodon-binding domain-like
超家族 Superfamily superfamily	c.51.1 — Class II aaRS ABD-related
家族 Family family	c.51.1.1 — Anticodon-binding domain of Class II aaRS

结构域编号 domain_id	d1h4qa2
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	d1h4qa3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.68 — IF3-like
超家族 Superfamily superfamily	d.68.5 — C-terminal domain of ProRS
家族 Family family	d.68.5.1 — C-terminal domain of ProRS

结构域编号 domain_id	d1h4qb1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.51 — Anticodon-binding domain-like
超家族 Superfamily superfamily	c.51.1 — Class II aaRS ABD-related
家族 Family family	c.51.1.1 — Anticodon-binding domain of Class II aaRS

结构域编号 domain_id	d1h4qb2
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	d1h4qb3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.68 — IF3-like
超家族 Superfamily superfamily	d.68.5 — C-terminal domain of ProRS
家族 Family family	d.68.5.1 — C-terminal domain of ProRS

CATH v4.4 (6 domains)

结构域编号 domain_id	1h4qA01
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	1h4qA02
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	800 — Anticodon-binding domain

结构域编号 domain_id	1h4qA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	110 — Translation Initiation Factor IF3
同源超家族 H-superfamily homologous superfamily	30 — C-terminal domain of ProRS

结构域编号 domain_id	1h4qB01
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	1h4qB02
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	800 — Anticodon-binding domain

结构域编号 domain_id	1h4qB03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	110 — Translation Initiation Factor IF3
同源超家族 H-superfamily homologous superfamily	30 — C-terminal domain of ProRS

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7. 引用文献 (5)

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晶胞边长 a length_a	141.290 Å
晶胞边长 b length_b	141.290 Å
晶胞边长 c length_c	237.560 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 43 21 2
空间群编号 int_tables_number	96
晶系 crystal_system	—

分辨率 resolution	3.000 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.2210
R_work r_work	0.2210
R_free r_free	0.2540

fit	/app/data/saxs_computation/h4/1h4q/1h4q.fit
pddf	/app/data/pr_computation/h4/1h4q/1h4q.pr.out
profile	/app/data/saxs_computation/h4/1h4q/1h4q.dat

Prolyl-tRNA synthetase from Thermus thermophilus complexed with tRNApro(CGG), ATP and prolinol

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 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 water

6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. 引用文献 (5)

8. 文件与曲线 (10)

Files (7)

Curves (3)