1j2b

Crystal Structure Of Archaeosine tRNA-Guanine Transglycosylase Complexed With lambda-form tRNA(Val)

Method: X-RAY DIFFRACTION D_max: 118.4 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	1j2b
沉积日期 deposition_date	2002-12-29
结构标题 title	Crystal Structure Of Archaeosine tRNA-Guanine Transglycosylase Complexed With lambda-form tRNA(Val)
关键词 keywords	transferase, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Structural Genomics, transferase-RNA COMPLEX; transferase/RNA
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	37.25 Å
回转半径 Rg (电子) rg_electron	35.56 Å
零角强度 I(0) i0	680061000.00
分子量 molecular_weight	180070.0 kDa
排除体积 excluded_volume	211510 Å³
包络体积 envelope_volume	273860 Å³
水化壳体积 shell_volume	61631 Å³
包络直径 envelope_diameter	123.6 Å
壳层 Rg shell_rg	44.02 Å
包络 Rg envelope_rg	35.55 Å
形状 Rg shape_rg	35.48 Å
总 Rg total_rg	36.20 Å
总原子数 total_atoms	12454
残基数 n_residues	1300
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	118.4 Å
Rg (实空间) rg_real	37.12 Å
Rg 误差 (实空间) rg_real_error	0.88 Å
I(0) (实空间) i0_real	6.8010e+08
I(0) 误差 (实空间) i0_real_error	1.1710e+07
Rg (倒空间) rg_reciprocal	37.21 Å
I(0) (倒空间) i0_reciprocal	680100000.0000
解质量估计 total_estimate	0.8948
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	45.1 Å
偏度 Skewness skewness	0.240
峰度 Kurtosis kurtosis	-0.442
角度范围 angular_range	— – 0.2100 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	65890000.0000
实空间数据点数 n_real_points	43
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.918; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.885

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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 (5)

Entity 1 polymer

描述 description	tRNA(Val)
分子量 formula_weight	24827.7 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	C,D
原子数 atom_count	12495

GGGCCCGUGGUCUAGUUGGUCAUGACGCCGCCCUUACGAGGCGGAGGUCCGGGGUUCAAGUCCCCGCGGGCCCACCA

Entity 2 polymer

描述 description	Archaeosine tRNA-guanine transglycosylase
分子量 formula_weight	66700.1 kDa
EC 编号 ec_number	2.4.2.29
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

MSRGDKMLKFEIKARDGAGRIGKLEVNGKKIETPAIMPVVNPKQMVVEPKELEKMGFEIIITNSYIIYKDEELRRKALELGIHRMLDYNGIIEVDSGSFQLMKYGSIEVSNREIIEFQHRIGVDIGTFLDIPTPPDAPREQAVKELEITLSRAREAEEIKEIPMNATIQGSTYTDLRRYAARRLSSMNFEIHPIGGVVPLLESYRFRDVVDIVISSKMALRPDRPVHLFGAGHPIVFALAVAMGVDLFDSASYALYAKDDRYMTPEGTKRLDELDYFPCSCPVCSKYTPQELREMPKEERTRLLALHNLWVIKEEIKRVKQAIKEGELWRLVDERARSHPKLYSAYKRLLEHYTFLEEFEPITKKSALFKISNESLRWPVVRRAKERAKSINERFGELVEHPIFGRVSRYLSLTYPFAQSEAEDDFKIEKPTKEDAIKYVMAIAEYQFGEGASRAFDDAKVELSKTGMPRQVKVNGKRLATVRADDGLLTLGIEGAKRLHRVLPYPRMRVVVNKEAEPFARKGKDVFAKFVIFADPGIRPYDEVLVVNENDELLATGQALLSGREMIVFQYGRAVKVRKGVE

来源 Source

来源生物 organism	Pyrococcus horikoshii
NCBI 分类编号 ncbi_taxonomy_id	53953
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 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	4

Entity 4 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 5 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	41

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6. 折叠分类 (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d1j2ba1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.122 — PUA domain-like
超家族 Superfamily superfamily	b.122.1 — PUA domain-like
家族 Family family	b.122.1.1 — PUA domain

结构域编号 domain_id	d1j2ba2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.20 — tRNA-guanine transglycosylase
家族 Family family	c.1.20.1 — tRNA-guanine transglycosylase

结构域编号 domain_id	d1j2ba3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.17 — Cystatin-like
超家族 Superfamily superfamily	d.17.6 — Pre-PUA domain
家族 Family family	d.17.6.1 — Archaeosine tRNA-guanine transglycosylase, C2 domain

结构域编号 domain_id	d1j2bb1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.122 — PUA domain-like
超家族 Superfamily superfamily	b.122.1 — PUA domain-like
家族 Family family	b.122.1.1 — PUA domain

结构域编号 domain_id	d1j2bb2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.20 — tRNA-guanine transglycosylase
家族 Family family	c.1.20.1 — tRNA-guanine transglycosylase

结构域编号 domain_id	d1j2bb3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.17 — Cystatin-like
超家族 Superfamily superfamily	d.17.6 — Pre-PUA domain
家族 Family family	d.17.6.1 — Archaeosine tRNA-guanine transglycosylase, C2 domain

CATH v4.4 (8 domains)

结构域编号 domain_id	1j2bA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	105 — Queuine tRNA-ribosyltransferase-like

结构域编号 domain_id	1j2bA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1020 — Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — ArcTGT, C1 domain

结构域编号 domain_id	1j2bA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
同源超家族 H-superfamily homologous superfamily	90 — ArcTGT, C2 domain

结构域编号 domain_id	1j2bA04
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	130 — Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4
同源超家族 H-superfamily homologous superfamily	10 — PUA domain

结构域编号 domain_id	1j2bB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	105 — Queuine tRNA-ribosyltransferase-like

结构域编号 domain_id	1j2bB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1020 — Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — ArcTGT, C1 domain

结构域编号 domain_id	1j2bB03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
同源超家族 H-superfamily homologous superfamily	90 — ArcTGT, C2 domain

结构域编号 domain_id	1j2bB04
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	130 — Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4
同源超家族 H-superfamily homologous superfamily	10 — PUA domain

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7. 引用文献 (1)

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晶胞边长 a length_a	230.834 Å
晶胞边长 b length_b	230.834 Å
晶胞边长 c length_c	269.255 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	120.00 °
晶胞分子数 Z z_pdb	36

空间群 space_group	H 3 2
空间群编号 int_tables_number	155
晶系 crystal_system	—

分辨率 resolution	3.300 Å
最低分辨率 resolution_low	48.540 Å
R 因子 r_factor	0.2250
R_work r_work	0.2250
R_free r_free	0.2880

fit	/app/data/saxs_computation/j2/1j2b/1j2b.fit
pddf	/app/data/pr_computation/j2/1j2b/1j2b.pr.out
profile	/app/data/saxs_computation/j2/1j2b/1j2b.dat

Crystal Structure Of Archaeosine tRNA-Guanine Transglycosylase Complexed With lambda-form tRNA(Val)

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 (5)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 water

6. 折叠分类 (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

CATH v4.4 (8 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)