1t77

Crystal structure of the PH-BEACH domains of human LRBA/BGL

Method: X-RAY DIFFRACTION D_max: 167.7 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

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1t77
沉积日期 deposition_date	2004-05-08
结构标题 title	Crystal structure of the PH-BEACH domains of human LRBA/BGL
关键词 keywords	PH-BEACH DOMAINS; VESICLE TRAFFICKING; SIGNAL TRANSDUCTION, SIGNALING PROTEIN; SIGNALING 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	50.23 Å
回转半径 Rg (电子) rg_electron	50.34 Å
零角强度 I(0) i0	498843000.00
分子量 molecular_weight	190640.0 kDa
排除体积 excluded_volume	240650 Å³
包络体积 envelope_volume	348040 Å³
水化壳体积 shell_volume	61500 Å³
包络直径 envelope_diameter	177.1 Å
壳层 Rg shell_rg	49.47 Å
包络 Rg envelope_rg	48.81 Å
形状 Rg shape_rg	50.32 Å
总 Rg total_rg	50.36 Å
总原子数 total_atoms	13516
残基数 n_residues	1656
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	167.7 Å
Rg (实空间) rg_real	50.38 Å
Rg 误差 (实空间) rg_real_error	1.67 Å
I(0) (实空间) i0_real	4.9880e+08
I(0) 误差 (实空间) i0_real_error	1.0080e+07
Rg (倒空间) rg_reciprocal	50.10 Å
I(0) (倒空间) i0_reciprocal	498700000.0000
解质量估计 total_estimate	0.8021
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	70.3 Å
偏度 Skewness skewness	0.389
峰度 Kurtosis kurtosis	-0.180
角度范围 angular_range	— – 0.1550 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	45110000.0000
实空间数据点数 n_real_points	32
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.711; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.927; Smooth: 0.361

▶

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

▶

5. 实体与聚合体信息 (2)

▼

6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1t77a1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.169 — BEACH domain
超家族 Superfamily superfamily	a.169.1 — BEACH domain
家族 Family family	a.169.1.1 — BEACH domain

结构域编号 domain_id	d1t77a2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.55 — PH domain-like barrel
超家族 Superfamily superfamily	b.55.1 — PH domain-like
家族 Family family	b.55.1.6 — PreBEACH PH-like domain

结构域编号 domain_id	d1t77b1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.169 — BEACH domain
超家族 Superfamily superfamily	a.169.1 — BEACH domain
家族 Family family	a.169.1.1 — BEACH domain

结构域编号 domain_id	d1t77b2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.55 — PH domain-like barrel
超家族 Superfamily superfamily	b.55.1 — PH domain-like
家族 Family family	b.55.1.6 — PreBEACH PH-like domain

结构域编号 domain_id	d1t77c1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.169 — BEACH domain
超家族 Superfamily superfamily	a.169.1 — BEACH domain
家族 Family family	a.169.1.1 — BEACH domain

结构域编号 domain_id	d1t77c2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.55 — PH domain-like barrel
超家族 Superfamily superfamily	b.55.1 — PH domain-like
家族 Family family	b.55.1.6 — PreBEACH PH-like domain

结构域编号 domain_id	d1t77d1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.169 — BEACH domain
超家族 Superfamily superfamily	a.169.1 — BEACH domain
家族 Family family	a.169.1.1 — BEACH domain

结构域编号 domain_id	d1t77d2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.55 — PH domain-like barrel
超家族 Superfamily superfamily	b.55.1 — PH domain-like
家族 Family family	b.55.1.6 — PreBEACH PH-like domain

CATH v4.4 (8 domains)

结构域编号 domain_id	1t77A01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	29 — PH-domain like
同源超家族 H-superfamily homologous superfamily	30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

结构域编号 domain_id	1t77A02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1540 — Neurobeachin; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — BEACH domain

结构域编号 domain_id	1t77B01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	29 — PH-domain like
同源超家族 H-superfamily homologous superfamily	30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

结构域编号 domain_id	1t77B02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1540 — Neurobeachin; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — BEACH domain

结构域编号 domain_id	1t77C01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	29 — PH-domain like
同源超家族 H-superfamily homologous superfamily	30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

结构域编号 domain_id	1t77C02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1540 — Neurobeachin; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — BEACH domain

结构域编号 domain_id	1t77D01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	29 — PH-domain like
同源超家族 H-superfamily homologous superfamily	30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

结构域编号 domain_id	1t77D02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1540 — Neurobeachin; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — BEACH domain

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	73.218 Å
晶胞边长 b length_b	102.239 Å
晶胞边长 c length_c	131.519 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.47 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

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	2.400 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.2110
R_work r_work	0.2100
R_free r_free	0.2580

描述 description	Lipopolysaccharide-responsive and beige-like anchor protein
分子量 formula_weight	47713.8 kDa
来源方法 src_method	man
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	14010

Crystal structure of the PH-BEACH domains of human LRBA/BGL

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 (2)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 water

6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	494

fit	/app/data/saxs_computation/t7/1t77/1t77.fit
pddf	/app/data/pr_computation/t7/1t77/1t77.pr.out
profile	/app/data/saxs_computation/t7/1t77/1t77.dat