2fa8

Crystal Structure of the Putative Selenoprotein W-related family Protein from Agrobacterium tumefaciens

Method: X-RAY DIFFRACTION D_max: 66.5 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

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2fa8
沉积日期 deposition_date	2005-12-07
结构标题 title	Crystal Structure of the Putative Selenoprotein W-related family Protein from Agrobacterium tumefaciens
关键词 keywords	;alph-beta structure, 4 helix bundle, Structural Genomics, PSI, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, 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	20.92 Å
回转半径 Rg (电子) rg_electron	19.48 Å
零角强度 I(0) i0	24749900.00
分子量 molecular_weight	38176.0 kDa
排除体积 excluded_volume	47885 Å³
包络体积 envelope_volume	55486 Å³
水化壳体积 shell_volume	23057 Å³
包络直径 envelope_diameter	66.6 Å
壳层 Rg shell_rg	26.60 Å
包络 Rg envelope_rg	19.76 Å
形状 Rg shape_rg	19.48 Å
总 Rg total_rg	20.42 Å
总原子数 total_atoms	2675
残基数 n_residues	331
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	66.5 Å
Rg (实空间) rg_real	20.75 Å
Rg 误差 (实空间) rg_real_error	0.27 Å
I(0) (实空间) i0_real	2.4750e+07
I(0) 误差 (实空间) i0_real_error	2.6580e+05
Rg (倒空间) rg_reciprocal	20.79 Å
I(0) (倒空间) i0_reciprocal	24750000.0000
解质量估计 total_estimate	0.8894
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	27.0 Å
偏度 Skewness skewness	0.088
峰度 Kurtosis kurtosis	-0.478
角度范围 angular_range	— – 0.3800 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	6559000.0000
实空间数据点数 n_real_points	70
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.858; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 1.000

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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 (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	d2fa8a1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.47 — Thioredoxin fold
超家族 Superfamily superfamily	c.47.1 — Thioredoxin-like
家族 Family family	c.47.1.23 — Selenoprotein W-related

结构域编号 domain_id	d2fa8b_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.47 — Thioredoxin fold
超家族 Superfamily superfamily	c.47.1 — Thioredoxin-like
家族 Family family	c.47.1.23 — Selenoprotein W-related

结构域编号 domain_id	d2fa8c_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.47 — Thioredoxin fold
超家族 Superfamily superfamily	c.47.1 — Thioredoxin-like
家族 Family family	c.47.1.23 — Selenoprotein W-related

结构域编号 domain_id	d2fa8d_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.47 — Thioredoxin fold
超家族 Superfamily superfamily	c.47.1 — Thioredoxin-like
家族 Family family	c.47.1.23 — Selenoprotein W-related

CATH v4.4 (4 domains)

结构域编号 domain_id	2fa8A00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	30 — Glutaredoxin
同源超家族 H-superfamily homologous superfamily	10 — Glutaredoxin

结构域编号 domain_id	2fa8B00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	30 — Glutaredoxin
同源超家族 H-superfamily homologous superfamily	10 — Glutaredoxin

结构域编号 domain_id	2fa8C00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	30 — Glutaredoxin
同源超家族 H-superfamily homologous superfamily	10 — Glutaredoxin

结构域编号 domain_id	2fa8D00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	30 — Glutaredoxin
同源超家族 H-superfamily homologous superfamily	10 — Glutaredoxin

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7. 引用文献 (1)

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晶胞边长 a length_a	53.078 Å
晶胞边长 b length_b	69.306 Å
晶胞边长 c length_c	95.578 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	16

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	1.900 Å
最低分辨率 resolution_low	46.420 Å
R 因子 r_factor	0.2007
R_work r_work	0.1981
R_free r_free	0.2481

描述 description	hypothetical protein Atu0228
分子量 formula_weight	11959.3 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	2995

Crystal Structure of the Putative Selenoprotein W-related family Protein from Agrobacterium tumefaciens

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

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	Agrobacterium tumefaciens str.
NCBI 分类编号 ncbi_taxonomy_id	176299
宿主生物 host_organism	Escherichia coli BL21(DE3)

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	198

fit	/app/data/saxs_computation/fa/2fa8/2fa8.fit
pddf	/app/data/pr_computation/fa/2fa8/2fa8.pr.out
profile	/app/data/saxs_computation/fa/2fa8/2fa8.dat