1ixr

RuvA-RuvB complex

Method: X-RAY DIFFRACTION D_max: 124.9 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	1ixr
沉积日期 deposition_date	2002-07-04
结构标题 title	RuvA-RuvB complex
关键词 keywords	heterooligomeric complex, octameric RuvA, AAA-ATPase domain, complex with nucleotide, Hydrolase; HYDROLASE
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	40.44 Å
回转半径 Rg (电子) rg_electron	40.89 Å
零角强度 I(0) i0	69417200.00
分子量 molecular_weight	69581.0 kDa
排除体积 excluded_volume	88560 Å³
包络体积 envelope_volume	134020 Å³
水化壳体积 shell_volume	30510 Å³
包络直径 envelope_diameter	134.7 Å
壳层 Rg shell_rg	41.03 Å
包络 Rg envelope_rg	39.56 Å
形状 Rg shape_rg	40.88 Å
总 Rg total_rg	40.95 Å
总原子数 total_atoms	4904
残基数 n_residues	634
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	124.9 Å
Rg (实空间) rg_real	40.79 Å
Rg 误差 (实空间) rg_real_error	0.99 Å
I(0) (实空间) i0_real	6.9420e+07
I(0) 误差 (实空间) i0_real_error	1.1070e+06
Rg (倒空间) rg_reciprocal	40.45 Å
I(0) (倒空间) i0_reciprocal	69390000.0000
解质量估计 total_estimate	0.7568
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	28.8 Å
偏度 Skewness skewness	0.407
峰度 Kurtosis kurtosis	-0.826
角度范围 angular_range	— – 0.1950 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	3832000.0000
实空间数据点数 n_real_points	40
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.776; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.497; Smooth: 0.011

▶

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

▶

5. 实体与聚合体信息 (3)

Entity 1 polymer

描述 description	Holliday junction DNA helicase ruvA
分子量 formula_weight	20441.1 kDa
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	4904

MIRYLRGLVLKKEAGGFVLLAGGVGFFLQAPTPFLQALEEGKEVGVHTHLLLKEEGLSLYGFPDEENLALFELLLSVSGVGPKVALALLSALPPRLLARALLEGDARLLTSASGVGRRLAERIALELKGKVPPHLLAGEKVESEAAEEAVMALAALGFKEAQARAVVLDLLAQNPKARAQDLIKEALKRLR

来源 Source

来源生物 organism	Thermus thermophilus
NCBI 分类编号 ncbi_taxonomy_id	274
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

描述 description	RuvB
分子量 formula_weight	34801.3 kDa
EC 编号 ec_number	3.6.1.3
突变 mutation	Y309R
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	C

MEDLALRPKTLDEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHELGVNLRVTSGPAIEKPGDLAAILANSLEEGDILFIDEIHRLSRQAEEHLYPAMEDFVMDIVIGQGPAARTIRLELPRFTLIGATTRPGLITAPLLSRFGIVEHLEYYTPEELAQGVMRDARLLGVRITEEAALEIGRRSRGTMRVAKRLFRRVRDFAQVAGEEVITRERALEALAALGLDELGLEKRDREILEVLILRFGGGPVGLATLATALSEDPGTLEEVHEPYLIRQGLLKRTPRGRVATELARRHL

来源 Source

来源生物 organism	Thermus thermophilus
NCBI 分类编号 ncbi_taxonomy_id	274
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 non-polymer

描述 description	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
分子量 formula_weight	506.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

▼

6. 折叠分类 (SCOP + CATH) 15 domains

SCOP 2.08 (7 domains)

结构域编号 domain_id	d1ixra1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.60 — SAM domain-like
超家族 Superfamily superfamily	a.60.2 — RuvA domain 2-like
家族 Family family	a.60.2.1 — DNA helicase RuvA subunit, middle domain

结构域编号 domain_id	d1ixra2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.40 — OB-fold
超家族 Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
家族 Family family	b.40.4.2 — DNA helicase RuvA subunit, N-terminal domain

结构域编号 domain_id	d1ixrb1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.5 — RuvA C-terminal domain-like
超家族 Superfamily superfamily	a.5.1 — DNA helicase RuvA subunit, C-terminal domain
家族 Family family	a.5.1.1 — DNA helicase RuvA subunit, C-terminal domain

结构域编号 domain_id	d1ixrb2
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.60 — SAM domain-like
超家族 Superfamily superfamily	a.60.2 — RuvA domain 2-like
家族 Family family	a.60.2.1 — DNA helicase RuvA subunit, middle domain

结构域编号 domain_id	d1ixrb3
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.40 — OB-fold
超家族 Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
家族 Family family	b.40.4.2 — DNA helicase RuvA subunit, N-terminal domain

结构域编号 domain_id	d1ixrc1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
超家族 Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
家族 Family family	a.4.5.11 — Helicase DNA-binding domain

结构域编号 domain_id	d1ixrc2
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.37.1.20 — Extended AAA-ATPase domain

CATH v4.4 (8 domains)

结构域编号 domain_id	1ixrA01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	140 — Nucleic acid-binding proteins

结构域编号 domain_id	1ixrA02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	150 — DNA polymerase; domain 1
同源超家族 H-superfamily homologous superfamily	20 — 5' to 3' exonuclease, C-terminal subdomain

结构域编号 domain_id	1ixrB01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	140 — Nucleic acid-binding proteins

结构域编号 domain_id	1ixrB02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	150 — DNA polymerase; domain 1
同源超家族 H-superfamily homologous superfamily	20 — 5' to 3' exonuclease, C-terminal subdomain

结构域编号 domain_id	1ixrB03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily	10 — Ubiquitin-associated (UBA) domain

结构域编号 domain_id	1ixrC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	1ixrC02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily	60 —

结构域编号 domain_id	1ixrC03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	10 — Arc Repressor Mutant, subunit A
同源超家族 H-superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	61.581 Å
晶胞边长 b length_b	195.113 Å
晶胞边长 c length_c	246.244 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	16

空间群 space_group	I 2 2 2
空间群编号 int_tables_number	23
晶系 crystal_system	—

分辨率 resolution	3.300 Å
最低分辨率 resolution_low	12.000 Å
R 因子 r_factor	—
R_work r_work	0.2680
R_free r_free	0.3350

fit	/app/data/saxs_computation/ix/1ixr/1ixr.fit
pddf	/app/data/pr_computation/ix/1ixr/1ixr.pr.out
profile	/app/data/saxs_computation/ix/1ixr/1ixr.dat

RuvA-RuvB complex

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

5. 实体与聚合体信息 (3)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

6. 折叠分类 (SCOP + CATH) 15 domains

SCOP 2.08 (7 domains)

CATH v4.4 (8 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)