1wyz

;X-Ray structure of the putative methyltransferase from Bacteroides thetaiotaomicron VPI-5482 at the resolution 2.5 A. Norteast Structural Genomics Consortium target Btr28 ;

Method: X-RAY DIFFRACTION D_max: 115.1 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

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1wyz
沉积日期 deposition_date	2005-02-21
结构标题 title	;X-Ray structure of the putative methyltransferase from Bacteroides thetaiotaomicron VPI-5482 at the resolution 2.5 A. Norteast Structural Genomics Consortium target Btr28 ;
关键词 keywords	Northeast Structural Genomics Consortium, BtR28, methyltransferase, PSI, Protein Structure Initiative, NESG, TRANSFERASE; TRANSFERASE
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	35.69 Å
回转半径 Rg (电子) rg_electron	35.33 Å
零角强度 I(0) i0	149535000.00
分子量 molecular_weight	101640.0 kDa
排除体积 excluded_volume	128640 Å³
包络体积 envelope_volume	167530 Å³
水化壳体积 shell_volume	40704 Å³
包络直径 envelope_diameter	122.1 Å
壳层 Rg shell_rg	40.48 Å
包络 Rg envelope_rg	34.97 Å
形状 Rg shape_rg	35.33 Å
总 Rg total_rg	35.69 Å
总原子数 total_atoms	7119
残基数 n_residues	888
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	115.1 Å
Rg (实空间) rg_real	35.87 Å
Rg 误差 (实空间) rg_real_error	0.90 Å
I(0) (实空间) i0_real	1.4950e+08
I(0) 误差 (实空间) i0_real_error	2.2010e+06
Rg (倒空间) rg_reciprocal	35.76 Å
I(0) (倒空间) i0_reciprocal	149500000.0000
解质量估计 total_estimate	0.8511
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	36.6 Å
偏度 Skewness skewness	0.445
峰度 Kurtosis kurtosis	-0.508
角度范围 angular_range	— – 0.2200 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	19970000.0000
实空间数据点数 n_real_points	45
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.825; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.929; Smooth: 0.655

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (2)

▼

6. 折叠分类 (SCOP + CATH) 15 domains

SCOP 2.08 (7 domains)

结构域编号 domain_id	d1wyza1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.90 — Tetrapyrrole methylase
超家族 Superfamily superfamily	c.90.1 — Tetrapyrrole methylase
家族 Family family	c.90.1.1 — Tetrapyrrole methylase

结构域编号 domain_id	d1wyzb2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.90 — Tetrapyrrole methylase
超家族 Superfamily superfamily	c.90.1 — Tetrapyrrole methylase
家族 Family family	c.90.1.1 — Tetrapyrrole methylase

结构域编号 domain_id	d1wyzb3
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	d1wyzc2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.90 — Tetrapyrrole methylase
超家族 Superfamily superfamily	c.90.1 — Tetrapyrrole methylase
家族 Family family	c.90.1.1 — Tetrapyrrole methylase

结构域编号 domain_id	d1wyzc3
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	d1wyzd2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.90 — Tetrapyrrole methylase
超家族 Superfamily superfamily	c.90.1 — Tetrapyrrole methylase
家族 Family family	c.90.1.1 — Tetrapyrrole methylase

结构域编号 domain_id	d1wyzd3
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 (8 domains)

结构域编号 domain_id	1wyzA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1010 — Cobalt-precorrin-4 Transmethylase; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Tetrapyrrole methylase, N-terminal domain

结构域编号 domain_id	1wyzA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	950 — Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2
同源超家族 H-superfamily homologous superfamily	10 — Tetrapyrrole methylase, C-terminal domain

结构域编号 domain_id	1wyzB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1010 — Cobalt-precorrin-4 Transmethylase; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Tetrapyrrole methylase, N-terminal domain

结构域编号 domain_id	1wyzB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	950 — Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2
同源超家族 H-superfamily homologous superfamily	10 — Tetrapyrrole methylase, C-terminal domain

结构域编号 domain_id	1wyzC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1010 — Cobalt-precorrin-4 Transmethylase; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Tetrapyrrole methylase, N-terminal domain

结构域编号 domain_id	1wyzC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	950 — Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2
同源超家族 H-superfamily homologous superfamily	10 — Tetrapyrrole methylase, C-terminal domain

结构域编号 domain_id	1wyzD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1010 — Cobalt-precorrin-4 Transmethylase; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Tetrapyrrole methylase, N-terminal domain

结构域编号 domain_id	1wyzD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	950 — Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2
同源超家族 H-superfamily homologous superfamily	10 — Tetrapyrrole methylase, C-terminal domain

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	85.785 Å
晶胞边长 b length_b	101.542 Å
晶胞边长 c length_c	108.802 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	16

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	2.500 Å
最低分辨率 resolution_low	28.740 Å
R 因子 r_factor	0.2260
R_work r_work	0.2260
R_free r_free	0.2930

描述 description	putative S-adenosylmethionine-dependent methyltransferase
分子量 formula_weight	27391.0 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	7245

;X-Ray structure of the putative methyltransferase from Bacteroides thetaiotaomicron VPI-5482 at the resolution 2.5 A. Norteast Structural Genomics Consortium target Btr28 ;

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) 15 domains

SCOP 2.08 (7 domains)

CATH v4.4 (8 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)

来源生物 organism	Bacteroides thetaiotaomicron
NCBI 分类编号 ncbi_taxonomy_id	226186
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	126

fit	/app/data/saxs_computation/wy/1wyz/1wyz.fit
pddf	/app/data/pr_computation/wy/1wyz/1wyz.pr.out
profile	/app/data/saxs_computation/wy/1wyz/1wyz.dat