8r9s

A soakable crystal form of human CDK7 in complex with AMP-PNP

Method: X-RAY DIFFRACTION D_max: 94.5 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	8r9s
沉积日期 deposition_date	2023-11-30
结构标题 title	A soakable crystal form of human CDK7 in complex with AMP-PNP
关键词 keywords	serine-threonine kinase, phosphorylation, cell cycle progression, ATP binding, CELL CYCLE; CELL CYCLE
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	28.22 Å
回转半径 Rg (电子) rg_electron	27.04 Å
零角强度 I(0) i0	67958200.00
分子量 molecular_weight	67622.0 kDa
排除体积 excluded_volume	86097 Å³
包络体积 envelope_volume	107990 Å³
水化壳体积 shell_volume	33006 Å³
包络直径 envelope_diameter	99.7 Å
壳层 Rg shell_rg	34.81 Å
包络 Rg envelope_rg	26.54 Å
形状 Rg shape_rg	27.01 Å
总 Rg total_rg	27.98 Å
总原子数 total_atoms	4846
残基数 n_residues	579
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	94.5 Å
Rg (实空间) rg_real	28.12 Å
Rg 误差 (实空间) rg_real_error	0.62 Å
I(0) (实空间) i0_real	6.7960e+07
I(0) 误差 (实空间) i0_real_error	9.5720e+05
Rg (倒空间) rg_reciprocal	28.16 Å
I(0) (倒空间) i0_reciprocal	67960000.0000
解质量估计 total_estimate	0.8921
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	33.7 Å
偏度 Skewness skewness	0.217
峰度 Kurtosis kurtosis	-0.512
角度范围 angular_range	— – 0.2800 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	20900000.0000
实空间数据点数 n_real_points	57
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.868; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; 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 (5)

Entity 1 polymer

描述 description	Cyclin-dependent kinase 7
分子量 formula_weight	42235.6 kDa
突变 mutation	W132R,S164D, T170E
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	4916

MSYYHHHHHHDYDIPTTENLYFQGSMALDVKSRAKRYEKLDFLGEGQFATVYKARDKNTNQIVAIKKIKLGHRSEAKDGINRTALREIKLLQELSHPNIIGLLDAFGHKSNISLVFDFMETDLEVIIKDNSLVLTPSHIKAYMLMTLQGLEYLHQHRILHRDLKPNNLLLDENGVLKLADFGLAKSFGDPNRAYEHQVVTRWYRAPELLFGARMYGVGVDMWAVGCILAELLLRVPFLPGDSDLDQLTRIFETLGTPTEEQWPDMCSLPDYVTFKSFPGIPLHHIFSAAGDDLLDLIQGLFLFNPCARITATQALKMKYFSNRPGPTPGCQLPRPNCPVETLKEQSNPALAIKRKRTEALEQGGLPKKLIF

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	Spodoptera frugiperda

Entity 2 non-polymer

描述 description	3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL
分子量 formula_weight	634.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 3 non-polymer

描述 description	DI(HYDROXYETHYL)ETHER
分子量 formula_weight	106.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	;[(3S)-1-[4-(dimethylamino)butanoyl]pyrrolidin-3-yl] 4-[(5-methyl-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-7-yl)amino]piperidine-1-carboxylate ;
分子量 formula_weight	499.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	70

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7. 引用文献 (1)

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晶胞边长 a length_a	40.294 Å
晶胞边长 b length_b	145.584 Å
晶胞边长 c length_c	66.833 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	95.70 °
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	2.780 Å
最低分辨率 resolution_low	35.120 Å
R 因子 r_factor	0.2401
R_work r_work	0.2372
R_free r_free	0.2962

fit	/app/data/saxs_computation/r9/8r9s/8r9s.fit
pddf	/app/data/pr_computation/r9/8r9s/8r9s.pr.out
profile	/app/data/saxs_computation/r9/8r9s/8r9s.dat

A soakable crystal form of human CDK7 in complex with AMP-PNP

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