SAXSdb — 1ovr

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1ovr
沉积日期 deposition_date	2003-03-27
结构标题 title	CRYSTAL STRUCTURE OF FOUR-HELIX BUNDLE MODEL di-Mn(II)-DF1-L13
关键词 keywords	ALPHA-HELICAL BUNDLE, PROTEIN DESIGN, DE NOVO PROTEIN; DE NOVO 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	29.13 Å
回转半径 Rg (电子) rg_electron	28.95 Å
零角强度 I(0) i0	7999880.00
分子量 molecular_weight	23782.0 kDa
排除体积 excluded_volume	30745 Å³
包络体积 envelope_volume	44205 Å³
水化壳体积 shell_volume	14196 Å³
包络直径 envelope_diameter	101.8 Å
壳层 Rg shell_rg	32.50 Å
包络 Rg envelope_rg	28.17 Å
形状 Rg shape_rg	28.95 Å
总 Rg total_rg	29.42 Å
总原子数 total_atoms	1669
残基数 n_residues	192
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	97.6 Å
Rg (实空间) rg_real	29.39 Å
Rg 误差 (实空间) rg_real_error	1.23 Å
I(0) (实空间) i0_real	8.0000e+06
I(0) 误差 (实空间) i0_real_error	1.3530e+05
Rg (倒空间) rg_reciprocal	29.29 Å
I(0) (倒空间) i0_reciprocal	7999000.0000
解质量估计 total_estimate	0.7320
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	16.3 Å
偏度 Skewness skewness	0.310
峰度 Kurtosis kurtosis	-0.748
角度范围 angular_range	— – 0.2700 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	445000.0000
实空间数据点数 n_real_points	55
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.451; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.320; Smooth: 0.840

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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)

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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	d1ovra_
类 Class class	k — Designed proteins
折叠类型 Fold fold	k.8 — Designed four-helix bundle protein
超家族 Superfamily superfamily	k.8.1 — Designed four-helix bundle protein
家族 Family family	k.8.1.1 — Designed four-helix bundle protein

结构域编号 domain_id	d1ovrb_
类 Class class	k — Designed proteins
折叠类型 Fold fold	k.8 — Designed four-helix bundle protein
超家族 Superfamily superfamily	k.8.1 — Designed four-helix bundle protein
家族 Family family	k.8.1.1 — Designed four-helix bundle protein

结构域编号 domain_id	d1ovrc_
类 Class class	k — Designed proteins
折叠类型 Fold fold	k.8 — Designed four-helix bundle protein
超家族 Superfamily superfamily	k.8.1 — Designed four-helix bundle protein
家族 Family family	k.8.1.1 — Designed four-helix bundle protein

结构域编号 domain_id	d1ovrd_
类 Class class	k — Designed proteins
折叠类型 Fold fold	k.8 — Designed four-helix bundle protein
超家族 Superfamily superfamily	k.8.1 — Designed four-helix bundle protein
家族 Family family	k.8.1.1 — Designed four-helix bundle protein

CATH v4.4 (4 domains)

结构域编号 domain_id	1ovrA00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	420 — Immunoglobulin FC, subunit C

结构域编号 domain_id	1ovrB00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	420 — Immunoglobulin FC, subunit C

结构域编号 domain_id	1ovrC00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	420 — Immunoglobulin FC, subunit C

结构域编号 domain_id	1ovrD00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	420 — Immunoglobulin FC, subunit C

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7. 引用文献 (4)

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晶胞边长 a length_a	88.888 Å
晶胞边长 b length_b	149.177 Å
晶胞边长 c length_c	38.578 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	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	2.990 Å
最低分辨率 resolution_low	15.000 Å
R 因子 r_factor	0.2293
R_work r_work	0.2258
R_free r_free	0.3054

描述 description	four-helix bundle model di-Mn(II)-DF1-L13
分子量 formula_weight	5870.9 kDa
来源方法 src_method	syn
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	1707

CRYSTAL STRUCTURE OF FOUR-HELIX BUNDLE MODEL di-Mn(II)-DF1-L13

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

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 (4)

8. 文件与曲线 (10)

Files (7)

Curves (3)

描述 description	MANGANESE (II) ION
分子量 formula_weight	54.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	5

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	38

fit	/app/data/saxs_computation/ov/1ovr/1ovr.fit
pddf	/app/data/pr_computation/ov/1ovr/1ovr.pr.out
profile	/app/data/saxs_computation/ov/1ovr/1ovr.dat