SAXSdb — 1r8a

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1r8a
沉积日期 deposition_date	2003-10-23
结构标题 title	Crystal Structures of an Archaeal Class I CCA-Adding Enzyme and Its Nucleotide Complexes
关键词 keywords	CCA Adding Enzyme, nucleotidyltransferase, TRANSFERASE; TRANSFERASE
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	28.65 Å
回转半径 Rg (电子) rg_electron	28.05 Å
零角强度 I(0) i0	42059000.00
分子量 molecular_weight	51517.0 kDa
排除体积 excluded_volume	65002 Å³
包络体积 envelope_volume	88270 Å³
水化壳体积 shell_volume	27373 Å³
包络直径 envelope_diameter	98.7 Å
壳层 Rg shell_rg	33.59 Å
包络 Rg envelope_rg	28.26 Å
形状 Rg shape_rg	28.06 Å
总 Rg total_rg	28.65 Å
总原子数 total_atoms	3633
残基数 n_residues	437
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	94.6 Å
Rg (实空间) rg_real	28.75 Å
Rg 误差 (实空间) rg_real_error	0.75 Å
I(0) (实空间) i0_real	4.2060e+07
I(0) 误差 (实空间) i0_real_error	6.2990e+05
Rg (倒空间) rg_reciprocal	28.71 Å
I(0) (倒空间) i0_reciprocal	42060000.0000
解质量估计 total_estimate	0.8747
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	31.0 Å
偏度 Skewness skewness	0.447
峰度 Kurtosis kurtosis	-0.245
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	7985000.0000
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: 0.880; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.906; Smooth: 0.820

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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	tRNA nucleotidyltransferase
分子量 formula_weight	51469.1 kDa
EC 编号 ec_number	2.7.7.25
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	3961

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 2 non-polymer

描述 description	MANGANESE (II) ION
分子量 formula_weight	54.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 non-polymer

描述 description	SODIUM ION
分子量 formula_weight	23.0 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	328

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6. 折叠分类 (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

结构域编号 domain_id	d1r8aa1
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	d1r8aa2
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	d1r8aa3
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	1r8aA01
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	1r8aA02
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	1r8aA03
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	1r8aA04
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

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7. 引用文献 (1)

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晶胞边长 a length_a	86.453 Å
晶胞边长 b length_b	78.726 Å
晶胞边长 c length_c	77.396 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	98.03 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	2.100 Å
最低分辨率 resolution_low	38.350 Å
R 因子 r_factor	0.1893
R_work r_work	0.1865
R_free r_free	0.2419

fit	/app/data/saxs_computation/r8/1r8a/1r8a.fit
pddf	/app/data/pr_computation/r8/1r8a/1r8a.pr.out
profile	/app/data/saxs_computation/r8/1r8a/1r8a.dat

Crystal Structures of an Archaeal Class I CCA-Adding Enzyme and Its Nucleotide Complexes

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