1yv3

The structural basis of blebbistatin inhibition and specificity for myosin II

Method: X-RAY DIFFRACTION D_max: 92.2 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	1yv3
沉积日期 deposition_date	2005-02-14
结构标题 title	The structural basis of blebbistatin inhibition and specificity for myosin II
关键词 keywords	myosin, blebbistatin, myosin II inhibitor, myosin-inhibitor complex, metastable state, CONTRACTILE PROTEIN; CONTRACTILE PROTEIN
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	28.59 Å
回转半径 Rg (电子) rg_electron	27.77 Å
零角强度 I(0) i0	96867400.00
分子量 molecular_weight	78147.0 kDa
排除体积 excluded_volume	97889 Å³
包络体积 envelope_volume	122000 Å³
水化壳体积 shell_volume	36195 Å³
包络直径 envelope_diameter	98.5 Å
壳层 Rg shell_rg	35.38 Å
包络 Rg envelope_rg	28.32 Å
形状 Rg shape_rg	27.78 Å
总 Rg total_rg	28.46 Å
总原子数 total_atoms	5521
残基数 n_residues	703
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	92.2 Å
Rg (实空间) rg_real	28.58 Å
Rg 误差 (实空间) rg_real_error	0.63 Å
I(0) (实空间) i0_real	9.6870e+07
I(0) 误差 (实空间) i0_real_error	1.4250e+06
Rg (倒空间) rg_reciprocal	28.59 Å
I(0) (倒空间) i0_reciprocal	96870000.0000
解质量估计 total_estimate	0.6880
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	33.5 Å
偏度 Skewness skewness	0.385
峰度 Kurtosis kurtosis	-0.213
角度范围 angular_range	— – 0.2750 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	16520000.0000
实空间数据点数 n_real_points	56
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.876; Stabil: 1.000; Sysdev: 0.156; Positv: 1.000; Valcen: 0.997; Smooth: 0.848

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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 (7)

Entity 1 polymer

描述 description	Myosin II heavy chain
分子量 formula_weight	86747.1 kDa
来源方法 src_method	nat
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	6219

GNPIHDRTSDYHKYLKVKQGDSDLFKLTVSDKRYIWYNPDPKERDSYECGEIVSETSDSFTFKTVDGQDRQVKKDDANQRNPIKFDGVEDMSELSYLNEPAVFHNLRVRYNQDLIYTYSGLFLVAVNPFKRIPIYTQEMVDIFKGRRRNEVAPHIFAISDVAYRSMLDDRQNQSLLITGESGAGKTENTKKVIQYLASVAGRNQANGSGVLEQQILQANPILEAFGNAKTTRNNNSSRFGKFIEIQFNSAGFISGASIQSYLLEKSRVVFQSETERNYHIFYQLLAGATAEEKKALHLAGPESFNYLNQSGCVDIKGVSDSEEFKITRQAMDIVGFSQEEQMSIFKIIAGILHLGNIKFEKGAGEGAVLKDKTALNAASTVFGVNPSVLEKALMEPRILAGRDLVAQHLNVEKSSSSRDALVKALYGRLFLWLVKKINNVLCQERKAYFIGVLDISGFEIFKVNSFEQLCINYTNEKLQQFFNHHMFKLEQEEYLKEKINWTFIDFGLDSQATIDLIDGRQPPGILALLDEQSVFPNATDNTLITKLHSHFSKKNAKYEEPRFSKTEFGVTHYAGQVMYEIQDWLEKNKDPLQQDLELCFKDSSDNVVTKLFNDPNIASRAKKGANFITVAAQYKEQLASLMATLETTNPHFVRCIIPNNKQLPAKLEDKVVLDQLRCNGVLEGIRITRKGFPNRIIYADFVKRYYLLAPNVPRDAEDSQKATDAVLKHLNIDPEQYRFGITKIFFRAGQLARIEEARELPN

Entity 2 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 non-polymer

描述 description	VANADATE ION
分子量 formula_weight	114.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	ADENOSINE-5'-DIPHOSPHATE
分子量 formula_weight	427.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 non-polymer

描述 description	(-)-1-PHENYL-1,2,3,4-TETRAHYDRO-4-HYDROXYPYRROLO[2,3-B]-7-METHYLQUINOLIN-4-ONE
分子量 formula_weight	292.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 6 non-polymer

描述 description	1,2-ETHANEDIOL
分子量 formula_weight	62.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 7 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	678

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6. 折叠分类 (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

结构域编号 domain_id	1yv3A01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
同源超家族 H-superfamily homologous superfamily	530 —

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7. 引用文献 (1)

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晶胞边长 a length_a	88.106 Å
晶胞边长 b length_b	145.770 Å
晶胞边长 c length_c	152.912 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	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	C 2 2 21
空间群编号 int_tables_number	20
晶系 crystal_system	—

分辨率 resolution	2.000 Å
最低分辨率 resolution_low	40.000 Å
R 因子 r_factor	0.1751
R_work r_work	0.1730
R_free r_free	0.2150

fit	/app/data/saxs_computation/yv/1yv3/1yv3.fit
pddf	/app/data/pr_computation/yv/1yv3/1yv3.pr.out
profile	/app/data/saxs_computation/yv/1yv3/1yv3.dat