SAXSdb — 1fyf

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1fyf
沉积日期 deposition_date	2000-09-29
结构标题 title	CRYSTAL STRUCTURE OF A TRUNCATED FORM OF THREONYL-TRNA SYNTHETASE COMPLEXED WITH A SERYL ADENYLATE ANALOG
关键词 keywords	AMINO ACID RECOGNITION, ZINC ION, TRNA-SYNTHETASE, ADENYLATE ANALOG, DELETION MUTANT, LIGASE; 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	28.49 Å
回转半径 Rg (电子) rg_electron	27.32 Å
零角强度 I(0) i0	147671000.00
分子量 molecular_weight	93966.0 kDa
排除体积 excluded_volume	116650 Å³
包络体积 envelope_volume	140090 Å³
水化壳体积 shell_volume	40920 Å³
包络直径 envelope_diameter	87.7 Å
壳层 Rg shell_rg	36.18 Å
包络 Rg envelope_rg	27.46 Å
形状 Rg shape_rg	27.31 Å
总 Rg total_rg	28.17 Å
总原子数 total_atoms	6593
残基数 n_residues	802
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	84.8 Å
Rg (实空间) rg_real	28.26 Å
Rg 误差 (实空间) rg_real_error	0.45 Å
I(0) (实空间) i0_real	1.4770e+08
I(0) 误差 (实空间) i0_real_error	2.0060e+06
Rg (倒空间) rg_reciprocal	28.34 Å
I(0) (倒空间) i0_reciprocal	147700000.0000
解质量估计 total_estimate	0.9069
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	37.9 Å
偏度 Skewness skewness	0.095
峰度 Kurtosis kurtosis	-0.547
角度范围 angular_range	— – 0.2800 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	56730000.0000
实空间数据点数 n_real_points	57
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.956; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.935

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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	THREONYL-TRNA SYNTHETASE
分子量 formula_weight	46725.2 kDa
EC 编号 ec_number	6.1.1.3
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
原子数 atom_count	7127

RDHRKIGKQLDLYHMQEEAPGMVFWHNDGWTIFRELEVFVRSKLKEYQYQEVKGPFMMDRVLWEKTGHWDNYKDAMFTTSSENREYCIKPMNCPGHVQIFNQGLKSYRDLPLRMAEFGSCHRNEPSGSLHGLMRVRGFTQDDAHIFCTEEQIRDEVNGCIRLVYDMYSTFGFEKIVVKLSTRPEKRIGSDEMWDRAEADLAVALEENNIPFEYQLGEGAFYGPKIEFTLYDCLDRAWQCGTVQLDFSLPSRLSASYVGEDNERKVPVMIHRAILGSMERFIGILTEEFAGFFPTWLAPVQVVIMNITDSQSEYVNELTQKLSNAGIRVKADLRNEKIGFKIREHTLRRVPYMLVCGDKEVESGKVAVRTRRGKDLGSMDVNEVIEKLQQEIRSRSLKQLEE

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 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 3 non-polymer

描述 description	5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE
分子量 formula_weight	433.4 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	534

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1fyfa1
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	d1fyfa2
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	d1fyfb1
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	d1fyfb2
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 (4 domains)

结构域编号 domain_id	1fyfA01
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	1fyfA02
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	1fyfB01
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	1fyfB02
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

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7. 引用文献 (3)

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晶胞边长 a length_a	86.950 Å
晶胞边长 b length_b	109.520 Å
晶胞边长 c length_c	115.370 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	1.650 Å
最低分辨率 resolution_low	19.930 Å
R 因子 r_factor	0.2180
R_work r_work	0.2180
R_free r_free	0.2370

fit	/app/data/saxs_computation/fy/1fyf/1fyf.fit
pddf	/app/data/pr_computation/fy/1fyf/1fyf.pr.out
profile	/app/data/saxs_computation/fy/1fyf/1fyf.dat

CRYSTAL STRUCTURE OF A TRUNCATED FORM OF THREONYL-TRNA SYNTHETASE COMPLEXED WITH A SERYL 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