1y8g

Catalytic and ubiqutin-associated domains of MARK2/PAR-1: Inactive double mutant with selenomethionine

Method: X-RAY DIFFRACTION D_max: 103.1 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	1y8g
沉积日期 deposition_date	2004-12-12
结构标题 title	Catalytic and ubiqutin-associated domains of MARK2/PAR-1: Inactive double mutant with selenomethionine
关键词 keywords	SERINE/THREONINE PROTEIN KINASE; MARK; PAR-1; KIN1; UBA DOMAIN, SIGNALING PROTEIN, TRANSFERASE; SIGNALING PROTEIN,TRANSFERASE
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	30.06 Å
回转半径 Rg (电子) rg_electron	29.22 Å
零角强度 I(0) i0	77008800.00
分子量 molecular_weight	70378.0 kDa
排除体积 excluded_volume	88442 Å³
包络体积 envelope_volume	110900 Å³
水化壳体积 shell_volume	32978 Å³
包络直径 envelope_diameter	108.7 Å
壳层 Rg shell_rg	35.04 Å
包络 Rg envelope_rg	28.89 Å
形状 Rg shape_rg	29.17 Å
总 Rg total_rg	29.93 Å
总原子数 total_atoms	4885
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	103.1 Å
Rg (实空间) rg_real	30.13 Å
Rg 误差 (实空间) rg_real_error	0.92 Å
I(0) (实空间) i0_real	7.7010e+07
I(0) 误差 (实空间) i0_real_error	1.1800e+06
Rg (倒空间) rg_reciprocal	30.10 Å
I(0) (倒空间) i0_reciprocal	77010000.0000
解质量估计 total_estimate	0.8769
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	35.0 Å
偏度 Skewness skewness	0.400
峰度 Kurtosis kurtosis	-0.271
角度范围 angular_range	— – 0.2650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	15420000.0000
实空间数据点数 n_real_points	54
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.832; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.936; Smooth: 0.972

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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)

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1y8ga_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.144 — Protein kinase-like (PK-like)
超家族 Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
家族 Family family	d.144.1.0 — automated matches

结构域编号 domain_id	d1y8gb_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.144 — Protein kinase-like (PK-like)
超家族 Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
家族 Family family	d.144.1.0 — automated matches

CATH v4.4 (6 domains)

结构域编号 domain_id	1y8gA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	200 — Phosphorylase Kinase; domain 1
同源超家族 H-superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

结构域编号 domain_id	1y8gA02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	510 — Transferase(Phosphotransferase); domain 1
同源超家族 H-superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

结构域编号 domain_id	1y8gA03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily	10 — Ubiquitin-associated (UBA) domain

结构域编号 domain_id	1y8gB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	200 — Phosphorylase Kinase; domain 1
同源超家族 H-superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

结构域编号 domain_id	1y8gB02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	510 — Transferase(Phosphotransferase); domain 1
同源超家族 H-superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

结构域编号 domain_id	1y8gB03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily	10 — Ubiquitin-associated (UBA) domain

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7. 引用文献 (1)

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晶胞边长 a length_a	118.822 Å
晶胞边长 b length_b	118.822 Å
晶胞边长 c length_c	105.380 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	120.00 °
晶胞分子数 Z z_pdb	12

空间群 space_group	P 61
空间群编号 int_tables_number	169
晶系 crystal_system	—

分辨率 resolution	2.501 Å
最低分辨率 resolution_low	46.300 Å
R 因子 r_factor	0.2014
R_work r_work	0.1978
R_free r_free	0.2683

描述 description	MAP/Microtubule affinity-regulating kinase 2
分子量 formula_weight	38070.4 kDa
EC 编号 ec_number	2.7.1.37
突变 mutation	T208A, S212A
来源方法 src_method	man
拷贝数 entity_count	2

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	5071

Catalytic and ubiqutin-associated domains of MARK2/PAR-1: Inactive double mutant with selenomethionine

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) 8 domains

SCOP 2.08 (2 domains)

CATH v4.4 (6 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI 分类编号 ncbi_taxonomy_id	10116
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	158

fit	/app/data/saxs_computation/y8/1y8g/1y8g.fit
pddf	/app/data/pr_computation/y8/1y8g/1y8g.pr.out
profile	/app/data/saxs_computation/y8/1y8g/1y8g.dat