SAXSdb — 1j3h

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1j3h
沉积日期 deposition_date	2003-01-31
结构标题 title	Crystal structure of apoenzyme cAMP-dependent protein kinase catalytic subunit
关键词 keywords	apoenzyme, cAMP-dependent protein kinase, catalytic subunit, open conformation, preformed active site, TRANSFERASE; 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	33.27 Å
回转半径 Rg (电子) rg_electron	32.63 Å
零角强度 I(0) i0	78410700.00
分子量 molecular_weight	70579.0 kDa
排除体积 excluded_volume	88285 Å³
包络体积 envelope_volume	118730 Å³
水化壳体积 shell_volume	31909 Å³
包络直径 envelope_diameter	115.8 Å
壳层 Rg shell_rg	37.25 Å
包络 Rg envelope_rg	32.38 Å
形状 Rg shape_rg	32.58 Å
总 Rg total_rg	33.19 Å
总原子数 total_atoms	5002
残基数 n_residues	656
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	111.5 Å
Rg (实空间) rg_real	33.57 Å
Rg 误差 (实空间) rg_real_error	0.86 Å
I(0) (实空间) i0_real	7.8410e+07
I(0) 误差 (实空间) i0_real_error	1.2800e+06
Rg (倒空间) rg_reciprocal	33.45 Å
I(0) (倒空间) i0_reciprocal	78400000.0000
解质量估计 total_estimate	0.8488
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	30.2 Å
偏度 Skewness skewness	0.469
峰度 Kurtosis kurtosis	-0.467
角度范围 angular_range	— – 0.2400 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	18840000.0000
实空间数据点数 n_real_points	49
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.812; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.787; Smooth: 0.809

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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) 6 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1j3ha_
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.144.1.7 — Protein kinases, catalytic subunit

结构域编号 domain_id	d1j3hb_
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.144.1.7 — Protein kinases, catalytic subunit

CATH v4.4 (4 domains)

结构域编号 domain_id	1j3hA01
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	1j3hA02
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	1j3hB01
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	1j3hB02
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

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7. 引用文献 (6)

Dynamic Features of cAMP-dependent Protein Kinase Revealed by Apoenzyme Crystal Structure

J.Mol.Biol. (2003)

PMID: 12614615 · DOI: 10.1016/S0022-2836(02)01446-8 PRIMARY

Crystal structure of a transition state mimic of the catalytic subunit of cAMP-dependent protein kinase

Nat.Struct.Biol. (2002)

DOI: 10.1038/nsb780

A binary complex of the catalytic subunit of cAMP-dependent protein kinase and adenosine further defines conformational flexibility

Structure (1997)

DOI: 10.1016/S0969-2126(97)00246-3

;Structure of the mammalian catalytic subunit of cAMP-dependent protein kinase and an inhibitor peptide displays an open conformation ;

Acta Crystallogr.,Sect.D (1993)

DOI: 10.1107/S0907444993002306

Crystal structures of the myristylated catalytic subunit of cAMP-dependent protein kinase reveal open and closed conformations

Protein Sci. (1993)

Crystal structure of the catalytic subunit of cAMP-dependent protein kinase complexed with MgATP and peptide inhibitor

Biochemistry (1993)

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晶胞边长 a length_a	48.776 Å
晶胞边长 b length_b	143.601 Å
晶胞边长 c length_c	62.809 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	105.71 °
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	2.900 Å
最低分辨率 resolution_low	19.960 Å
R 因子 r_factor	—
R_work r_work	0.2570
R_free r_free	0.2910

描述 description	cAMP-dependent protein kinase, alpha-catalytic subunit
分子量 formula_weight	40733.4 kDa
EC 编号 ec_number	2.7.1.37
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	5002

Crystal structure of apoenzyme cAMP-dependent protein kinase catalytic subunit

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 non-polymer

6. 折叠分类 (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. 引用文献 (6)

8. 文件与曲线 (10)

Files (7)

Curves (3)

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

描述 description	(4S)-2-METHYL-2,4-PENTANEDIOL
分子量 formula_weight	118.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

fit	/app/data/saxs_computation/j3/1j3h/1j3h.fit
pddf	/app/data/pr_computation/j3/1j3h/1j3h.pr.out
profile	/app/data/saxs_computation/j3/1j3h/1j3h.dat