1zo1

IF2, IF1, and tRNA fitted to cryo-EM data OF E. COLI 70S initiation complex

Method: ELECTRON MICROSCOPY D_max: 159.1 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	1zo1
沉积日期 deposition_date	2005-05-12
结构标题 title	IF2, IF1, and tRNA fitted to cryo-EM data OF E. COLI 70S initiation complex
关键词 keywords	E. COLI, RIBOSOME, INITIATION OF PROTEIN SYNTHESIS, INITIATION FACTOR, CRYO-ELETRON MICROSCOPY, translation-RNA COMPLEX; translation/RNA
实验方法 method	ELECTRON MICROSCOPY

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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	53.21 Å
回转半径 Rg (电子) rg_electron	52.07 Å
零角强度 I(0) i0	164526000.00
分子量 molecular_weight	86793.0 kDa
排除体积 excluded_volume	101040 Å³
包络体积 envelope_volume	188280 Å³
水化壳体积 shell_volume	34505 Å³
包络直径 envelope_diameter	168.2 Å
壳层 Rg shell_rg	46.81 Å
包络 Rg envelope_rg	49.01 Å
形状 Rg shape_rg	51.93 Å
总 Rg total_rg	52.23 Å
总原子数 total_atoms	5992
残基数 n_residues	648
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	159.1 Å
Rg (实空间) rg_real	53.73 Å
Rg 误差 (实空间) rg_real_error	1.67 Å
I(0) (实空间) i0_real	1.6450e+08
I(0) 误差 (实空间) i0_real_error	3.4880e+06
Rg (倒空间) rg_reciprocal	52.72 Å
I(0) (倒空间) i0_reciprocal	164300000.0000
解质量估计 total_estimate	0.7220
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	31.8 Å
偏度 Skewness skewness	0.338
峰度 Kurtosis kurtosis	-0.995
角度范围 angular_range	— – 0.1500 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	2959000.0000
实空间数据点数 n_real_points	31
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.690; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.316; Smooth: 0.000

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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 (3)

Entity 1 polymer

描述 description	P/I-site tRNA
分子量 formula_weight	24518.6 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	F
原子数 atom_count	5992

GCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGAUCUGGAGGUCCUGUGUUCGAUCCACAGAAUUCGCACCA

Entity 2 polymer

描述 description	translation initiation factor 2
分子量 formula_weight	54209.8 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	I

EPRAPVVTIMGHVDHGKTSLLEYIRSTKVASGEAGGITQHIGAYHVETENGMITFLDTPGHAAFTSMRARGAQATDIVVLVVAADDGVMPQTIEAIQHAKAAQVPVVVAVNKIDKPEADPDRVKNELSQYGILPEEWGGESQFVHVSAKAGTGIDELLDAILLQAEVLELKAVRKGMASGAVIESFLDKGRGPVATVLVREGTLHKGDIVLCGFEYGRVRAMRNELGQEVLEAGPSIPVEILGLSGVPAAGDEVTVVRDEKKAREVALYRQGKFREVKLARQQKSKLENMFANMTEGEVHEVNIVLKADVQGSVEAISDSLLKLSTDEVKVKIIGSGVGGITETDATLAAASNAILVGFNVRADASARKVIEAESLDLRYYSVIYNLIDEVKAAMSGMLSPELKQQIIGLAEVRDVFKSPKFGAIAGCMVTEGVVKRHNPIRVLRDNVVIYEGELESLRRFKDDVNEVRNGMECGIGVKNYNDVRTGDVIEVFEIIEIQRT

Entity 3 polymer

描述 description	translation Initiation Factor 1
分子量 formula_weight	8116.5 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	W

AKEKDTIRTEGVVTEALPNATFRVKLDSGPEILAYISGKMRMHYIRILPGDRVVVEITPYDPTRGRIVYRK

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6. 折叠分类 (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

结构域编号 domain_id	d1zo1w1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.40 — OB-fold
超家族 Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
家族 Family family	b.40.4.5 — Cold shock DNA-binding domain-like

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7. 引用文献 (1)

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晶胞边长 a length_a	1.000 Å
晶胞边长 b length_b	1.000 Å
晶胞边长 c length_c	1.000 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	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	13.80 Å
分辨率测定方法 resolution_method	MULTI-REFERENCE
颗粒数 num_particles	20283

fit	/app/data/saxs_computation/zo/1zo1/1zo1.fit
pddf	/app/data/pr_computation/zo/1zo1/1zo1.pr.out
profile	/app/data/saxs_computation/zo/1zo1/1zo1.dat

IF2, IF1, and tRNA fitted to cryo-EM data OF E. COLI 70S initiation complex

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

冷冻电镜 EM 3D

5. 实体与聚合体信息 (3)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

6. 折叠分类 (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)