SAXSdb — 2gvm

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2gvm
沉积日期 deposition_date	2006-05-03
结构标题 title	Crystal structure of hydrophobin HFBI with detergent
关键词 keywords	hydrophobin, amphiphile, surfactant, high solvent content, SURFACE ACTIVE PROTEIN; SURFACE ACTIVE 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	22.20 Å
回转半径 Rg (电子) rg_electron	20.62 Å
零角强度 I(0) i0	15828200.00
分子量 molecular_weight	30870.0 kDa
排除体积 excluded_volume	39219 Å³
包络体积 envelope_volume	47484 Å³
水化壳体积 shell_volume	19861 Å³
包络直径 envelope_diameter	68.5 Å
壳层 Rg shell_rg	26.10 Å
包络 Rg envelope_rg	20.70 Å
形状 Rg shape_rg	20.65 Å
总 Rg total_rg	21.34 Å
总原子数 total_atoms	2130
残基数 n_residues	280
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	68.2 Å
Rg (实空间) rg_real	22.11 Å
Rg 误差 (实空间) rg_real_error	0.45 Å
I(0) (实空间) i0_real	1.5830e+07
I(0) 误差 (实空间) i0_real_error	2.1280e+05
Rg (倒空间) rg_reciprocal	22.13 Å
I(0) (倒空间) i0_reciprocal	15830000.0000
解质量估计 total_estimate	0.9027
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	32.6 Å
偏度 Skewness skewness	0.095
峰度 Kurtosis kurtosis	-0.545
角度范围 angular_range	— – 0.3600 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	1419000.0000
实空间数据点数 n_real_points	68
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.927; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.962

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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	Hydrophobin-1
分子量 formula_weight	7543.6 kDa
来源方法 src_method	nat
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	2248

SNGNGNVCPPGLFSNPQCCATQVLGLIGLDCKVPSQNVYDGTDFRNVCAKTGAQPLCCVAPVAGQALLCQTAVGA

Entity 2 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 non-polymer

描述 description	LAURYL DIMETHYLAMINE-N-OXIDE
分子量 formula_weight	229.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	10

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	118

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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	d2gvma_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.138 — Hydrophobin II, HfbII
超家族 Superfamily superfamily	b.138.1 — Hydrophobin II, HfbII
家族 Family family	b.138.1.1 — Hydrophobin II, HfbII

结构域编号 domain_id	d2gvmb_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.138 — Hydrophobin II, HfbII
超家族 Superfamily superfamily	b.138.1 — Hydrophobin II, HfbII
家族 Family family	b.138.1.1 — Hydrophobin II, HfbII

结构域编号 domain_id	d2gvmc_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.138 — Hydrophobin II, HfbII
超家族 Superfamily superfamily	b.138.1 — Hydrophobin II, HfbII
家族 Family family	b.138.1.1 — Hydrophobin II, HfbII

结构域编号 domain_id	d2gvmd_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.138 — Hydrophobin II, HfbII
超家族 Superfamily superfamily	b.138.1 — Hydrophobin II, HfbII
家族 Family family	b.138.1.1 — Hydrophobin II, HfbII

CATH v4.4 (4 domains)

结构域编号 domain_id	2gvmA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	120 — hfbii hydrophobin
同源超家族 H-superfamily homologous superfamily	10 — Hydrophobin

结构域编号 domain_id	2gvmB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	120 — hfbii hydrophobin
同源超家族 H-superfamily homologous superfamily	10 — Hydrophobin

结构域编号 domain_id	2gvmC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	120 — hfbii hydrophobin
同源超家族 H-superfamily homologous superfamily	10 — Hydrophobin

结构域编号 domain_id	2gvmD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	120 — hfbii hydrophobin
同源超家族 H-superfamily homologous superfamily	10 — Hydrophobin

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7. 引用文献 (1)

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晶胞边长 a length_a	91.900 Å
晶胞边长 b length_b	121.600 Å
晶胞边长 c length_c	121.200 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	C 2 2 21
空间群编号 int_tables_number	20
晶系 crystal_system	—

分辨率 resolution	2.300 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.2330
R_work r_work	0.2330
R_free r_free	0.2470

fit	/app/data/saxs_computation/gv/2gvm/2gvm.fit
pddf	/app/data/pr_computation/gv/2gvm/2gvm.pr.out
profile	/app/data/saxs_computation/gv/2gvm/2gvm.dat

Crystal structure of hydrophobin HFBI with detergent

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

Entity 2 non-polymer

Entity 3 non-polymer

Entity 4 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)