2h4o

X-ray Crystal Structure of Protein yonK from Bacillus subtilis. Northeast Structural Genomics Consortium Target SR415

Method: X-RAY DIFFRACTION D_max: 74.7 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	2h4o
沉积日期 deposition_date	2006-05-24
结构标题 title	X-ray Crystal Structure of Protein yonK from Bacillus subtilis. Northeast Structural Genomics Consortium Target SR415
关键词 keywords	;PSI, PROTEIN STRUCTURE INITIATIVE, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM, NESG, Bsu2107 (YonK protein), STRUCTURAL GENOMICS, 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	25.19 Å
回转半径 Rg (电子) rg_electron	24.00 Å
零角强度 I(0) i0	15216000.00
分子量 molecular_weight	28863.0 kDa
排除体积 excluded_volume	35878 Å³
包络体积 envelope_volume	56799 Å³
水化壳体积 shell_volume	20484 Å³
包络直径 envelope_diameter	76.5 Å
壳层 Rg shell_rg	30.15 Å
包络 Rg envelope_rg	23.39 Å
形状 Rg shape_rg	23.96 Å
总 Rg total_rg	25.04 Å
总原子数 total_atoms	2004
残基数 n_residues	240
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	74.7 Å
Rg (实空间) rg_real	25.08 Å
Rg 误差 (实空间) rg_real_error	0.48 Å
I(0) (实空间) i0_real	1.5220e+07
I(0) 误差 (实空间) i0_real_error	2.1370e+05
Rg (倒空间) rg_reciprocal	25.11 Å
I(0) (倒空间) i0_reciprocal	15220000.0000
解质量估计 total_estimate	0.9061
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	72.3 Å
偏度 Skewness skewness	0.012
峰度 Kurtosis kurtosis	-0.724
角度范围 angular_range	— – 0.3150 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	1801000.0000
实空间数据点数 n_real_points	64
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.934; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; 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 (2)

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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	d2h4oa1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.368 — YonK-like
超家族 Superfamily superfamily	d.368.1 — YonK-like
家族 Family family	d.368.1.1 — Yonk-like

结构域编号 domain_id	d2h4ob_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.368 — YonK-like
超家族 Superfamily superfamily	d.368.1 — YonK-like
家族 Family family	d.368.1.1 — Yonk-like

结构域编号 domain_id	d2h4oc_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.368 — YonK-like
超家族 Superfamily superfamily	d.368.1 — YonK-like
家族 Family family	d.368.1.1 — Yonk-like

结构域编号 domain_id	d2h4od_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.368 — YonK-like
超家族 Superfamily superfamily	d.368.1 — YonK-like
家族 Family family	d.368.1.1 — Yonk-like

CATH v4.4 (4 domains)

结构域编号 domain_id	2h4oA00
类 Class class	6 — Special
架构 Architecture architecture	20 — Other non-globular
拓扑 Topology topology	120 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	2h4oB00
类 Class class	6 — Special
架构 Architecture architecture	20 — Other non-globular
拓扑 Topology topology	120 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	2h4oC00
类 Class class	6 — Special
架构 Architecture architecture	20 — Other non-globular
拓扑 Topology topology	120 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	2h4oD00
类 Class class	6 — Special
架构 Architecture architecture	20 — Other non-globular
拓扑 Topology topology	120 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	10 —

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7. 引用文献 (1)

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晶胞边长 a length_a	101.016 Å
晶胞边长 b length_b	72.201 Å
晶胞边长 c length_c	48.935 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	113.78 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	16

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	2.800 Å
最低分辨率 resolution_low	28.340 Å
R 因子 r_factor	0.2630
R_work r_work	0.2630
R_free r_free	0.3010

描述 description	YonK protein
分子量 formula_weight	9012.5 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	2032

X-ray Crystal Structure of Protein yonK from Bacillus subtilis. Northeast Structural Genomics Consortium Target SR415

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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)

来源生物 organism	Bacillus subtilis
NCBI 分类编号 ncbi_taxonomy_id	1423
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	28

fit	/app/data/saxs_computation/h4/2h4o/2h4o.fit
pddf	/app/data/pr_computation/h4/2h4o/2h4o.pr.out
profile	/app/data/saxs_computation/h4/2h4o/2h4o.dat