9nu0

Crystal structure of calcium-dependent protein kinase 1 (CDPK1) from Cryptosporidium parvum in complex with inhibitor WIN-III-6.

Method: X-RAY DIFFRACTION D_max: 88.8 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	9nu0
沉积日期 deposition_date	2025-03-19
最后修订 last_revision	2026-04-01
结构标题 title	Crystal structure of calcium-dependent protein kinase 1 (CDPK1) from Cryptosporidium parvum in complex with inhibitor WIN-III-6.
关键词 keywords	SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, TRANSFERASE, Cryptosporidium parvum, CDPK1; 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	24.65 Å
回转半径 Rg (电子) rg_electron	23.89 Å
零角强度 I(0) i0	80973100.00
分子量 molecular_weight	47197.0 kDa
排除体积 excluded_volume	45709 Å³
包络体积 envelope_volume	76838 Å³
水化壳体积 shell_volume	27125 Å³
包络直径 envelope_diameter	86.1 Å
壳层 Rg shell_rg	30.77 Å
包络 Rg envelope_rg	24.06 Å
形状 Rg shape_rg	23.88 Å
总 Rg total_rg	24.51 Å
总原子数 total_atoms	3560
残基数 n_residues	450
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	88.8 Å
Rg (实空间) rg_real	24.63 Å
Rg 误差 (实空间) rg_real_error	0.71 Å
I(0) (实空间) i0_real	8.0970e+07
I(0) 误差 (实空间) i0_real_error	1.3110e+06
Rg (倒空间) rg_reciprocal	24.63 Å
I(0) (倒空间) i0_reciprocal	80970000.0000
解质量估计 total_estimate	0.6968
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	28.2 Å
偏度 Skewness skewness	0.346
峰度 Kurtosis kurtosis	-0.272
角度范围 angular_range	— – 0.3200 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	14280000.0000
实空间数据点数 n_real_points	64
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.713; Stabil: 1.000; Sysdev: 0.338; Positv: 1.000; Valcen: 0.901; Smooth: 1.000

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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 (4)

Entity 1 polymer

描述 description	Calmodulin-domain protein kinase 1
分子量 formula_weight	56710.4 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	3742

MGSSHHHHHHSSGRENLYFQGHMGTFAERYNIVCMLGKGSFGEVLKCKDRITQQEYAVKVINKASAKNKDTSTILREVELLKKLDHPNIMKLFEILEDSSSFYIVGELYTGGELFDEIIKRKRFSEHDAARIIKQVFSGITYMHKHNIVHRDLKPENILLESKEKDCDIKIIDFGLSTCFQQNTKMKDRIGTAYYIAPEVLRGTYDEKCDVWSAGVILYILLSGTPPFYGKNEYDILKRVETGKYAFDLPQWRTISDDAKDLIRKMLTFHPSLRITATQCLEHPWIQKYSSETPTISDLPSLESAMTNIRQFQAEKKLAQAALLYMASKLTTLDETKQLTEIFRKLDTNNDGMLDRDELVRGYHEFMRLKGVDSNSLIQNEGSTIEDQIDSLMPLLDMDGSGSIEYSEFIASAIDRTILLSRERMERAFKMFDKDGSGKISTKELFKLFSQADSSIQMEELESIIEQVDNNKDGEVDFNEFVEMLQNFVRNE

来源 Source

来源生物 organism	Cryptosporidium parvum Iowa II
NCBI 分类编号 ncbi_taxonomy_id	353152
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 3 non-polymer

描述 description	(6M)-6-[2-chloro-4-(cyclopropylmethoxy)phenyl]-8-methyl-2-(methylamino)pyrido[2,3-d]pyrimidin-7(8H)-one
分子量 formula_weight	370.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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	134

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7. 引用文献 (1)

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晶胞边长 a length_a	60.157 Å
晶胞边长 b length_b	56.637 Å
晶胞边长 c length_c	80.660 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	104.30 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	2

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	1.940 Å
最低分辨率 resolution_low	45.860 Å
R 因子 r_factor	0.1891
R_work r_work	0.1872
R_free r_free	0.2274

fit	/app/data/saxs_computation/nu/9nu0/9nu0.fit
pddf	/app/data/pr_computation/nu/9nu0/9nu0.pr.out
profile	/app/data/saxs_computation/nu/9nu0/9nu0.dat

Crystal structure of calcium-dependent protein kinase 1 (CDPK1) from Cryptosporidium parvum in complex with inhibitor WIN-III-6.

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