2jj9

Crystal structure of myosin-2 in complex with ADP-metavanadate

Method: X-RAY DIFFRACTION D_max: 93.8 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

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2jj9
沉积日期 deposition_date	2008-03-25
结构标题 title	Crystal structure of myosin-2 in complex with ADP-metavanadate
关键词 keywords	;CALMODULIN-BINDING, NUCLEOTIDE-BINDING, MOTOR PROTEIN, ACTIN-BINDING, PHOSPHOPROTEIN, MYOSIN, CYTOPLASM, ATP-ANALOG, METHYLATION, COILED COIL, ATP-BINDING, MOTOR-DOMAIN, CONTRACTILE PROTEIN ;; CONTRACTILE PROTEIN
实验方法 method	X-RAY DIFFRACTION

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	28.64 Å
回转半径 Rg (电子) rg_electron	27.76 Å
零角强度 I(0) i0	100425000.00
分子量 molecular_weight	79049.0 kDa
排除体积 excluded_volume	98950 Å³
包络体积 envelope_volume	122220 Å³
水化壳体积 shell_volume	36348 Å³
包络直径 envelope_diameter	97.9 Å
壳层 Rg shell_rg	35.33 Å
包络 Rg envelope_rg	28.23 Å
形状 Rg shape_rg	27.75 Å
总 Rg total_rg	28.50 Å
总原子数 total_atoms	5571
残基数 n_residues	692
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

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	93.8 Å
Rg (实空间) rg_real	28.62 Å
Rg 误差 (实空间) rg_real_error	0.75 Å
I(0) (实空间) i0_real	1.0040e+08
I(0) 误差 (实空间) i0_real_error	1.7010e+06
Rg (倒空间) rg_reciprocal	28.63 Å
I(0) (倒空间) i0_reciprocal	100400000.0000
解质量估计 total_estimate	0.8809
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	34.1 Å
偏度 Skewness skewness	0.386
峰度 Kurtosis kurtosis	-0.194
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	18320000.0000
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: 0.852; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.897

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (4)

Entity 1 polymer

描述 description	MYOSIN-2 HEAVY CHAIN
分子量 formula_weight	90014.6 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	6079

MHHHHHHHDGTENPIHDRTSDYHKYLKVKQGDSDLFKLTVSDKRYIWYNPDPKERDSYECGEIVSETSDSFTFKTVDGQDRQVKKDDANQRNPIKFDGVEDMSELSYLNEPAVFHNLRVRYNQDLIYTYSGLFLVAVNPFKRIPIYTQEMVDIFKGRRRNEVAPHIFAISDVAYRSMLDDRQNQSLLITGESGAGKTENTKKVIQYLASVAGRNQANGSGVLEQQILQANPILEAFGNAKTTRNNNSSRFGKFIEIQFNSAGFISGASIQSYLLEKSRVVFQSETERNYHIFYQLLAGATAEEKKALHLAGPESFNYLNQSGCVDIKGVSDSEEFKITRQAMDIVGFSQEEQMSIFKIIAGILHLGNIKFEKGAGEGAVLKDKTALNAASTVFGVNPSVLEKALMEPRILAGRDLVAQHLNVEKSSSSRDALVKALYGRLFLWLVKKINNVLCQERKAYFIGVLDISGFEIFKVNSFEQLCINYTNEKLQQFFNHHMFKLEQEEYLKEKINWTFIDFGLDSQATIDLIDGRQPPGILALLDEQSVFPNATDNTLITKLHSHFSKKNAKYEEPRFSKTEFGVTHYAGQVMYEIQDWLEKNKDPLQQDLELCFKDSSDNVVTKLFNDPNIASRAKKGANFITVAAQYKEQLASLMATLETTNPHFVRCIIPNNKQLPAKLEDKVVLDQLRCNGVLEGIRITRKGFPNRIIYADFVKRYYLLAPNVPRDAEDSQKATDAVLKHLNIDPEQYRFGITKIFFRAGQLARIEEAREQRLESNEPPMDFDDDIPF

Entity 2 non-polymer

描述 description	ADP METAVANADATE
分子量 formula_weight	527.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 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	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	508

▼

6. 折叠分类 (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

结构域编号 domain_id	2jj9A02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	360 — Myosin S1 fragment, N-terminal

结构域编号 domain_id	2jj9A03
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 —

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	89.417 Å
晶胞边长 b length_b	147.218 Å
晶胞边长 c length_c	153.837 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	2.300 Å
最低分辨率 resolution_low	8.000 Å
R 因子 r_factor	0.2250
R_work r_work	0.2250
R_free r_free	0.2750

fit	/app/data/saxs_computation/jj/2jj9/2jj9.fit
pddf	/app/data/pr_computation/jj/2jj9/2jj9.pr.out
profile	/app/data/saxs_computation/jj/2jj9/2jj9.dat

Crystal structure of myosin-2 in complex with ADP-metavanadate

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