1gz0

;23S RIBOSOMAL RNA G2251 2'O-METHYLTRANSFERASE RLMB ;

Method: X-RAY DIFFRACTION D_max: 137.0 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	1gz0
沉积日期 deposition_date	2002-05-03
结构标题 title	;23S RIBOSOMAL RNA G2251 2'O-METHYLTRANSFERASE RLMB ;
关键词 keywords	;TRANSFERASE, METHYLTRANSFERASE, 2'O-METHYLTRANSFERASE, KNOT, MONTREAL- KINGSTON BACTERIAL STRUCTURAL GENOMICS INITIATIVE, BSGI, STRUCTURAL GENOMICS ;; 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	42.63 Å
回转半径 Rg (电子) rg_electron	42.32 Å
零角强度 I(0) i0	642775000.00
分子量 molecular_weight	199600.0 kDa
排除体积 excluded_volume	245920 Å³
包络体积 envelope_volume	346740 Å³
水化壳体积 shell_volume	66844 Å³
包络直径 envelope_diameter	153.0 Å
壳层 Rg shell_rg	48.62 Å
包络 Rg envelope_rg	42.00 Å
形状 Rg shape_rg	42.37 Å
总 Rg total_rg	42.44 Å
总原子数 total_atoms	13776
残基数 n_residues	1749
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	137.0 Å
Rg (实空间) rg_real	42.46 Å
Rg 误差 (实空间) rg_real_error	0.96 Å
I(0) (实空间) i0_real	6.4280e+08
I(0) 误差 (实空间) i0_real_error	1.1210e+07
Rg (倒空间) rg_reciprocal	42.63 Å
I(0) (倒空间) i0_reciprocal	642900000.0000
解质量估计 total_estimate	0.8868
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	55.5 Å
偏度 Skewness skewness	0.154
峰度 Kurtosis kurtosis	-0.416
角度范围 angular_range	— – 0.1850 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	61130000.0000
实空间数据点数 n_real_points	38
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.888; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.872

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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 (2)

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6. 折叠分类 (SCOP + CATH) 32 domains

SCOP 2.08 (18 domains)

结构域编号 domain_id	d1gz0a1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.116 — alpha/beta knot
超家族 Superfamily superfamily	c.116.1 — alpha/beta knot
家族 Family family	c.116.1.1 — SpoU-like RNA 2'-O ribose methyltransferase

结构域编号 domain_id	d1gz0a2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.79 — Bacillus chorismate mutase-like
超家族 Superfamily superfamily	d.79.3 — L30e-like
家族 Family family	d.79.3.3 — RNA 2'-O ribose methyltransferase substrate binding domain

结构域编号 domain_id	d1gz0b1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.116 — alpha/beta knot
超家族 Superfamily superfamily	c.116.1 — alpha/beta knot
家族 Family family	c.116.1.1 — SpoU-like RNA 2'-O ribose methyltransferase

结构域编号 domain_id	d1gz0b2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.79 — Bacillus chorismate mutase-like
超家族 Superfamily superfamily	d.79.3 — L30e-like
家族 Family family	d.79.3.3 — RNA 2'-O ribose methyltransferase substrate binding domain

结构域编号 domain_id	d1gz0b3
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d1gz0c1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.116 — alpha/beta knot
超家族 Superfamily superfamily	c.116.1 — alpha/beta knot
家族 Family family	c.116.1.1 — SpoU-like RNA 2'-O ribose methyltransferase

结构域编号 domain_id	d1gz0c2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.79 — Bacillus chorismate mutase-like
超家族 Superfamily superfamily	d.79.3 — L30e-like
家族 Family family	d.79.3.3 — RNA 2'-O ribose methyltransferase substrate binding domain

结构域编号 domain_id	d1gz0d1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.116 — alpha/beta knot
超家族 Superfamily superfamily	c.116.1 — alpha/beta knot
家族 Family family	c.116.1.1 — SpoU-like RNA 2'-O ribose methyltransferase

结构域编号 domain_id	d1gz0d2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.79 — Bacillus chorismate mutase-like
超家族 Superfamily superfamily	d.79.3 — L30e-like
家族 Family family	d.79.3.3 — RNA 2'-O ribose methyltransferase substrate binding domain

结构域编号 domain_id	d1gz0d3
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d1gz0e1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.116 — alpha/beta knot
超家族 Superfamily superfamily	c.116.1 — alpha/beta knot
家族 Family family	c.116.1.1 — SpoU-like RNA 2'-O ribose methyltransferase

结构域编号 domain_id	d1gz0f1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.116 — alpha/beta knot
超家族 Superfamily superfamily	c.116.1 — alpha/beta knot
家族 Family family	c.116.1.1 — SpoU-like RNA 2'-O ribose methyltransferase

