2ba0

Archaeal exosome core

Method: X-RAY DIFFRACTION D_max: 118.6 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	2ba0
沉积日期 deposition_date	2005-10-13
结构标题 title	Archaeal exosome core
关键词 keywords	EXOSOME, RNASE PH, RNA DEGRADATION, EXORIBONUCLEASE, RNA BINDING, S1DOMAIN, KH DOMAIN, ARCHAEAL, RNA BINDING PROTEIN; RNA BINDING 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	39.92 Å
回转半径 Rg (电子) rg_electron	39.06 Å
零角强度 I(0) i0	818879000.00
分子量 molecular_weight	239240.0 kDa
排除体积 excluded_volume	302110 Å³
包络体积 envelope_volume	413380 Å³
水化壳体积 shell_volume	83014 Å³
包络直径 envelope_diameter	125.7 Å
壳层 Rg shell_rg	48.89 Å
包络 Rg envelope_rg	38.08 Å
形状 Rg shape_rg	39.04 Å
总 Rg total_rg	39.67 Å
总原子数 total_atoms	16809
残基数 n_residues	2154
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	118.6 Å
Rg (实空间) rg_real	39.64 Å
Rg 误差 (实空间) rg_real_error	0.54 Å
I(0) (实空间) i0_real	8.1890e+08
I(0) 误差 (实空间) i0_real_error	1.2520e+07
Rg (倒空间) rg_reciprocal	39.92 Å
I(0) (倒空间) i0_reciprocal	819100000.0000
解质量估计 total_estimate	0.8975
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	56.3 Å
偏度 Skewness skewness	-0.028
峰度 Kurtosis kurtosis	-0.564
角度范围 angular_range	— – 0.2000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	194800000.0000
实空间数据点数 n_real_points	41
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.921; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.951; Smooth: 0.949

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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 (4)

Entity 1 polymer

描述 description	Archaeal exosome RNA binding protein RRP4
分子量 formula_weight	25589.9 kDa
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C
原子数 atom_count	16910

MRKIVLPGDLLSTNPRAAGYGTYVEGGKVYAKIIGLFDQTETHVRVIPLKGRYTPSVGDVVIGIIREVAANGWAVDIYSPYQAFLPVSENPEMKPNKKPNEVLDIGDAIIAKVLNIDPKMKVTLTMKDRICRPIRFGRIVAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQNGLIWVNGDRRKVSIAEEAIYLIEQEAHTEGLTDRVAEFIKRRKADVGIQHHHHHH

来源 Source

来源生物 organism	Archaeoglobus fulgidus
NCBI 分类编号 ncbi_taxonomy_id	2234
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	Archaeal exosome RNA binding protein RRP41
分子量 formula_weight	28888.3 kDa
EC 编号 ec_number	3.1.13.-
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	F,E,D

MSEFNEKPEKLIVDGLRLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNKVIAAVFGPREVHPRHLQDPSKAIIRYRYNMAPFSVEERKRPGPDRRSIEISKVSKEAFEAVIMKELFPRSAIDIFVEVLQADAGSRTACLNAASVALVDAGVPMKGMITSVAVGKADGQLVLDPMKEEDNFGEADMPFAFLIRNGKIESIALLQMDGRMTRDEVKQAIELAKKGALQIYEMQREAILRRYIEVGEEMDEITEGGEDA

来源 Source

来源生物 organism	Archaeoglobus fulgidus
NCBI 分类编号 ncbi_taxonomy_id	2234
宿主生物 host_organism	Escherichia coli

Entity 3 polymer

描述 description	Archaeal exosome RNA binding protein RRP42
分子量 formula_weight	28677.6 kDa
EC 编号 ec_number	3.1.13.-
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	I,H,G

MPEDILVDIKRDYVLSKLRDNERIDGRGFDEFRKVEIIPNVIEKAEGSALVKLGDTQVVVGVKMQPGEPYPDTPDRGVIIVNAELVPLASPTFEPGPPDENSIELARVVDRGIRESEAVDLSKLVIEEGEKVWIVFVDIHALDDDGNLLDASALAAIAALMNTKVPAERFDLGEDYLLPVRDLPVSVTSLIVGNKYLVDPSREEMSVGDTTLTITTDKDDNVVAMQKSGGYLLDEKLFDELLDVSINCARKLREKFKEI

