SAXSdb — 1g7t

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1g7t
沉积日期 deposition_date	2000-11-14
结构标题 title	X-RAY STRUCTURE OF TRANSLATION INITIATION FACTOR IF2/EIF5B COMPLEXED WITH GDPNP
关键词 keywords	translational GTPase, 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	34.50 Å
回转半径 Rg (电子) rg_electron	34.65 Å
零角强度 I(0) i0	61593200.00
分子量 molecular_weight	62733.0 kDa
排除体积 excluded_volume	78922 Å³
包络体积 envelope_volume	105210 Å³
水化壳体积 shell_volume	28347 Å³
包络直径 envelope_diameter	122.3 Å
壳层 Rg shell_rg	36.45 Å
包络 Rg envelope_rg	34.92 Å
形状 Rg shape_rg	34.66 Å
总 Rg total_rg	34.80 Å
总原子数 total_atoms	4406
残基数 n_residues	569
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	34.97 Å
Rg 误差 (实空间) rg_real_error	1.15 Å
I(0) (实空间) i0_real	6.1590e+07
I(0) 误差 (实空间) i0_real_error	1.1010e+06
Rg (倒空间) rg_reciprocal	34.68 Å
I(0) (倒空间) i0_reciprocal	61580000.0000
解质量估计 total_estimate	0.7558
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	28.3 Å
偏度 Skewness skewness	0.591
峰度 Kurtosis kurtosis	-0.522
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	12950000.0000
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: 0.529; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.499; Smooth: 0.736

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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	TRANSLATION INITIATION FACTOR IF2/EIF5B
分子量 formula_weight	66340.4 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	4734

MKIRSPIVSVLGHVDHGKTTLLDHIRGSAVASREAGGITQHIGATEIPMDVIEGICGDFLKKFSIRETLPGLFFIDTPGHEAFTTLRKRGGALADLAILIVDINEGFKPQTQEALNILRMYRTPFVVAANKIDRIHGWRVHEGRPFMETFSKQDIQVQQKLDTKVYELVGKLHEEGFESERFDRVTDFASQVSIIPISAITGEGIPELLTMLMGLAQQYLREQLKIEEDSPARGTILEVKEETGLGMTIDAVIYDGILRKDDTIAMMTSKDVISTRIRSLLKPRPLEEMRESRKKFQKVDEVVAAAGIKIVAPGIDDVMAGSPLRVVTDPEKVREEILSEIEDIKIDTDEAGVVVKADTLGSLEAVVKILRDMYVPIKVADIGDVSRRDVVNAGIALQEDRVYGAIIAFNVKVIPSAAQELKNSDIKLFQGNVIYRLMEEYEEWVRGIEEEKKKKWMEAIIKPASIRLIPKLVFRQSKPAIGGVEVLTGVIRQGYPLMNDDGETVGTVESMQDKGENLKSASRGQKVAMAIKDAVYGKTIHEGDTLYVDIPENHYHILKEQLSGDLTDEELDLMDKIAEIKRKKNPDWGMKAPF

来源 Source

来源生物 organism	Methanothermobacter thermautotrophicus
NCBI 分类编号 ncbi_taxonomy_id	145262
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
分子量 formula_weight	522.2 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	328

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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	d1g7ta1
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	d1g7ta2
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	d1g7ta3
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.20 — Initiation factor IF2/eIF5b, domain 3
超家族 Superfamily superfamily	c.20.1 — Initiation factor IF2/eIF5b, domain 3
家族 Family family	c.20.1.1 — Initiation factor IF2/eIF5b, domain 3

结构域编号 domain_id	d1g7ta4
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

CATH v4.4 (4 domains)

结构域编号 domain_id	1g7tA01
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	1g7tA02
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	1g7tA03
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	10050 — Translation initiation factor IF- 2, domain 3

结构域编号 domain_id	1g7tA04
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

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7. 引用文献 (1)

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晶胞边长 a length_a	48.799 Å
晶胞边长 b length_b	53.680 Å
晶胞边长 c length_c	94.926 Å
晶胞夹角 α angle_alpha	105.17 °
晶胞夹角 β angle_beta	94.76 °
晶胞夹角 γ angle_gamma	100.17 °
晶胞分子数 Z z_pdb	1

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	2.000 Å
最低分辨率 resolution_low	22.000 Å
R 因子 r_factor	—
R_work r_work	0.2310
R_free r_free	0.2670

fit	/app/data/saxs_computation/g7/1g7t/1g7t.fit
pddf	/app/data/pr_computation/g7/1g7t/1g7t.pr.out
profile	/app/data/saxs_computation/g7/1g7t/1g7t.dat

X-RAY STRUCTURE OF TRANSLATION INITIATION FACTOR IF2/EIF5B COMPLEXED WITH GDPNP

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