1ktv

Crystal Structure of Elongation Factor G Dimer Without Nucleotide

Method: X-RAY DIFFRACTION D_max: 137.7 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	1ktv
沉积日期 deposition_date	2002-01-17
结构标题 title	Crystal Structure of Elongation Factor G Dimer Without Nucleotide
关键词 keywords	apo form, TRANSLATION; TRANSLATION
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	39.19 Å
回转半径 Rg (电子) rg_electron	38.78 Å
零角强度 I(0) i0	289251000.00
分子量 molecular_weight	140770.0 kDa
排除体积 excluded_volume	177700 Å³
包络体积 envelope_volume	242650 Å³
水化壳体积 shell_volume	53267 Å³
包络直径 envelope_diameter	145.4 Å
壳层 Rg shell_rg	43.51 Å
包络 Rg envelope_rg	38.19 Å
形状 Rg shape_rg	38.79 Å
总 Rg total_rg	39.06 Å
总原子数 total_atoms	9914
残基数 n_residues	1264
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	137.7 Å
Rg (实空间) rg_real	39.14 Å
Rg 误差 (实空间) rg_real_error	1.16 Å
I(0) (实空间) i0_real	2.8930e+08
I(0) 误差 (实空间) i0_real_error	4.5480e+06
Rg (倒空间) rg_reciprocal	39.17 Å
I(0) (倒空间) i0_reciprocal	289300000.0000
解质量估计 total_estimate	0.8784
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	48.2 Å
偏度 Skewness skewness	0.282
峰度 Kurtosis kurtosis	-0.353
角度范围 angular_range	— – 0.2000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	24180000.0000
实空间数据点数 n_real_points	41
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.818; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.977

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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 (1)

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6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1ktva1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.43 — Reductase/isomerase/elongation factor common domain
超家族 Superfamily superfamily	b.43.3 — Translation proteins
家族 Family family	b.43.3.1 — Elongation factors

结构域编号 domain_id	d1ktva2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.8 — G proteins

结构域编号 domain_id	d1ktva3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.14 — Ribosomal protein S5 domain 2-like
超家族 Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
家族 Family family	d.14.1.1 — Translational machinery components

结构域编号 domain_id	d1ktva4
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.58.11 — EF-G C-terminal domain-like
家族 Family family	d.58.11.1 — EF-G/eEF-2 domains III and V

结构域编号 domain_id	d1ktvb1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.43 — Reductase/isomerase/elongation factor common domain
超家族 Superfamily superfamily	b.43.3 — Translation proteins
家族 Family family	b.43.3.1 — Elongation factors

结构域编号 domain_id	d1ktvb2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.8 — G proteins

结构域编号 domain_id	d1ktvb3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.14 — Ribosomal protein S5 domain 2-like
超家族 Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
家族 Family family	d.14.1.1 — Translational machinery components

结构域编号 domain_id	d1ktvb4
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.58.11 — EF-G C-terminal domain-like
家族 Family family	d.58.11.1 — EF-G/eEF-2 domains III and V

CATH v4.4 (10 domains)

结构域编号 domain_id	1ktvA01
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	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	1ktvA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
同源超家族 H-superfamily homologous superfamily	10 — Translation factors

结构域编号 domain_id	1ktvA03
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	870 — Elongation Factor G (Translational Gtpase), domain 3

结构域编号 domain_id	1ktvA04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	230 — Ribosomal Protein S5; domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1ktvA05
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	240 —

结构域编号 domain_id	1ktvB01
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	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	1ktvB02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
同源超家族 H-superfamily homologous superfamily	10 — Translation factors

结构域编号 domain_id	1ktvB03
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	870 — Elongation Factor G (Translational Gtpase), domain 3

结构域编号 domain_id	1ktvB04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	230 — Ribosomal Protein S5; domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1ktvB05
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	240 —

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7. 引用文献 (1)

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晶胞边长 a length_a	86.987 Å
晶胞边长 b length_b	103.548 Å
晶胞边长 c length_c	176.447 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	3.800 Å
最低分辨率 resolution_low	39.730 Å
R 因子 r_factor	—
R_work r_work	0.2870
R_free r_free	0.3740

描述 description	ELONGATION FACTOR G
分子量 formula_weight	76977.1 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	9914

Crystal Structure of Elongation Factor G Dimer Without Nucleotide

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 (1)

Entity 1 polymer

聚合体 Polymer

来源 Source

6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (8 domains)

CATH v4.4 (10 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)

来源生物 organism	Thermus thermophilus
NCBI 分类编号 ncbi_taxonomy_id	274
宿主生物 host_organism	Escherichia coli BL21(DE3)

fit	/app/data/saxs_computation/kt/1ktv/1ktv.fit
pddf	/app/data/pr_computation/kt/1ktv/1ktv.pr.out
profile	/app/data/saxs_computation/kt/1ktv/1ktv.dat