1kxz

MT0146, the Precorrin-6y methyltransferase (CbiT) homolog from M. Thermoautotrophicum, P1 spacegroup

Method: X-RAY DIFFRACTION D_max: 154.6 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	1kxz
沉积日期 deposition_date	2002-02-01
结构标题 title	MT0146, the Precorrin-6y methyltransferase (CbiT) homolog from M. Thermoautotrophicum, P1 spacegroup
关键词 keywords	structural genomics, beta barrel, rossmann fold, tetramer, methyltransferase, decarboxylase, TRANSFERASE, LYASE; TRANSFERASE, LYASE
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	45.60 Å
回转半径 Rg (电子) rg_electron	45.92 Å
零角强度 I(0) i0	421984000.00
分子量 molecular_weight	162890.0 kDa
排除体积 excluded_volume	200750 Å³
包络体积 envelope_volume	266630 Å³
水化壳体积 shell_volume	50997 Å³
包络直径 envelope_diameter	153.5 Å
壳层 Rg shell_rg	46.80 Å
包络 Rg envelope_rg	45.08 Å
形状 Rg shape_rg	45.96 Å
总 Rg total_rg	45.81 Å
总原子数 total_atoms	11136
残基数 n_residues	1424
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	154.6 Å
Rg (实空间) rg_real	46.02 Å
Rg 误差 (实空间) rg_real_error	1.60 Å
I(0) (实空间) i0_real	4.2200e+08
I(0) 误差 (实空间) i0_real_error	7.8490e+06
Rg (倒空间) rg_reciprocal	45.61 Å
I(0) (倒空间) i0_reciprocal	421800000.0000
解质量估计 total_estimate	0.8023
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	39.8 Å
偏度 Skewness skewness	0.446
峰度 Kurtosis kurtosis	-0.651
角度范围 angular_range	— – 0.1750 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	36800000.0000
实空间数据点数 n_real_points	36
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.708; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.659; Smooth: 0.642

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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) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1kxza_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
超家族 Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
家族 Family family	c.66.1.22 — Precorrin-6Y methyltransferase (CbiT)

结构域编号 domain_id	d1kxzb_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
超家族 Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
家族 Family family	c.66.1.22 — Precorrin-6Y methyltransferase (CbiT)

结构域编号 domain_id	d1kxzc_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
超家族 Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
家族 Family family	c.66.1.22 — Precorrin-6Y methyltransferase (CbiT)

结构域编号 domain_id	d1kxzd_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
超家族 Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
家族 Family family	c.66.1.22 — Precorrin-6Y methyltransferase (CbiT)

结构域编号 domain_id	d1kxze_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
超家族 Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
家族 Family family	c.66.1.22 — Precorrin-6Y methyltransferase (CbiT)

结构域编号 domain_id	d1kxzf_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
超家族 Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
家族 Family family	c.66.1.22 — Precorrin-6Y methyltransferase (CbiT)

结构域编号 domain_id	d1kxzg_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
超家族 Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
家族 Family family	c.66.1.22 — Precorrin-6Y methyltransferase (CbiT)

结构域编号 domain_id	d1kxzh_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
超家族 Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
家族 Family family	c.66.1.22 — Precorrin-6Y methyltransferase (CbiT)

CATH v4.4 (8 domains)

结构域编号 domain_id	1kxzA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

结构域编号 domain_id	1kxzB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

结构域编号 domain_id	1kxzC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

结构域编号 domain_id	1kxzD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

结构域编号 domain_id	1kxzE00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

结构域编号 domain_id	1kxzF00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

结构域编号 domain_id	1kxzG00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

结构域编号 domain_id	1kxzH00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

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7. 引用文献 (1)

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晶胞边长 a length_a	59.100 Å
晶胞边长 b length_b	76.000 Å
晶胞边长 c length_c	97.200 Å
晶胞夹角 α angle_alpha	70.90 °
晶胞夹角 β angle_beta	78.80 °
晶胞夹角 γ angle_gamma	66.70 °
晶胞分子数 Z z_pdb	8

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	2.700 Å
最低分辨率 resolution_low	36.650 Å
R 因子 r_factor	—
R_work r_work	0.2120
R_free r_free	0.2570

描述 description	Precorrin-6y methyltransferase/putative decarboxylase
分子量 formula_weight	21112.1 kDa
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	11247

MT0146, the Precorrin-6y methyltransferase (CbiT) homolog from M. Thermoautotrophicum, P1 spacegroup

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) 16 domains

SCOP 2.08 (8 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	Methanothermobacter thermautotrophicus
NCBI 分类编号 ncbi_taxonomy_id	145262
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	111

fit	/app/data/saxs_computation/kx/1kxz/1kxz.fit
pddf	/app/data/pr_computation/kx/1kxz/1kxz.pr.out
profile	/app/data/saxs_computation/kx/1kxz/1kxz.dat