SAXSdb — 1xwa

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1xwa
沉积日期 deposition_date	2004-10-29
结构标题 title	Drospohila thioredoxin, oxidized, P41212
关键词 keywords	Dimerization, Drosophila melanogaster, redox regulation, thioredoxin, x-ray crystal structure, ELECTRON TRANSPORT; ELECTRON TRANSPORT
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	45.31 Å
回转半径 Rg (电子) rg_electron	44.86 Å
零角强度 I(0) i0	32466500.00
分子量 molecular_weight	47659.0 kDa
排除体积 excluded_volume	60148 Å³
包络体积 envelope_volume	102830 Å³
水化壳体积 shell_volume	20037 Å³
包络直径 envelope_diameter	119.2 Å
壳层 Rg shell_rg	48.41 Å
包络 Rg envelope_rg	41.29 Å
形状 Rg shape_rg	44.86 Å
总 Rg total_rg	45.10 Å
总原子数 total_atoms	3313
残基数 n_residues	429
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	134.8 Å
Rg (实空间) rg_real	45.09 Å
Rg 误差 (实空间) rg_real_error	1.27 Å
I(0) (实空间) i0_real	3.2470e+07
I(0) 误差 (实空间) i0_real_error	5.8250e+05
Rg (倒空间) rg_reciprocal	45.31 Å
I(0) (倒空间) i0_reciprocal	32470000.0000
解质量估计 total_estimate	0.5996
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	61.6 Å
偏度 Skewness skewness	-0.342
峰度 Kurtosis kurtosis	-0.967
角度范围 angular_range	— – 0.1750 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	747000.0000
实空间数据点数 n_real_points	36
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.008; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.769; 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 (4)

Entity 1 polymer

描述 description	thioredoxin
分子量 formula_weight	12104.0 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	3731

AAAAAMVYQVKDKADLDGQLTKASGKLVVLDFFATWCGPCKMISPKLVELSTQFADNVVVLKVDVDECEDIAMEYNISSMPTFVFLKNGVKVEEFAGANAKRLEDVIKANI

来源 Source

来源生物 organism	Drosophila melanogaster
通用名 common_name	fruit fly
NCBI 分类编号 ncbi_taxonomy_id	7227
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	CADMIUM ION
分子量 formula_weight	112.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 3 non-polymer

描述 description	CHLORIDE ION
分子量 formula_weight	35.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	418

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6. 折叠分类 (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

结构域编号 domain_id	d1xwaa1
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.47.1.1 — Thioltransferase

结构域编号 domain_id	d1xwaa2
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	d1xwab_
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.47.1.1 — Thioltransferase

结构域编号 domain_id	d1xwac_
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.47.1.1 — Thioltransferase

结构域编号 domain_id	d1xwad_
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.47.1.1 — Thioltransferase

CATH v4.4 (4 domains)

结构域编号 domain_id	1xwaA00
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	1xwaB00
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	1xwaC00
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	1xwaD00
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	92.544 Å
晶胞边长 b length_b	92.544 Å
晶胞边长 c length_c	97.624 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	32

空间群 space_group	P 41 21 2
空间群编号 int_tables_number	92
晶系 crystal_system	—

分辨率 resolution	2.200 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	—
R_work r_work	0.2260
R_free r_free	0.2880

fit	/app/data/saxs_computation/xw/1xwa/1xwa.fit
pddf	/app/data/pr_computation/xw/1xwa/1xwa.pr.out
profile	/app/data/saxs_computation/xw/1xwa/1xwa.dat

Drospohila thioredoxin, oxidized, P41212

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 (4)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 non-polymer

Entity 3 non-polymer

Entity 4 water

6. 折叠分类 (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

CATH v4.4 (4 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)