SAXSdb — 1swg

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1swg
沉积日期 deposition_date	1997-07-12
结构标题 title	CIRCULAR PERMUTED STREPTAVIDIN E51/A46 IN COMPLEX WITH BIOTIN
关键词 keywords	BIOTIN BINDING PROTEIN, CIRCULAR PERMUTATION, BIOTIN, BIOTIN-BINDING PROTEIN; BIOTIN-BINDING PROTEIN
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	22.40 Å
回转半径 Rg (电子) rg_electron	21.35 Å
零角强度 I(0) i0	44495000.00
分子量 molecular_weight	49791.0 kDa
排除体积 excluded_volume	61371 Å³
包络体积 envelope_volume	70267 Å³
水化壳体积 shell_volume	26435 Å³
包络直径 envelope_diameter	70.4 Å
壳层 Rg shell_rg	28.81 Å
包络 Rg envelope_rg	21.66 Å
形状 Rg shape_rg	21.32 Å
总 Rg total_rg	22.27 Å
总原子数 total_atoms	3525
残基数 n_residues	463
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	66.7 Å
Rg (实空间) rg_real	22.25 Å
Rg 误差 (实空间) rg_real_error	0.33 Å
I(0) (实空间) i0_real	4.4490e+07
I(0) 误差 (实空间) i0_real_error	5.7040e+05
Rg (倒空间) rg_reciprocal	22.29 Å
I(0) (倒空间) i0_reciprocal	44500000.0000
解质量估计 total_estimate	0.8330
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	29.3 Å
偏度 Skewness skewness	0.113
峰度 Kurtosis kurtosis	-0.528
角度范围 angular_range	— – 0.3550 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	13560000.0000
实空间数据点数 n_real_points	67
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.948; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; 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 (3)

Entity 1 polymer

描述 description	CIRCULARLY PERMUTED CORE-STREPTAVIDIN E51/A46
分子量 formula_weight	13329.4 kDa
突变 mutation	;DELETION OF SURFACE LOOP RESIDUES 45 - 50 FROM THE SEQUENCE. THE OLD N- AND C-TERMINI (S139, A13, RESPECTIVELY) ARE CONNECTED INTRODUCING THE FOUR ADDITIONAL RESIDUES GGGS ;
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	3860

MESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVKPSAASGGGSAEAGITGTWYNQLGSTFIVTAGADGALTGTYESA

来源 Source

来源生物 organism	Streptomyces avidinii
NCBI 分类编号 ncbi_taxonomy_id	1895
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	BIOTIN
分子量 formula_weight	244.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 3 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	335

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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	d1swga_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.61 — Streptavidin-like
超家族 Superfamily superfamily	b.61.1 — Avidin/streptavidin
家族 Family family	b.61.1.1 — Avidin/streptavidin

结构域编号 domain_id	d1swgb_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.61 — Streptavidin-like
超家族 Superfamily superfamily	b.61.1 — Avidin/streptavidin
家族 Family family	b.61.1.1 — Avidin/streptavidin

结构域编号 domain_id	d1swgc_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.61 — Streptavidin-like
超家族 Superfamily superfamily	b.61.1 — Avidin/streptavidin
家族 Family family	b.61.1.1 — Avidin/streptavidin

结构域编号 domain_id	d1swgd_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.61 — Streptavidin-like
超家族 Superfamily superfamily	b.61.1 — Avidin/streptavidin
家族 Family family	b.61.1.1 — Avidin/streptavidin

CATH v4.4 (4 domains)

结构域编号 domain_id	1swgA00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	128 — Lipocalin
同源超家族 H-superfamily homologous superfamily	30 — Avidin-like

结构域编号 domain_id	1swgB00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	128 — Lipocalin
同源超家族 H-superfamily homologous superfamily	30 — Avidin-like

结构域编号 domain_id	1swgC00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	128 — Lipocalin
同源超家族 H-superfamily homologous superfamily	30 — Avidin-like

结构域编号 domain_id	1swgD00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	128 — Lipocalin
同源超家族 H-superfamily homologous superfamily	30 — Avidin-like

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7. 引用文献 (3)

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晶胞边长 a length_a	71.900 Å
晶胞边长 b length_b	78.600 Å
晶胞边长 c length_c	90.800 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	1.800 Å
最低分辨率 resolution_low	10.000 Å
R 因子 r_factor	0.1900
R_work r_work	—
R_free r_free	0.2450

fit	/app/data/saxs_computation/sw/1swg/1swg.fit
pddf	/app/data/pr_computation/sw/1swg/1swg.pr.out
profile	/app/data/saxs_computation/sw/1swg/1swg.dat

CIRCULAR PERMUTED STREPTAVIDIN E51/A46 IN COMPLEX WITH BIOTIN

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 (3)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 non-polymer

Entity 3 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 (3)

8. 文件与曲线 (10)

Files (7)

Curves (3)