来源 Source

来源生物 organism	Archaeoglobus fulgidus
NCBI 分类编号 ncbi_taxonomy_id	2234
宿主生物 host_organism	Escherichia coli

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	101

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6. 折叠分类 (SCOP + CATH) 36 domains

SCOP 2.08 (21 domains)

结构域编号 domain_id	d2ba0a1
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.40.4.5 — Cold shock DNA-binding domain-like

结构域编号 domain_id	d2ba0a2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.84 — Barrel-sandwich hybrid
超家族 Superfamily superfamily	b.84.4 — Ribosomal L27 protein-like
家族 Family family	b.84.4.2 — ECR1 N-terminal domain-like

结构域编号 domain_id	d2ba0a3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.51 — Eukaryotic type KH-domain (KH-domain type I)
超家族 Superfamily superfamily	d.51.1 — Eukaryotic type KH-domain (KH-domain type I)
家族 Family family	d.51.1.1 — Eukaryotic type KH-domain (KH-domain type I)

结构域编号 domain_id	d2ba0b1
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.40.4.5 — Cold shock DNA-binding domain-like

结构域编号 domain_id	d2ba0b2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.84 — Barrel-sandwich hybrid
超家族 Superfamily superfamily	b.84.4 — Ribosomal L27 protein-like
家族 Family family	b.84.4.2 — ECR1 N-terminal domain-like

结构域编号 domain_id	d2ba0b3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.51 — Eukaryotic type KH-domain (KH-domain type I)
超家族 Superfamily superfamily	d.51.1 — Eukaryotic type KH-domain (KH-domain type I)
家族 Family family	d.51.1.1 — Eukaryotic type KH-domain (KH-domain type I)

结构域编号 domain_id	d2ba0c1
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.40.4.5 — Cold shock DNA-binding domain-like

结构域编号 domain_id	d2ba0c2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.84 — Barrel-sandwich hybrid
超家族 Superfamily superfamily	b.84.4 — Ribosomal L27 protein-like
家族 Family family	b.84.4.2 — ECR1 N-terminal domain-like

结构域编号 domain_id	d2ba0c3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.51 — Eukaryotic type KH-domain (KH-domain type I)
超家族 Superfamily superfamily	d.51.1 — Eukaryotic type KH-domain (KH-domain type I)
家族 Family family	d.51.1.1 — Eukaryotic type KH-domain (KH-domain type I)

结构域编号 domain_id	d2ba0d1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.14 — Ribosomal protein S5 domain 2-like
超家族 Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
家族 Family family	d.14.1.4 — Ribonuclease PH domain 1-like

结构域编号 domain_id	d2ba0d2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.101 — Ribonuclease PH domain 2-like
超家族 Superfamily superfamily	d.101.1 — Ribonuclease PH domain 2-like
家族 Family family	d.101.1.1 — Ribonuclease PH domain 2-like

结构域编号 domain_id	d2ba0e1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.14 — Ribosomal protein S5 domain 2-like
超家族 Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
家族 Family family	d.14.1.4 — Ribonuclease PH domain 1-like

结构域编号 domain_id	d2ba0e2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.101 — Ribonuclease PH domain 2-like
超家族 Superfamily superfamily	d.101.1 — Ribonuclease PH domain 2-like
家族 Family family	d.101.1.1 — Ribonuclease PH domain 2-like

结构域编号 domain_id	d2ba0f1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.14 — Ribosomal protein S5 domain 2-like
超家族 Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
家族 Family family	d.14.1.4 — Ribonuclease PH domain 1-like

结构域编号 domain_id	d2ba0f2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.101 — Ribonuclease PH domain 2-like
超家族 Superfamily superfamily	d.101.1 — Ribonuclease PH domain 2-like
家族 Family family	d.101.1.1 — Ribonuclease PH domain 2-like

