SAXSdb — 1ses

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1ses
沉积日期 deposition_date	1994-02-21
结构标题 title	CRYSTAL STRUCTURES AT 2.5 ANGSTROMS RESOLUTION OF SERYL-TRNA SYNTHETASE COMPLEXED WITH TWO DIFFERENT ANALOGUES OF SERYL-ADENYLATE
关键词 keywords	LIGASE, 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	32.97 Å
回转半径 Rg (电子) rg_electron	32.67 Å
零角强度 I(0) i0	146337000.00
分子量 molecular_weight	96415.0 kDa
排除体积 excluded_volume	120880 Å³
包络体积 envelope_volume	154610 Å³
水化壳体积 shell_volume	40453 Å³
包络直径 envelope_diameter	120.4 Å
壳层 Rg shell_rg	37.94 Å
包络 Rg envelope_rg	34.18 Å
形状 Rg shape_rg	32.64 Å
总 Rg total_rg	33.21 Å
总原子数 total_atoms	6799
残基数 n_residues	842
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	112.1 Å
Rg (实空间) rg_real	33.16 Å
Rg 误差 (实空间) rg_real_error	1.04 Å
I(0) (实空间) i0_real	1.4630e+08
I(0) 误差 (实空间) i0_real_error	2.3680e+06
Rg (倒空间) rg_reciprocal	33.08 Å
I(0) (倒空间) i0_reciprocal	146300000.0000
解质量估计 total_estimate	0.8632
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	35.0 Å
偏度 Skewness skewness	0.475
峰度 Kurtosis kurtosis	-0.296
角度范围 angular_range	— – 0.2400 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	24510000.0000
实空间数据点数 n_real_points	49
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.806; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.917; Smooth: 0.884

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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	SERYL-tRNA SYNTHETASE
分子量 formula_weight	47878.8 kDa
EC 编号 ec_number	6.1.1.11
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	6929

MVDLKRLRQEPEVFHRAIREKGVALDLEALLALDREVQELKKRLQEVQTERNQVAKRVPKAPPEEKEALIARGKALGEEAKRLEEALREKEARLEALLLQVPLPPWPGAPVGGEEANREIKRVGGPPEFSFPPLDHVALMEKNGWWEPRISQVSGSRSYALKGDLALYELALLRFAMDFMARRGFLPMTLPSYAREKAFLGTGHFPAYRDQVWAIAETDLYLTGTAEVVLNALHSGEILPYEALPLRYAGYAPAFRSEAGSFGKDVRGLMRVHQFHKVEQYVLTEASLEASDRAFQELLENAEEILRLLELPYRLVEVATGDMGPGKWRQVDIEVYLPSEGRYRETHSCSALLDWQARRANLRYRDPEGRVRYAYTLNNTALATPRILAMLLENHQLQDGRVRVPQALIPYMGKEVLEPCG

来源 Source

来源生物 organism	Thermus thermophilus
NCBI 分类编号 ncbi_taxonomy_id	274

Entity 2 non-polymer

描述 description	SERYL-HYDROXAMATE-ADENOSINE MONOPHOSPHATE
分子量 formula_weight	449.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	ADENOSINE MONOPHOSPHATE
分子量 formula_weight	347.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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	130

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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	d1sesa1
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.2.7.1 — Seryl-tRNA synthetase (SerRS)

结构域编号 domain_id	d1sesa2
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	d1sesb1
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.2.7.1 — Seryl-tRNA synthetase (SerRS)

结构域编号 domain_id	d1sesb2
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	1sesA01
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	40 — Serine-tRNA synthetase, tRNA binding domain

结构域编号 domain_id	1sesA02
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	1sesB01
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	40 — Serine-tRNA synthetase, tRNA binding domain

结构域编号 domain_id	1sesB02
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

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7. 引用文献 (9)

Crystal structures at 2.5 angstrom resolution of seryl-tRNA synthetase complexed with two analogs of seryl adenylate.

Science (1994)

PMID: 8128224 PRIMARY

The 2.9 Angstroms Crystal Structure of T. Thermophilus Seryl-tRNA Synthetase Complexed with tRNA-Ser

Science (1994)

Refined Crystal Structure of the Seryl-tRNA Synthetase from Thermus Thermophilus at 2.5 Angstroms Resolution

J.Mol.Biol. (1993)

Crystallization of the Seryl-tRNA Synthetase: TRNA-Ser Complex of Escherichia Coli

FEBS Lett. (1993)

;A New Crystal Form of the Complex between Seryl-tRNA Synthetase and tRNA-Ser from Thermus Thermophilus that Diffracts to 2.8 Angstroms Resolution ;

FEBS Lett. (1992)

Crystallization of the Seryl-tRNA Synthetase-tRNA-Ser Complex from Thermus Thermophilus

J.Mol.Biol. (1992)

Sequence, Structural and Evolutionary Relationships between Class 2 Aminoacyl-tRNA Synthetases

Nucleic Acids Res. (1991)

Seryl-tRNA Synthetase from Escherichia Coli at 2.5 Angstroms Resolution: A Second Class of Synthetase Structure

Nature (1990)

Crystals of Seryl-tRNA Synthetase from Thermus Thermophilus. Preliminary Crystallographic Data

J.Mol.Biol. (1990)

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晶胞边长 a length_a	85.100 Å
晶胞边长 b length_b	125.200 Å
晶胞边长 c length_c	62.400 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	108.80 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

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	2.500 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.1760
R_work r_work	0.1760
R_free r_free	—

fit	/app/data/saxs_computation/se/1ses/1ses.fit
pddf	/app/data/pr_computation/se/1ses/1ses.pr.out
profile	/app/data/saxs_computation/se/1ses/1ses.dat

CRYSTAL STRUCTURES AT 2.5 ANGSTROMS RESOLUTION OF SERYL-TRNA SYNTHETASE COMPLEXED WITH TWO DIFFERENT ANALOGUES OF SERYL-ADENYLATE

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution