SAXSdb — 1hqj

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1hqj
沉积日期 deposition_date	2000-12-18
结构标题 title	CRYSTAL STRUCTURE OF A DE NOVO DESIGNED TRIMERIC COILED-COIL PEPTIDE
关键词 keywords	coiled coil, de novo design, alpha-helix, trimer, DE NOVO PROTEIN; DE NOVO PROTEIN
实验方法 method	X-RAY DIFFRACTION

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	19.70 Å
回转半径 Rg (电子) rg_electron	18.85 Å
零角强度 I(0) i0	16192700.00
分子量 molecular_weight	25529.0 kDa
排除体积 excluded_volume	29372 Å³
包络体积 envelope_volume	35631 Å³
水化壳体积 shell_volume	16304 Å³
包络直径 envelope_diameter	67.4 Å
壳层 Rg shell_rg	24.29 Å
包络 Rg envelope_rg	18.98 Å
形状 Rg shape_rg	18.77 Å
总 Rg total_rg	19.68 Å
总原子数 total_atoms	1663
残基数 n_residues	168
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

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	67.7 Å
Rg (实空间) rg_real	19.70 Å
Rg 误差 (实空间) rg_real_error	0.57 Å
I(0) (实空间) i0_real	1.6190e+07
I(0) 误差 (实空间) i0_real_error	2.1890e+05
Rg (倒空间) rg_reciprocal	19.70 Å
I(0) (倒空间) i0_reciprocal	16190000.0000
解质量估计 total_estimate	0.8681
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	65.7 Å
偏度 Skewness skewness	0.339
峰度 Kurtosis kurtosis	-0.289
角度范围 angular_range	— – 0.4050 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	2825000.0000
实空间数据点数 n_real_points	72
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.794; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.918; Smooth: 0.984

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (4)

Entity 1 polymer

描述 description	ZJU-GLU-LEU-GLU-ALA-ARG-ILE-ARG-GLU-LEU-GLU-ALA-ARG-ILE-LYS-NH2
分子量 formula_weight	2031.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	12

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H,I,J,K,L
原子数 atom_count	1870

DELERRIRELEARIK

Entity 2 non-polymer

描述 description	LEAD (II) ION
分子量 formula_weight	207.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	9

Entity 3 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

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	147

▼

6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (12 domains)

结构域编号 domain_id	d1hqja_
类 Class class	k — Designed proteins
折叠类型 Fold fold	k.40 — Designed trimeric coiled-coil
超家族 Superfamily superfamily	k.40.1 — Designed trimeric coiled-coil
家族 Family family	k.40.1.1 — Designed trimeric coiled-coil

结构域编号 domain_id	d1hqjb_
类 Class class	k — Designed proteins
折叠类型 Fold fold	k.40 — Designed trimeric coiled-coil
超家族 Superfamily superfamily	k.40.1 — Designed trimeric coiled-coil
家族 Family family	k.40.1.1 — Designed trimeric coiled-coil

结构域编号 domain_id	d1hqjc_
类 Class class	k — Designed proteins
折叠类型 Fold fold	k.40 — Designed trimeric coiled-coil
超家族 Superfamily superfamily	k.40.1 — Designed trimeric coiled-coil
家族 Family family	k.40.1.1 — Designed trimeric coiled-coil

结构域编号 domain_id	d1hqjd_
类 Class class	k — Designed proteins
折叠类型 Fold fold	k.40 — Designed trimeric coiled-coil
超家族 Superfamily superfamily	k.40.1 — Designed trimeric coiled-coil
家族 Family family	k.40.1.1 — Designed trimeric coiled-coil

结构域编号 domain_id	d1hqje_
类 Class class	k — Designed proteins
折叠类型 Fold fold	k.40 — Designed trimeric coiled-coil
超家族 Superfamily superfamily	k.40.1 — Designed trimeric coiled-coil
家族 Family family	k.40.1.1 — Designed trimeric coiled-coil

结构域编号 domain_id	d1hqjf_
类 Class class	k — Designed proteins
折叠类型 Fold fold	k.40 — Designed trimeric coiled-coil
超家族 Superfamily superfamily	k.40.1 — Designed trimeric coiled-coil
家族 Family family	k.40.1.1 — Designed trimeric coiled-coil

结构域编号 domain_id	d1hqjg_
类 Class class	k — Designed proteins
折叠类型 Fold fold	k.40 — Designed trimeric coiled-coil
超家族 Superfamily superfamily	k.40.1 — Designed trimeric coiled-coil
家族 Family family	k.40.1.1 — Designed trimeric coiled-coil

结构域编号 domain_id	d1hqjh_
类 Class class	k — Designed proteins
折叠类型 Fold fold	k.40 — Designed trimeric coiled-coil
超家族 Superfamily superfamily	k.40.1 — Designed trimeric coiled-coil
家族 Family family	k.40.1.1 — Designed trimeric coiled-coil

结构域编号 domain_id	d1hqji_
类 Class class	k — Designed proteins
折叠类型 Fold fold	k.40 — Designed trimeric coiled-coil
超家族 Superfamily superfamily	k.40.1 — Designed trimeric coiled-coil
家族 Family family	k.40.1.1 — Designed trimeric coiled-coil

结构域编号 domain_id	d1hqjj_
类 Class class	k — Designed proteins
折叠类型 Fold fold	k.40 — Designed trimeric coiled-coil
超家族 Superfamily superfamily	k.40.1 — Designed trimeric coiled-coil
家族 Family family	k.40.1.1 — Designed trimeric coiled-coil

结构域编号 domain_id	d1hqjk_
类 Class class	k — Designed proteins
折叠类型 Fold fold	k.40 — Designed trimeric coiled-coil
超家族 Superfamily superfamily	k.40.1 — Designed trimeric coiled-coil
家族 Family family	k.40.1.1 — Designed trimeric coiled-coil

结构域编号 domain_id	d1hqjl_
类 Class class	k — Designed proteins
折叠类型 Fold fold	k.40 — Designed trimeric coiled-coil
超家族 Superfamily superfamily	k.40.1 — Designed trimeric coiled-coil
家族 Family family	k.40.1.1 — Designed trimeric coiled-coil

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	44.334 Å
晶胞边长 b length_b	44.874 Å
晶胞边长 c length_c	81.043 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	48

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	1.200 Å
最低分辨率 resolution_low	10.000 Å
R 因子 r_factor	—
R_work r_work	—
R_free r_free	0.2230

fit	/app/data/saxs_computation/hq/1hqj/1hqj.fit
pddf	/app/data/pr_computation/hq/1hqj/1hqj.pr.out
profile	/app/data/saxs_computation/hq/1hqj/1hqj.dat

CRYSTAL STRUCTURE OF A DE NOVO DESIGNED TRIMERIC COILED-COIL PEPTIDE

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) 12 domains

SCOP 2.08 (12 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)