8dgq

Crystal structure of p120RasGAP SH2-SH3-SH2 in complex with p190RhoGAP doubly phosphorylated peptide

Method: X-RAY DIFFRACTION D_max: 84.4 Å Quality: EXCELLENT

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	8dgq
沉积日期 deposition_date	2022-06-24
结构标题 title	Crystal structure of p120RasGAP SH2-SH3-SH2 in complex with p190RhoGAP doubly phosphorylated peptide
关键词 keywords	SH2 domain, SH3 domain, phosphotyrosine, 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	27.90 Å
回转半径 Rg (电子) rg_electron	27.09 Å
零角强度 I(0) i0	79403600.00
分子量 molecular_weight	68353.0 kDa
排除体积 excluded_volume	84940 Å³
包络体积 envelope_volume	108280 Å³
水化壳体积 shell_volume	33226 Å³
包络直径 envelope_diameter	88.8 Å
壳层 Rg shell_rg	34.40 Å
包络 Rg envelope_rg	26.75 Å
形状 Rg shape_rg	27.06 Å
总 Rg total_rg	27.95 Å
总原子数 total_atoms	4819
残基数 n_residues	584
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	84.4 Å
Rg (实空间) rg_real	27.74 Å
Rg 误差 (实空间) rg_real_error	0.46 Å
I(0) (实空间) i0_real	7.9400e+07
I(0) 误差 (实空间) i0_real_error	1.1120e+06
Rg (倒空间) rg_reciprocal	27.79 Å
I(0) (倒空间) i0_reciprocal	79410000.0000
解质量估计 total_estimate	0.9091
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	37.0 Å
偏度 Skewness skewness	0.137
峰度 Kurtosis kurtosis	-0.512
角度范围 angular_range	— – 0.2850 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	25220000.0000
实空间数据点数 n_real_points	58
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.959; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.941

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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 (4)

Entity 1 polymer

描述 description	Ras GTPase-activating protein 1
分子量 formula_weight	31551.5 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	5079

GSTAPPTNQWYHGKLDRTIAEERLRQAGKSGSYLIRESDRRPGSFVLSFLSQMNVVNHFRIIAMSGDYYIGGRRFSSLSDLIGYYSHVSSLLKGEKLLYPVAPPEPVEDRRRVRAILPYTKVPDTDEISFLKGDMFIVHNELEDGWMWVTNLRTDEQGLIVEDLVEEVGREEDPHEGKIWFHGKISKQEAYNLLMTVGQVSSFLVRPSDNTPGDYSLYFRTNENIQRFKISPTPNNQFMMGGRYYNSIGDIIDHYRKEQIVEGYYLKEPVPMQ

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)

Entity 2 polymer

描述 description	Rho GTPase-activating protein 35
分子量 formula_weight	3467.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	U,V

DPSDYAEPMDAVVKPRNEEENIYSVPHDS

Entity 3 non-polymer

描述 description	MALONATE ION
分子量 formula_weight	102.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

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	233

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6. 折叠分类 (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

结构域编号 domain_id	8dgqA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	505 — SHC Adaptor Protein
同源超家族 H-superfamily homologous superfamily	10 — SH2 domain

结构域编号 domain_id	8dgqA02
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	8dgqB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	505 — SHC Adaptor Protein
同源超家族 H-superfamily homologous superfamily	10 — SH2 domain

结构域编号 domain_id	8dgqB02
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 (1)

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晶胞边长 a length_a	55.210 Å
晶胞边长 b length_b	113.500 Å
晶胞边长 c length_c	119.070 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	8

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	1.950 Å
最低分辨率 resolution_low	49.650 Å
R 因子 r_factor	0.2150
R_work r_work	0.2135
R_free r_free	0.2556

fit	/app/data/saxs_computation/dg/8dgq/8dgq.fit
pddf	/app/data/pr_computation/dg/8dgq/8dgq.pr.out
profile	/app/data/saxs_computation/dg/8dgq/8dgq.dat

Crystal structure of p120RasGAP SH2-SH3-SH2 in complex with p190RhoGAP doubly phosphorylated 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

来源 Source

Entity 2 polymer

聚合体 Polymer

Entity 3 non-polymer

Entity 4 water

6. 折叠分类 (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)