SAXSdb — 2dr5

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2dr5
沉积日期 deposition_date	2006-06-08
结构标题 title	Complex structure of CCA adding enzyme with mini-helix lacking CCA
关键词 keywords	protein-rna complex, TRANSFERASE-RNA COMPLEX; TRANSFERASE/RNA
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	28.03 Å
回转半径 Rg (电子) rg_electron	27.85 Å
零角强度 I(0) i0	76593200.00
分子量 molecular_weight	61965.0 kDa
排除体积 excluded_volume	74676 Å³
包络体积 envelope_volume	100170 Å³
水化壳体积 shell_volume	30828 Å³
包络直径 envelope_diameter	100.4 Å
壳层 Rg shell_rg	34.15 Å
包络 Rg envelope_rg	27.75 Å
形状 Rg shape_rg	27.85 Å
总 Rg total_rg	28.44 Å
总原子数 total_atoms	4324
残基数 n_residues	469
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	96.3 Å
Rg (实空间) rg_real	28.07 Å
Rg 误差 (实空间) rg_real_error	0.82 Å
I(0) (实空间) i0_real	7.6590e+07
I(0) 误差 (实空间) i0_real_error	1.2680e+06
Rg (倒空间) rg_reciprocal	28.06 Å
I(0) (倒空间) i0_reciprocal	76590000.0000
解质量估计 total_estimate	0.8729
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	33.8 Å
偏度 Skewness skewness	0.395
峰度 Kurtosis kurtosis	-0.189
角度范围 angular_range	— – 0.2850 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	11270000.0000
实空间数据点数 n_real_points	58
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.822; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.964; Smooth: 0.914

▶

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	tRNA (32-MER)
分子量 formula_weight	10294.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	B
原子数 atom_count	4427

GGCCCGGGGCGGUUCGAUUCCGCCCUGGGCCA

Entity 2 polymer

描述 description	CCA-adding enzyme
分子量 formula_weight	51469.1 kDa
EC 编号 ec_number	2.7.7.25, 2.7.7.21
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

MKVEEILEKALELVIPDEEEVRKGREAEEELRRRLDELGVEYVFVGSYARNTWLKGSLEIDVFLLFPEEFSKEELRERGLEIGKAVLDSYEIRYAEHPYVHGVVKGVEVDVVPCYKLKEPKNIKSAVDRTPFHHKWLEGRIKGKENEVRLLKGFLKANGIYGAEYKVRGFSGYLCELLIVFYGSFLETVKNARRWTRRTVIDVAKGEVRKGEEFFVVDPVDEKRNVAANLSLDNLARFVHLCREFMEAPSLGFFKPKHPLEIEPERLRKIVEERGTAVFAVKFRKPDIVDDNLYPQLERASRKIFEFLERENFMPLRSAFKASEEFCYLLFECQIKEISRVFRRMGPQFEDERNVKKFLSRNRAFRPFIENGRWWAFEMRKFTTPEEGVRSYASTHWHTLGKNVGESIREYFEIISGEKLFKEPVTAELCEMMGVKD

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 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	103

▼

6. 折叠分类 (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

结构域编号 domain_id	d2dr5a1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.160 — PAP/OAS1 substrate-binding domain
超家族 Superfamily superfamily	a.160.1 — PAP/OAS1 substrate-binding domain
家族 Family family	a.160.1.3 — Archaeal tRNA CCA-adding enzyme substrate-binding domain

结构域编号 domain_id	d2dr5a2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.218 — Nucleotidyltransferase
超家族 Superfamily superfamily	d.218.1 — Nucleotidyltransferase
家族 Family family	d.218.1.7 — Archaeal tRNA CCA-adding enzyme catalytic domain

结构域编号 domain_id	d2dr5a3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.16 — PAP/Archaeal CCA-adding enzyme, C-terminal domain
家族 Family family	d.58.16.2 — Archaeal tRNA CCA-adding enzyme

CATH v4.4 (4 domains)

结构域编号 domain_id	2dr5A01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1410 — Poly(a)-polymerase, middle domain
同源超家族 H-superfamily homologous superfamily	30 — CCA tRNA nucleotidyltransferase, domain 2

结构域编号 domain_id	2dr5A02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	460 — Beta Polymerase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Beta Polymerase, domain 2

结构域编号 domain_id	2dr5A03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	590 — Poly(A) polymerase predicted RNA binding domain

结构域编号 domain_id	2dr5A04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	1550 — Archaeal tRNA CCA-adding enzyme catalytic domain

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	58.112 Å
晶胞边长 b length_b	58.112 Å
晶胞边长 c length_c	441.926 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	P 43 21 2
空间群编号 int_tables_number	96
晶系 crystal_system	—

分辨率 resolution	2.800 Å
最低分辨率 resolution_low	10.000 Å
R 因子 r_factor	0.2360
R_work r_work	0.2360
R_free r_free	0.2920

fit	/app/data/saxs_computation/dr/2dr5/2dr5.fit
pddf	/app/data/pr_computation/dr/2dr5/2dr5.pr.out
profile	/app/data/saxs_computation/dr/2dr5/2dr5.dat

Complex structure of CCA adding enzyme with mini-helix lacking CCA

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 (4)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

Entity 4 water

6. 折叠分类 (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

CATH v4.4 (4 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)