SAXSdb — 1r89

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1r89
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, Incoming nucleotide, nucleotidyltransferase superfamily, 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	28.36 Å
回转半径 Rg (电子) rg_electron	27.94 Å
零角强度 I(0) i0	45619700.00
分子量 molecular_weight	52598.0 kDa
排除体积 excluded_volume	65849 Å³
包络体积 envelope_volume	87770 Å³
水化壳体积 shell_volume	27261 Å³
包络直径 envelope_diameter	98.0 Å
壳层 Rg shell_rg	33.58 Å
包络 Rg envelope_rg	28.14 Å
形状 Rg shape_rg	27.96 Å
总 Rg total_rg	28.47 Å
总原子数 total_atoms	3694
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	95.0 Å
Rg (实空间) rg_real	28.50 Å
Rg 误差 (实空间) rg_real_error	0.74 Å
I(0) (实空间) i0_real	4.5620e+07
I(0) 误差 (实空间) i0_real_error	7.6750e+05
Rg (倒空间) rg_reciprocal	28.46 Å
I(0) (倒空间) i0_reciprocal	45620000.0000
解质量估计 total_estimate	0.8727
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	28.9 Å
偏度 Skewness skewness	0.438
峰度 Kurtosis kurtosis	-0.267
角度范围 angular_range	— – 0.2800 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	10090000.0000
实空间数据点数 n_real_points	57
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.862; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.903; Smooth: 0.851

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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 (7)

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	4024

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	3

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 non-polymer

描述 description	CHLORIDE ION
分子量 formula_weight	35.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 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 6 non-polymer

描述 description	CYTIDINE-5'-TRIPHOSPHATE
分子量 formula_weight	483.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 7 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	330

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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	d1r89a1
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	d1r89a2
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	d1r89a3
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	1r89A01
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	1r89A02
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	1r89A03
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	1r89A04
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	86.151 Å
晶胞边长 b length_b	79.954 Å
晶胞边长 c length_c	78.145 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	97.53 °
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	1.800 Å
最低分辨率 resolution_low	38.630 Å
R 因子 r_factor	0.1872
R_work r_work	0.1850
R_free r_free	0.2264

fit	/app/data/saxs_computation/r8/1r89/1r89.fit
pddf	/app/data/pr_computation/r8/1r89/1r89.pr.out
profile	/app/data/saxs_computation/r8/1r89/1r89.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