1sem

STRUCTURAL DETERMINANTS OF PEPTIDE-BINDING ORIENTATION AND OF SEQUENCE SPECIFICITY IN SH3 DOMAINS

Method: X-RAY DIFFRACTION D_max: 58.2 Å Quality: GOOD

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1sem
沉积日期 deposition_date	1995-03-28
结构标题 title	STRUCTURAL DETERMINANTS OF PEPTIDE-BINDING ORIENTATION AND OF SEQUENCE SPECIFICITY IN SH3 DOMAINS
关键词 keywords	SRC-HOMOLOGY 3 (SH3) DOMAIN, PEPTIDE-BINDING PROTEIN, GUANINE NUCLEOTIDE EXCHANGE FACTOR, SIGNAL TRANSDUCTION PROTEIN; SIGNAL TRANSDUCTION 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	17.38 Å
回转半径 Rg (电子) rg_electron	16.17 Å
零角强度 I(0) i0	4286370.00
分子量 molecular_weight	14934.0 kDa
排除体积 excluded_volume	18707 Å³
包络体积 envelope_volume	21916 Å³
水化壳体积 shell_volume	12012 Å³
包络直径 envelope_diameter	56.1 Å
壳层 Rg shell_rg	20.85 Å
包络 Rg envelope_rg	16.34 Å
形状 Rg shape_rg	16.15 Å
总 Rg total_rg	17.14 Å
总原子数 total_atoms	1061
残基数 n_residues	129
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	58.2 Å
Rg (实空间) rg_real	17.40 Å
Rg 误差 (实空间) rg_real_error	0.36 Å
I(0) (实空间) i0_real	4.2860e+06
I(0) 误差 (实空间) i0_real_error	4.7090e+04
Rg (倒空间) rg_reciprocal	17.40 Å
I(0) (倒空间) i0_reciprocal	4286000.0000
解质量估计 total_estimate	0.8682
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	17.6 Å
偏度 Skewness skewness	0.334
峰度 Kurtosis kurtosis	-0.512
角度范围 angular_range	— – 0.4600 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	1888000.0000
实空间数据点数 n_real_points	77
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.782; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.936; Smooth: 0.999

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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	SEM-5
分子量 formula_weight	6799.5 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	1128

ETKFVQALFDFNPQESGELAFKRGDVITLINKDDPNWWEGQLNNRRGIFPSNYVCPYN

来源 Source

来源生物 organism	Caenorhabditis elegans
NCBI 分类编号 ncbi_taxonomy_id	6239
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	10-RESIDUE PROLINE-RICH PEPTIDE FROM MSOS (ACE-PRO-PRO-PRO-VAL-PRO-PRO-ARG-ARG-ARG)
分子量 formula_weight	1100.3 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C,D

XPPPVPPRRR

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	67

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6. 折叠分类 (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1sema_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.34 — SH3-like barrel
超家族 Superfamily superfamily	b.34.2 — SH3-domain
家族 Family family	b.34.2.1 — SH3-domain

结构域编号 domain_id	d1semb_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.34 — SH3-like barrel
超家族 Superfamily superfamily	b.34.2 — SH3-domain
家族 Family family	b.34.2.1 — SH3-domain

CATH v4.4 (2 domains)

结构域编号 domain_id	1semA00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	40 — SH3 Domains

结构域编号 domain_id	1semB00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	40 — SH3 Domains

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7. 引用文献 (3)

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晶胞边长 a length_a	26.912 Å
晶胞边长 b length_b	68.410 Å
晶胞边长 c length_c	35.029 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	94.71 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	2.000 Å
最低分辨率 resolution_low	7.000 Å
R 因子 r_factor	0.1890
R_work r_work	0.1890
R_free r_free	—

fit	/app/data/saxs_computation/se/1sem/1sem.fit
pddf	/app/data/pr_computation/se/1sem/1sem.pr.out
profile	/app/data/saxs_computation/se/1sem/1sem.dat

STRUCTURAL DETERMINANTS OF PEPTIDE-BINDING ORIENTATION AND OF SEQUENCE SPECIFICITY IN SH3 DOMAINS

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

5. 实体与聚合体信息 (3)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

Entity 3 water

6. 折叠分类 (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. 引用文献 (3)

8. 文件与曲线 (10)

Files (7)

Curves (3)