1svj

The solution structure of the nucleotide binding domain of KdpB

Method: SOLUTION NMR D_max: 52.4 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

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1svj
沉积日期 deposition_date	2004-03-29
结构标题 title	The solution structure of the nucleotide binding domain of KdpB
关键词 keywords	alpha-beta sandwich, HYDROLASE; HYDROLASE
实验方法 method	SOLUTION NMR

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	15.45 Å
回转半径 Rg (电子) rg_electron	13.92 Å
零角强度 I(0) i0	4680720.00
分子量 molecular_weight	14800.0 kDa
排除体积 excluded_volume	18372 Å³
包络体积 envelope_volume	20732 Å³
水化壳体积 shell_volume	12495 Å³
包络直径 envelope_diameter	50.4 Å
壳层 Rg shell_rg	19.85 Å
包络 Rg envelope_rg	14.55 Å
形状 Rg shape_rg	13.91 Å
总 Rg total_rg	15.15 Å
总原子数 total_atoms	2098
残基数 n_residues	136
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

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	52.4 Å
Rg (实空间) rg_real	15.36 Å
Rg 误差 (实空间) rg_real_error	0.33 Å
I(0) (实空间) i0_real	4.6810e+06
I(0) 误差 (实空间) i0_real_error	5.2130e+04
Rg (倒空间) rg_reciprocal	15.37 Å
I(0) (倒空间) i0_reciprocal	4681000.0000
解质量估计 total_estimate	0.8576
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	20.6 Å
偏度 Skewness skewness	0.200
峰度 Kurtosis kurtosis	-0.182
角度范围 angular_range	— – 0.5000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	1343000.0000
实空间数据点数 n_real_points	80
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.727; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.966

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (1)

▼

6. 折叠分类 (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

结构域编号 domain_id	d1svja_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.220 — Metal cation-transporting ATPase, ATP-binding domain N
超家族 Superfamily superfamily	d.220.1 — Metal cation-transporting ATPase, ATP-binding domain N
家族 Family family	d.220.1.1 — Metal cation-transporting ATPase, ATP-binding domain N

CATH v4.4 (1 domains)

结构域编号 domain_id	1svjA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1110 — Calcium-transporting ATPase, cytoplasmic domain N
同源超家族 H-superfamily homologous superfamily	10 — Calcium-transporting ATPase, cytoplasmic domain N

▶

7. 引用文献 (1)

▶

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	—

描述 description	Potassium-transporting ATPase B chain
分子量 formula_weight	17168.3 kDa
EC 编号 ec_number	3.6.3.12
来源方法 src_method	man
拷贝数 entity_count	1

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	2098

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli BL21(DE3)

The solution structure of the nucleotide binding domain of KdpB

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

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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/sv/1svj/1svj.fit
pddf	/app/data/pr_computation/sv/1svj/1svj.pr.out
profile	/app/data/saxs_computation/sv/1svj/1svj.dat