1vk0

X-ray Structure of Gene Product from Arabidopsis Thaliana At5g06450

Method: X-RAY DIFFRACTION D_max: 102.7 Å Quality: EXCELLENT

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	1vk0
沉积日期 deposition_date	2004-04-12
结构标题 title	X-ray Structure of Gene Product from Arabidopsis Thaliana At5g06450
关键词 keywords	;Protein, homohexamer, Arabidopsis thaliana, At5g06450, Structural Genomics, Protein Structure Initiative, Center for Eukaryotic Structural Genomics, CESG, unknown function ;; structural genomics, unknown function
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	34.35 Å
回转半径 Rg (电子) rg_electron	33.23 Å
零角强度 I(0) i0	267895000.00
分子量 molecular_weight	135150.0 kDa
排除体积 excluded_volume	170380 Å³
包络体积 envelope_volume	214220 Å³
水化壳体积 shell_volume	51739 Å³
包络直径 envelope_diameter	102.6 Å
壳层 Rg shell_rg	42.06 Å
包络 Rg envelope_rg	32.42 Å
形状 Rg shape_rg	33.19 Å
总 Rg total_rg	33.99 Å
总原子数 total_atoms	9546
残基数 n_residues	1194
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	102.7 Å
Rg (实空间) rg_real	34.16 Å
Rg 误差 (实空间) rg_real_error	0.59 Å
I(0) (实空间) i0_real	2.6790e+08
I(0) 误差 (实空间) i0_real_error	4.0560e+06
Rg (倒空间) rg_reciprocal	34.28 Å
I(0) (倒空间) i0_reciprocal	267900000.0000
解质量估计 total_estimate	0.9101
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	46.9 Å
偏度 Skewness skewness	0.061
峰度 Kurtosis kurtosis	-0.694
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	109900000.0000
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: 0.969; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.929

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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) 18 domains

SCOP 2.08 (12 domains)

结构域编号 domain_id	d1vk0a1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.55 — Ribonuclease H-like motif
超家族 Superfamily superfamily	c.55.3 — Ribonuclease H-like
家族 Family family	c.55.3.5 — DnaQ-like 3'-5' exonuclease

结构域编号 domain_id	d1vk0a2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d1vk0b1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.55 — Ribonuclease H-like motif
超家族 Superfamily superfamily	c.55.3 — Ribonuclease H-like
家族 Family family	c.55.3.5 — DnaQ-like 3'-5' exonuclease

结构域编号 domain_id	d1vk0b2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d1vk0c1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.55 — Ribonuclease H-like motif
超家族 Superfamily superfamily	c.55.3 — Ribonuclease H-like
家族 Family family	c.55.3.5 — DnaQ-like 3'-5' exonuclease

结构域编号 domain_id	d1vk0c2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d1vk0d1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.55 — Ribonuclease H-like motif
超家族 Superfamily superfamily	c.55.3 — Ribonuclease H-like
家族 Family family	c.55.3.5 — DnaQ-like 3'-5' exonuclease

结构域编号 domain_id	d1vk0d2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d1vk0e1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.55 — Ribonuclease H-like motif
超家族 Superfamily superfamily	c.55.3 — Ribonuclease H-like
家族 Family family	c.55.3.5 — DnaQ-like 3'-5' exonuclease

结构域编号 domain_id	d1vk0e2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d1vk0f1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.55 — Ribonuclease H-like motif
超家族 Superfamily superfamily	c.55.3 — Ribonuclease H-like
家族 Family family	c.55.3.5 — DnaQ-like 3'-5' exonuclease

结构域编号 domain_id	d1vk0f2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

CATH v4.4 (6 domains)

结构域编号 domain_id	1vk0A00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	420 — Nucleotidyltransferase; domain 5
同源超家族 H-superfamily homologous superfamily	10 — Ribonuclease H-like superfamily/Ribonuclease H

结构域编号 domain_id	1vk0B00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	420 — Nucleotidyltransferase; domain 5
同源超家族 H-superfamily homologous superfamily	10 — Ribonuclease H-like superfamily/Ribonuclease H

结构域编号 domain_id	1vk0C00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	420 — Nucleotidyltransferase; domain 5
同源超家族 H-superfamily homologous superfamily	10 — Ribonuclease H-like superfamily/Ribonuclease H

结构域编号 domain_id	1vk0D00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	420 — Nucleotidyltransferase; domain 5
同源超家族 H-superfamily homologous superfamily	10 — Ribonuclease H-like superfamily/Ribonuclease H

结构域编号 domain_id	1vk0E00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	420 — Nucleotidyltransferase; domain 5
同源超家族 H-superfamily homologous superfamily	10 — Ribonuclease H-like superfamily/Ribonuclease H

结构域编号 domain_id	1vk0F00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	420 — Nucleotidyltransferase; domain 5
同源超家族 H-superfamily homologous superfamily	10 — Ribonuclease H-like superfamily/Ribonuclease H

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7. 引用文献 (1)

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晶胞边长 a length_a	120.831 Å
晶胞边长 b length_b	120.831 Å
晶胞边长 c length_c	185.222 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	120.00 °
晶胞分子数 Z z_pdb	36

空间群 space_group	P 32 2 1
空间群编号 int_tables_number	154
晶系 crystal_system	—

分辨率 resolution	2.100 Å
最低分辨率 resolution_low	34.922 Å
R 因子 r_factor	0.1829
R_work r_work	0.1803
R_free r_free	0.2326

描述 description	hypothetical protein
分子量 formula_weight	23243.1 kDa
来源方法 src_method	man
拷贝数 entity_count	6

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F
原子数 atom_count	10215

X-ray Structure of Gene Product from Arabidopsis Thaliana At5g06450

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) 18 domains

SCOP 2.08 (12 domains)

CATH v4.4 (6 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)

来源生物 organism	Arabidopsis thaliana
通用名 common_name	thale cress
NCBI 分类编号 ncbi_taxonomy_id	3702
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	645

fit	/app/data/saxs_computation/vk/1vk0/1vk0.fit
pddf	/app/data/pr_computation/vk/1vk0/1vk0.pr.out
profile	/app/data/saxs_computation/vk/1vk0/1vk0.dat