SAXSdb — 1jx2

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1jx2
沉积日期 deposition_date	2001-09-05
结构标题 title	CRYSTAL STRUCTURE OF THE NUCLEOTIDE-FREE DYNAMIN A GTPASE DOMAIN, DETERMINED AS MYOSIN FUSION
关键词 keywords	dynamin, GTPase, myosin, fusion-protein, Dictyostelium, HYDROLASE; HYDROLASE
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	41.71 Å
回转半径 Rg (电子) rg_electron	42.35 Å
零角强度 I(0) i0	205408000.00
分子量 molecular_weight	118270.0 kDa
排除体积 excluded_volume	148870 Å³
包络体积 envelope_volume	202050 Å³
水化壳体积 shell_volume	44220 Å³
包络直径 envelope_diameter	159.3 Å
壳层 Rg shell_rg	41.89 Å
包络 Rg envelope_rg	42.46 Å
形状 Rg shape_rg	42.30 Å
总 Rg total_rg	42.50 Å
总原子数 total_atoms	8337
残基数 n_residues	1039
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	149.8 Å
Rg (实空间) rg_real	42.30 Å
Rg 误差 (实空间) rg_real_error	1.42 Å
I(0) (实空间) i0_real	2.0540e+08
I(0) 误差 (实空间) i0_real_error	3.4950e+06
Rg (倒空间) rg_reciprocal	41.71 Å
I(0) (倒空间) i0_reciprocal	205300000.0000
解质量估计 total_estimate	0.7487
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	35.5 Å
偏度 Skewness skewness	0.683
峰度 Kurtosis kurtosis	-0.202
角度范围 angular_range	— – 0.1900 Å⁻¹
当前正则化参数 α current_alpha	0.0003
最高正则化参数 α highest_alpha	40090000.0000
实空间数据点数 n_real_points	39
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.471; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.636; Smooth: 0.680

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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	Myosin-2 heavy chain,Dynamin-A
分子量 formula_weight	124573.5 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	8713

MHHHHHHHDGTEDPIHDRTSDYHKYLKVKQGDSDLFKLTVSDKRYIWYNPDPKERDSYECGEIVSETSDSFTFKTVDGQDRQVKKDDANQRNPIKFDGVEDMSELSYLNEPAVFHNLRVRYNQDLIYTYSGLFLVAVNPFKRIPIYTQEMVDIFKGRRRNEVAPHIFAISDVAYRSMLDDRQNQSLLITGESGAGKTENTKKVIQYLASVAGRNQANGSGVLEQQILQANPILEAFGNAKTTRNNNSSRFGKFIEIQFNSAGFISGASIQSYLLEKSRVVFQSETERNYHIFYQLLAGATAEEKKALHLAGPESFNYLNQSGCVDIKGVSDSEEFKITRQAMDIVGFSQEEQMSIFKIIAGILHLGNIKFEKGAGEGAVLKDKTALNAASTVFGVNPSVLEKALMEPRILAGRDLVAQHLNVEKSSSSRDALVKALYGRLFLWLVKKINNVLCQERKAYFIGVLDISGFEIFKVNSFEQLCINYTNEKLQQFFNHHMFKLEQEEYLKEKINWTFIDFGLDSQATIDLIDGRQPPGILALLDEQSVFPNATDNTLITKLHSHFSKKNAKYEEPRFSKTEFGVTHYAGQVMYEIQDWLEKNKDPLQQDLELCFKDSSDNVVTKLFNDPNIASRAKKGANFITVAAQYKEQLASLMATLETTNPHFVRCIIPNNKQLPAKLEDKVVLDQLRCNGVLEGIRITRKGFPNRIIYADFVKRYYLLAPNVPRDAEDSQKATDAVLKHLNIDPEQYRFGITKIFFRAGQLARIEEAREQRISEITRGLVPRGSDQLIPVINKLQDVFNTLGSDPLDLPQIVVVGSQSSGKSSVLENIVGRDFLPRGSGIVTRRPLILQLTHLPIADDGSQTQEWGEFLHKPNDMFYDFSEIREEIIRDTDRMTGKNKGISAQPINLKIYSPHVVNLTLVDLPGITKVPVGDQPTDIEQQIRRMVMAYIKKQNAIIVAVTPANTDLANSDALQLAKEVDPEGKRTIGVITKLDLMDKGTDAMEVLTGRVIPLTLGFIGVINRSQEDIIAKKSIRESLKSEILYFKNHPIYKSIANRSGTAYLSKTLNKLLMFHIRDTLPDLKVKVSKMLSDVQGELSTY

来源 Source

来源生物 organism	Dictyostelium discoideum
通用名 common_name	Slime mold
NCBI 分类编号 ncbi_taxonomy_id	44689
宿主生物 host_organism	Dictyostelium discoideum

Entity 2 non-polymer

描述 description	beta-D-glucopyranose
分子量 formula_weight	180.2 kDa
来源方法 src_method	man
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 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 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	376

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6. 折叠分类 (SCOP + CATH) 7 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1jx2a1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.34 — SH3-like barrel
超家族 Superfamily superfamily	b.34.3 — Myosin S1 fragment, N-terminal domain
家族 Family family	b.34.3.1 — Myosin S1 fragment, N-terminal domain

结构域编号 domain_id	d1jx2a2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.9 — Motor proteins

结构域编号 domain_id	d1jx2a3
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d1jx2a4
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.8 — G proteins

CATH v4.4 (3 domains)

结构域编号 domain_id	1jx2A01
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	1jx2A02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	850 — Kinesin
同源超家族 H-superfamily homologous superfamily	10 — Kinesin motor domain

结构域编号 domain_id	1jx2A04
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	54.450 Å
晶胞边长 b length_b	62.040 Å
晶胞边长 c length_c	181.200 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	94.79 °
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	2.300 Å
最低分辨率 resolution_low	14.960 Å
R 因子 r_factor	0.1970
R_work r_work	0.1970
R_free r_free	0.2550

fit	/app/data/saxs_computation/jx/1jx2/1jx2.fit
pddf	/app/data/pr_computation/jx/1jx2/1jx2.pr.out
profile	/app/data/saxs_computation/jx/1jx2/1jx2.dat

CRYSTAL STRUCTURE OF THE NUCLEOTIDE-FREE DYNAMIN A GTPASE DOMAIN, DETERMINED AS MYOSIN FUSION

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