1hkx

Crystal structure of calcium/calmodulin-dependent protein kinase

Method: X-RAY DIFFRACTION D_max: 136.5 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	1hkx
沉积日期 deposition_date	2003-03-12
结构标题 title	Crystal structure of calcium/calmodulin-dependent protein kinase
关键词 keywords	TRANSFERASE, SERINE/THREONINE-PROTEIN KINASE, CALMODULIN-BINDING, PHOSPHORYLATION, ATP-BINDING, ALTERNATIVE SPLICING; 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	44.44 Å
回转半径 Rg (电子) rg_electron	43.35 Å
零角强度 I(0) i0	810443000.00
分子量 molecular_weight	223740.0 kDa
排除体积 excluded_volume	274720 Å³
包络体积 envelope_volume	404680 Å³
水化壳体积 shell_volume	76239 Å³
包络直径 envelope_diameter	145.5 Å
壳层 Rg shell_rg	50.98 Å
包络 Rg envelope_rg	41.15 Å
形状 Rg shape_rg	43.19 Å
总 Rg total_rg	44.20 Å
总原子数 total_atoms	15628
残基数 n_residues	1935
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	136.5 Å
Rg (实空间) rg_real	44.19 Å
Rg 误差 (实空间) rg_real_error	1.03 Å
I(0) (实空间) i0_real	8.1040e+08
I(0) 误差 (实空间) i0_real_error	1.3740e+07
Rg (倒空间) rg_reciprocal	44.44 Å
I(0) (倒空间) i0_reciprocal	810700000.0000
解质量估计 total_estimate	0.8964
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	68.2 Å
偏度 Skewness skewness	0.004
峰度 Kurtosis kurtosis	-0.684
角度范围 angular_range	— – 0.1800 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	69890000.0000
实空间数据点数 n_real_points	37
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.924; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.886

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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 (5)

Entity 1 polymer

描述 description	CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II ALPHA CHAIN
分子量 formula_weight	16882.0 kDa
EC 编号 ec_number	2.7.1.123
来源方法 src_method	man
拷贝数 entity_count	14

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N
原子数 atom_count	15690

GPHMTTIEDEDTKVRKQEIIKVTEQLIEAISNGDFESYTKMCDPGMTAFEPEALGNLVEGLDFHRFYFENLWSRNSKPVHTTILNPHIHLMGDESACIAYIRITQYLDAGGIPRTAQSEETRVWHRRDGKWQIVHFHRSGAPSVLPH

来源 Source

来源生物 organism	MUS MUSCULUS
通用名 common_name	MOUSE
NCBI 分类编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 non-polymer

描述 description	2,3-DIHYDROXY-1,4-DITHIOBUTANE
分子量 formula_weight	154.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	CHLORIDE ION
分子量 formula_weight	35.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	14

Entity 4 non-polymer

描述 description	HEXATANTALUM DODECABROMIDE
分子量 formula_weight	2044.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 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	62

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6. 折叠分类 (SCOP + CATH) 28 domains

SCOP 2.08 (14 domains)

结构域编号 domain_id	d1hkxa_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.17 — Cystatin-like
超家族 Superfamily superfamily	d.17.4 — NTF2-like
家族 Family family	d.17.4.7 — Association domain of calcium/calmodulin-dependent protein kinase type II alpha subunit, CAMK2A

结构域编号 domain_id	d1hkxb_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.17 — Cystatin-like
超家族 Superfamily superfamily	d.17.4 — NTF2-like
家族 Family family	d.17.4.7 — Association domain of calcium/calmodulin-dependent protein kinase type II alpha subunit, CAMK2A

结构域编号 domain_id	d1hkxc_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.17 — Cystatin-like
超家族 Superfamily superfamily	d.17.4 — NTF2-like
家族 Family family	d.17.4.7 — Association domain of calcium/calmodulin-dependent protein kinase type II alpha subunit, CAMK2A

