2cxi

Crystal Structure Of An N-terminal Fragment Of The Phenylalanyl-tRNA Synthetase Beta-Subunit From Pyrococcus Horikoshii

Method: X-RAY DIFFRACTION D_max: 118.5 Å Quality: REASONABLE

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	2cxi
沉积日期 deposition_date	2005-06-29
结构标题 title	Crystal Structure Of An N-terminal Fragment Of The Phenylalanyl-tRNA Synthetase Beta-Subunit From Pyrococcus Horikoshii
关键词 keywords	;Aminoacyl-tRNA synthetase, Ligase, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI ;; 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	36.45 Å
回转半径 Rg (电子) rg_electron	35.93 Å
零角强度 I(0) i0	215622000.00
分子量 molecular_weight	122030.0 kDa
排除体积 excluded_volume	153860 Å³
包络体积 envelope_volume	194940 Å³
水化壳体积 shell_volume	46008 Å³
包络直径 envelope_diameter	123.2 Å
壳层 Rg shell_rg	41.50 Å
包络 Rg envelope_rg	35.56 Å
形状 Rg shape_rg	35.94 Å
总 Rg total_rg	36.26 Å
总原子数 total_atoms	8526
残基数 n_residues	1017
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	118.5 Å
Rg (实空间) rg_real	36.40 Å
Rg 误差 (实空间) rg_real_error	0.83 Å
I(0) (实空间) i0_real	2.1560e+08
I(0) 误差 (实空间) i0_real_error	3.6220e+06
Rg (倒空间) rg_reciprocal	36.44 Å
I(0) (倒空间) i0_reciprocal	215600000.0000
解质量估计 total_estimate	0.6726
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	46.8 Å
偏度 Skewness skewness	0.239
峰度 Kurtosis kurtosis	-0.464
角度范围 angular_range	— – 0.2150 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	31490000.0000
实空间数据点数 n_real_points	44
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.922; Stabil: 1.000; Sysdev: 0.048; Positv: 1.000; Valcen: 0.983; Smooth: 0.847

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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 (2)

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6. 折叠分类 (SCOP + CATH) 9 domains

CATH v4.4 (9 domains)

结构域编号 domain_id	2cxiA01
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	2cxiA02
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	2cxiA03
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	2cxiB01
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	2cxiB02
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	2cxiB03
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	2cxiC01
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	2cxiC02
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	2cxiC03
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 —

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7. 引用文献 (1)

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晶胞边长 a length_a	142.779 Å
晶胞边长 b length_b	81.973 Å
晶胞边长 c length_c	139.096 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	116.79 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	12

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	1.940 Å
最低分辨率 resolution_low	41.520 Å
R 因子 r_factor	0.1898
R_work r_work	0.1877
R_free r_free	0.2307

描述 description	Phenylalanyl-tRNA synthetase beta chain
分子量 formula_weight	40915.6 kDa
EC 编号 ec_number	6.1.1.20
来源方法 src_method	man
拷贝数 entity_count	3

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C
原子数 atom_count	9228

Crystal Structure Of An N-terminal Fragment Of The Phenylalanyl-tRNA Synthetase Beta-Subunit From Pyrococcus Horikoshii

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 (2)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 water

6. 折叠分类 (SCOP + CATH) 9 domains

CATH v4.4 (9 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)

来源生物 organism	Pyrococcus horikoshii
NCBI 分类编号 ncbi_taxonomy_id	70601
宿主生物 host_organism	Escherichia coli

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	684

fit	/app/data/saxs_computation/cx/2cxi/2cxi.fit
pddf	/app/data/pr_computation/cx/2cxi/2cxi.pr.out
profile	/app/data/saxs_computation/cx/2cxi/2cxi.dat