结构域编号 domain_id	d2ba0g1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.14 — Ribosomal protein S5 domain 2-like
超家族 Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
家族 Family family	d.14.1.4 — Ribonuclease PH domain 1-like

结构域编号 domain_id	d2ba0g2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.101 — Ribonuclease PH domain 2-like
超家族 Superfamily superfamily	d.101.1 — Ribonuclease PH domain 2-like
家族 Family family	d.101.1.1 — Ribonuclease PH domain 2-like

结构域编号 domain_id	d2ba0h1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.14 — Ribosomal protein S5 domain 2-like
超家族 Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
家族 Family family	d.14.1.4 — Ribonuclease PH domain 1-like

结构域编号 domain_id	d2ba0h2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.101 — Ribonuclease PH domain 2-like
超家族 Superfamily superfamily	d.101.1 — Ribonuclease PH domain 2-like
家族 Family family	d.101.1.1 — Ribonuclease PH domain 2-like

结构域编号 domain_id	d2ba0i1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.14 — Ribosomal protein S5 domain 2-like
超家族 Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
家族 Family family	d.14.1.4 — Ribonuclease PH domain 1-like

结构域编号 domain_id	d2ba0i2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.101 — Ribonuclease PH domain 2-like
超家族 Superfamily superfamily	d.101.1 — Ribonuclease PH domain 2-like
家族 Family family	d.101.1.1 — Ribonuclease PH domain 2-like

CATH v4.4 (15 domains)

结构域编号 domain_id	2ba0A01
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	100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain

结构域编号 domain_id	2ba0A02
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	2ba0A03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1370 — Ribosomal Protein S8; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — K Homology domain, type 1

结构域编号 domain_id	2ba0B01
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	100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain

结构域编号 domain_id	2ba0B02
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	2ba0B03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1370 — Ribosomal Protein S8; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — K Homology domain, type 1

结构域编号 domain_id	2ba0C01
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	100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain

结构域编号 domain_id	2ba0C02
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	2ba0C03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1370 — Ribosomal Protein S8; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — K Homology domain, type 1

结构域编号 domain_id	2ba0D01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	230 — Ribosomal Protein S5; domain 2
同源超家族 H-superfamily homologous superfamily	70 — GHMP Kinase, N-terminal domain

结构域编号 domain_id	2ba0E01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	230 — Ribosomal Protein S5; domain 2
同源超家族 H-superfamily homologous superfamily	70 — GHMP Kinase, N-terminal domain

结构域编号 domain_id	2ba0F01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	230 — Ribosomal Protein S5; domain 2
同源超家族 H-superfamily homologous superfamily	70 — GHMP Kinase, N-terminal domain

结构域编号 domain_id	2ba0G01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	230 — Ribosomal Protein S5; domain 2
同源超家族 H-superfamily homologous superfamily	70 — GHMP Kinase, N-terminal domain

结构域编号 domain_id	2ba0H01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	230 — Ribosomal Protein S5; domain 2
同源超家族 H-superfamily homologous superfamily	70 — GHMP Kinase, N-terminal domain

结构域编号 domain_id	2ba0I01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	230 — Ribosomal Protein S5; domain 2
同源超家族 H-superfamily homologous superfamily	70 — GHMP Kinase, N-terminal domain

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7. 引用文献 (1)

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晶胞边长 a length_a	101.570 Å
晶胞边长 b length_b	129.590 Å
晶胞边长 c length_c	102.330 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	101.56 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	6

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	2.700 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	—
R_work r_work	0.2160
R_free r_free	0.2640

Archaeal exosome core

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

5. 实体与聚合体信息 (4)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 polymer

聚合体 Polymer

来源 Source

Entity 4 water

6. 折叠分类 (SCOP + CATH) 36 domains

SCOP 2.08 (21 domains)

CATH v4.4 (15 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/ba/2ba0/2ba0.fit
pddf	/app/data/pr_computation/ba/2ba0/2ba0.pr.out
profile	/app/data/saxs_computation/ba/2ba0/2ba0.dat