结构域编号 domain_id	d1hkxd_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.17 — Cystatin-like
超家族 Superfamily superfamily	d.17.4 — NTF2-like
家族 Family family	d.17.4.7 — Association domain of calcium/calmodulin-dependent protein kinase type II alpha subunit, CAMK2A

结构域编号 domain_id	d1hkxe_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.17 — Cystatin-like
超家族 Superfamily superfamily	d.17.4 — NTF2-like
家族 Family family	d.17.4.7 — Association domain of calcium/calmodulin-dependent protein kinase type II alpha subunit, CAMK2A

结构域编号 domain_id	d1hkxf_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.17 — Cystatin-like
超家族 Superfamily superfamily	d.17.4 — NTF2-like
家族 Family family	d.17.4.7 — Association domain of calcium/calmodulin-dependent protein kinase type II alpha subunit, CAMK2A

结构域编号 domain_id	d1hkxg_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.17 — Cystatin-like
超家族 Superfamily superfamily	d.17.4 — NTF2-like
家族 Family family	d.17.4.7 — Association domain of calcium/calmodulin-dependent protein kinase type II alpha subunit, CAMK2A

结构域编号 domain_id	d1hkxh_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.17 — Cystatin-like
超家族 Superfamily superfamily	d.17.4 — NTF2-like
家族 Family family	d.17.4.7 — Association domain of calcium/calmodulin-dependent protein kinase type II alpha subunit, CAMK2A

结构域编号 domain_id	d1hkxi_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.17 — Cystatin-like
超家族 Superfamily superfamily	d.17.4 — NTF2-like
家族 Family family	d.17.4.7 — Association domain of calcium/calmodulin-dependent protein kinase type II alpha subunit, CAMK2A

结构域编号 domain_id	d1hkxj_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.17 — Cystatin-like
超家族 Superfamily superfamily	d.17.4 — NTF2-like
家族 Family family	d.17.4.7 — Association domain of calcium/calmodulin-dependent protein kinase type II alpha subunit, CAMK2A

结构域编号 domain_id	d1hkxk_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.17 — Cystatin-like
超家族 Superfamily superfamily	d.17.4 — NTF2-like
家族 Family family	d.17.4.7 — Association domain of calcium/calmodulin-dependent protein kinase type II alpha subunit, CAMK2A

结构域编号 domain_id	d1hkxl_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.17 — Cystatin-like
超家族 Superfamily superfamily	d.17.4 — NTF2-like
家族 Family family	d.17.4.7 — Association domain of calcium/calmodulin-dependent protein kinase type II alpha subunit, CAMK2A

结构域编号 domain_id	d1hkxm_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.17 — Cystatin-like
超家族 Superfamily superfamily	d.17.4 — NTF2-like
家族 Family family	d.17.4.7 — Association domain of calcium/calmodulin-dependent protein kinase type II alpha subunit, CAMK2A

结构域编号 domain_id	d1hkxn_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.17 — Cystatin-like
超家族 Superfamily superfamily	d.17.4 — NTF2-like
家族 Family family	d.17.4.7 — Association domain of calcium/calmodulin-dependent protein kinase type II alpha subunit, CAMK2A

CATH v4.4 (14 domains)

结构域编号 domain_id	1hkxA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	1hkxB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	1hkxC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	1hkxD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	1hkxE00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	1hkxF00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	1hkxG00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	1hkxH00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	1hkxI00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	1hkxJ00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	1hkxK00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	1hkxL00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	1hkxM00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	1hkxN00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
同源超家族 H-superfamily homologous superfamily	50 —

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7. 引用文献 (1)

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晶胞边长 a length_a	147.946 Å
晶胞边长 b length_b	118.043 Å
晶胞边长 c length_c	157.820 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	110.91 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	56

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	2.650 Å
最低分辨率 resolution_low	19.840 Å
R 因子 r_factor	0.2460
R_work r_work	0.2460
R_free r_free	0.2790

fit	/app/data/saxs_computation/hk/1hkx/1hkx.fit
pddf	/app/data/pr_computation/hk/1hkx/1hkx.pr.out
profile	/app/data/saxs_computation/hk/1hkx/1hkx.dat