1lb1

Crystal Structure of the Dbl and Pleckstrin homology domains of Dbs in complex with RhoA

Method: X-RAY DIFFRACTION D_max: 213.7 Å Quality: REASONABLE

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	1lb1
沉积日期 deposition_date	2002-04-01
结构标题 title	Crystal Structure of the Dbl and Pleckstrin homology domains of Dbs in complex with RhoA
关键词 keywords	GUANINE NUCLEOTIDE EXCHANGE FACTOR, SMALL G-PROTEIN, RHOA, DBS, DH domain, PH domain, SIGNALING PROTEIN; SIGNALING 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	76.24 Å
回转半径 Rg (电子) rg_electron	76.52 Å
零角强度 I(0) i0	744487000.00
分子量 molecular_weight	231490.0 kDa
排除体积 excluded_volume	290130 Å³
包络体积 envelope_volume	546910 Å³
水化壳体积 shell_volume	63498 Å³
包络直径 envelope_diameter	234.8 Å
壳层 Rg shell_rg	71.26 Å
包络 Rg envelope_rg	71.28 Å
形状 Rg shape_rg	76.50 Å
总 Rg total_rg	76.50 Å
总原子数 total_atoms	16236
残基数 n_residues	2008
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	213.7 Å
Rg (实空间) rg_real	76.53 Å
Rg 误差 (实空间) rg_real_error	1.60 Å
I(0) (实空间) i0_real	7.4440e+08
I(0) 误差 (实空间) i0_real_error	1.3270e+07
Rg (倒空间) rg_reciprocal	74.59 Å
I(0) (倒空间) i0_reciprocal	741200000.0000
解质量估计 total_estimate	0.6931
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	96.2 Å
偏度 Skewness skewness	0.149
峰度 Kurtosis kurtosis	-1.008
角度范围 angular_range	— – 0.1000 Å⁻¹
当前正则化参数 α current_alpha	0.0005
最高正则化参数 α highest_alpha	12230000.0000
实空间数据点数 n_real_points	21
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.501; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.502; Smooth: 0.000

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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 (2)

Entity 1 polymer

描述 description	Guanine nucleotide exchange factor DBS
分子量 formula_weight	41252.3 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,C,E,G
原子数 atom_count	16236

MGEEEESLAILRRHVMNELLDTERAYVEELLCVLEGYAAEMDNPLMAHLISTGLQNKKNILFGNMEEIYHFHNRIFLRELESCIDCPELVGRCFLERMEEFQIYEKYCQNKPRSESLWRQCSDCPFFQECQKKLDHKLSLDSYLLKPVQRITKYQLLLKEMLKYSKHCEGAEDLQEALSSILGILKAVNDSMHLIAITGYDGNLGDLGKLLMQGSFSVWTDHKKGHTKVKELARFKPMQRHLFLHEKAVLFCKKREENGEGYEKAPSYSYKQSLNMTAVGITENVKGDTKKFEIWYNAREEVYIIQAPTPEIKAAWVNEIRKVLTSQLQACREASQHRALEQSHSLEHHHHHH

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI 分类编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

描述 description	Transforming protein RhoA
分子量 formula_weight	21585.8 kDa
突变 mutation	C190S
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B,D,F,H

GAMAAIRKKLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENYVADIEVDGKQVELALWDTAGQEDYDRLRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRNDEHTRRELAKMKQEPVKPEEGRDMANRIGAFGYMECSAKTKDGVREVFEMATRAALQARRGKKKSGS

来源 Source

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 BL21(DE3)

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6. 折叠分类 (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

结构域编号 domain_id	d1lb1a1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.87 — DBL homology domain (DH-domain)
超家族 Superfamily superfamily	a.87.1 — DBL homology domain (DH-domain)
家族 Family family	a.87.1.1 — DBL homology domain (DH-domain)

结构域编号 domain_id	d1lb1a2
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.55.1.1 — Pleckstrin-homology domain (PH domain)

结构域编号 domain_id	d1lb1b_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.8 — G proteins

结构域编号 domain_id	d1lb1c1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.87 — DBL homology domain (DH-domain)
超家族 Superfamily superfamily	a.87.1 — DBL homology domain (DH-domain)
家族 Family family	a.87.1.1 — DBL homology domain (DH-domain)

结构域编号 domain_id	d1lb1c2
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.55.1.1 — Pleckstrin-homology domain (PH domain)

结构域编号 domain_id	d1lb1d_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.8 — G proteins

结构域编号 domain_id	d1lb1e1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.87 — DBL homology domain (DH-domain)
超家族 Superfamily superfamily	a.87.1 — DBL homology domain (DH-domain)
家族 Family family	a.87.1.1 — DBL homology domain (DH-domain)

结构域编号 domain_id	d1lb1e2
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.55.1.1 — Pleckstrin-homology domain (PH domain)

结构域编号 domain_id	d1lb1f_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.8 — G proteins

结构域编号 domain_id	d1lb1g1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.87 — DBL homology domain (DH-domain)
超家族 Superfamily superfamily	a.87.1 — DBL homology domain (DH-domain)
家族 Family family	a.87.1.1 — DBL homology domain (DH-domain)

结构域编号 domain_id	d1lb1g2
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.55.1.1 — Pleckstrin-homology domain (PH domain)

结构域编号 domain_id	d1lb1h_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.8 — G proteins

CATH v4.4 (12 domains)

结构域编号 domain_id	1lb1A01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	900 — Dbl Homology Domain; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Dbl homology (DH) domain

结构域编号 domain_id	1lb1A02
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	1lb1B00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	1lb1C01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	900 — Dbl Homology Domain; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Dbl homology (DH) domain

结构域编号 domain_id	1lb1C02
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	1lb1D00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	1lb1E01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	900 — Dbl Homology Domain; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Dbl homology (DH) domain

结构域编号 domain_id	1lb1E02
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	1lb1F00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	1lb1G01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	900 — Dbl Homology Domain; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Dbl homology (DH) domain

结构域编号 domain_id	1lb1G02
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	1lb1H00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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7. 引用文献 (1)

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晶胞边长 a length_a	158.897 Å
晶胞边长 b length_b	158.897 Å
晶胞边长 c length_c	151.791 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	16

空间群 space_group	P 43
空间群编号 int_tables_number	78
晶系 crystal_system	—

分辨率 resolution	2.810 Å
最低分辨率 resolution_low	47.700 Å
R 因子 r_factor	—
R_work r_work	0.2360
R_free r_free	0.2660

fit	/app/data/saxs_computation/lb/1lb1/1lb1.fit
pddf	/app/data/pr_computation/lb/1lb1/1lb1.pr.out
profile	/app/data/saxs_computation/lb/1lb1/1lb1.dat

Crystal Structure of the Dbl and Pleckstrin homology domains of Dbs in complex with RhoA

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 polymer

聚合体 Polymer

来源 Source

6. 折叠分类 (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)