结构域编号 domain_id	d1gz0f2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.79 — Bacillus chorismate mutase-like
超家族 Superfamily superfamily	d.79.3 — L30e-like
家族 Family family	d.79.3.3 — RNA 2'-O ribose methyltransferase substrate binding domain

结构域编号 domain_id	d1gz0f3
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d1gz0g1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.116 — alpha/beta knot
超家族 Superfamily superfamily	c.116.1 — alpha/beta knot
家族 Family family	c.116.1.1 — SpoU-like RNA 2'-O ribose methyltransferase

结构域编号 domain_id	d1gz0h1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.116 — alpha/beta knot
超家族 Superfamily superfamily	c.116.1 — alpha/beta knot
家族 Family family	c.116.1.1 — SpoU-like RNA 2'-O ribose methyltransferase

结构域编号 domain_id	d1gz0h2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.79 — Bacillus chorismate mutase-like
超家族 Superfamily superfamily	d.79.3 — L30e-like
家族 Family family	d.79.3.3 — RNA 2'-O ribose methyltransferase substrate binding domain

结构域编号 domain_id	d1gz0h3
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

CATH v4.4 (14 domains)

结构域编号 domain_id	1gz0A01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
同源超家族 H-superfamily homologous superfamily	30 — Ribosomal protein L30/S12

结构域编号 domain_id	1gz0A02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1280 — Alpha/beta knot
同源超家族 H-superfamily homologous superfamily	10 — SPOUT methyltransferase, trefoil knot domain

结构域编号 domain_id	1gz0B01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
同源超家族 H-superfamily homologous superfamily	30 — Ribosomal protein L30/S12

结构域编号 domain_id	1gz0B02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1280 — Alpha/beta knot
同源超家族 H-superfamily homologous superfamily	10 — SPOUT methyltransferase, trefoil knot domain

结构域编号 domain_id	1gz0C01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
同源超家族 H-superfamily homologous superfamily	30 — Ribosomal protein L30/S12

结构域编号 domain_id	1gz0C02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1280 — Alpha/beta knot
同源超家族 H-superfamily homologous superfamily	10 — SPOUT methyltransferase, trefoil knot domain

结构域编号 domain_id	1gz0D01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
同源超家族 H-superfamily homologous superfamily	30 — Ribosomal protein L30/S12

结构域编号 domain_id	1gz0D02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1280 — Alpha/beta knot
同源超家族 H-superfamily homologous superfamily	10 — SPOUT methyltransferase, trefoil knot domain

结构域编号 domain_id	1gz0E00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1280 — Alpha/beta knot
同源超家族 H-superfamily homologous superfamily	10 — SPOUT methyltransferase, trefoil knot domain

结构域编号 domain_id	1gz0F01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
同源超家族 H-superfamily homologous superfamily	30 — Ribosomal protein L30/S12

结构域编号 domain_id	1gz0F02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1280 — Alpha/beta knot
同源超家族 H-superfamily homologous superfamily	10 — SPOUT methyltransferase, trefoil knot domain

结构域编号 domain_id	1gz0G00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1280 — Alpha/beta knot
同源超家族 H-superfamily homologous superfamily	10 — SPOUT methyltransferase, trefoil knot domain

结构域编号 domain_id	1gz0H01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
同源超家族 H-superfamily homologous superfamily	30 — Ribosomal protein L30/S12

结构域编号 domain_id	1gz0H02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1280 — Alpha/beta knot
同源超家族 H-superfamily homologous superfamily	10 — SPOUT methyltransferase, trefoil knot domain

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7. 引用文献 (1)

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晶胞边长 a length_a	87.478 Å
晶胞边长 b length_b	132.288 Å
晶胞边长 c length_c	90.710 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	96.40 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	16

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	2.500 Å
最低分辨率 resolution_low	46.860 Å
R 因子 r_factor	0.2310
R_work r_work	0.2310
R_free r_free	0.2790

描述 description	HYPOTHETICAL TRNA/RRNA METHYLTRANSFERASE YJFH
分子量 formula_weight	27944.9 kDa
EC 编号 ec_number	2.1.1.-
来源方法 src_method	man
拷贝数 entity_count	8

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H
原子数 atom_count	13953

;23S RIBOSOMAL RNA G2251 2'O-METHYLTRANSFERASE RLMB ;

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 (2)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 water

6. 折叠分类 (SCOP + CATH) 32 domains

SCOP 2.08 (18 domains)

CATH v4.4 (14 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)

来源生物 organism	ESCHERICHIA COLI
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	ESCHERICHIA COLI

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	177

fit	/app/data/saxs_computation/gz/1gz0/1gz0.fit
pddf	/app/data/pr_computation/gz/1gz0/1gz0.pr.out
profile	/app/data/saxs_computation/gz/1gz0/1gz0.dat