1k3r

Crystal Structure of the Methyltransferase with a Knot from Methanobacterium thermoautotrophicum

Method: X-RAY DIFFRACTION D_max: 95.8 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	1k3r
沉积日期 deposition_date	2001-10-03
结构标题 title	Crystal Structure of the Methyltransferase with a Knot from Methanobacterium thermoautotrophicum
关键词 keywords	beta barrel, Structural Genomics, PSI, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, UNKNOWN FUNCTION; STRUCTURAL GENOMICS, UNKNOWN FUNCTION
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	26.26 Å
回转半径 Rg (电子) rg_electron	25.59 Å
零角强度 I(0) i0	54389200.00
分子量 molecular_weight	59126.0 kDa
排除体积 excluded_volume	74882 Å³
包络体积 envelope_volume	89952 Å³
水化壳体积 shell_volume	30041 Å³
包络直径 envelope_diameter	104.0 Å
壳层 Rg shell_rg	32.14 Å
包络 Rg envelope_rg	26.10 Å
形状 Rg shape_rg	25.53 Å
总 Rg total_rg	26.48 Å
总原子数 total_atoms	4158
残基数 n_residues	526
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	95.8 Å
Rg (实空间) rg_real	26.31 Å
Rg 误差 (实空间) rg_real_error	0.79 Å
I(0) (实空间) i0_real	5.4390e+07
I(0) 误差 (实空间) i0_real_error	7.7970e+05
Rg (倒空间) rg_reciprocal	26.30 Å
I(0) (倒空间) i0_reciprocal	54390000.0000
解质量估计 total_estimate	0.8300
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	31.9 Å
偏度 Skewness skewness	0.510
峰度 Kurtosis kurtosis	0.211
角度范围 angular_range	— – 0.3000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	12230000.0000
实空间数据点数 n_real_points	61
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.637; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.922; Smooth: 0.952

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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) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1k3ra1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.40 — OB-fold
超家族 Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
家族 Family family	b.40.4.10 — Hypothetical protein MTH1 (MT0001), insert domain

结构域编号 domain_id	d1k3ra2
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.116.1.2 — Hypothetical protein MTH1 (MT0001), dimerisation domain

结构域编号 domain_id	d1k3rb1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.40 — OB-fold
超家族 Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
家族 Family family	b.40.4.10 — Hypothetical protein MTH1 (MT0001), insert domain

结构域编号 domain_id	d1k3rb2
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.116.1.2 — Hypothetical protein MTH1 (MT0001), dimerisation domain

CATH v4.4 (4 domains)

结构域编号 domain_id	1k3rA01
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	1k3rA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	140 — Nucleic acid-binding proteins

结构域编号 domain_id	1k3rB01
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	1k3rB02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	140 — Nucleic acid-binding proteins

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7. 引用文献 (1)

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晶胞边长 a length_a	101.307 Å
晶胞边长 b length_b	51.353 Å
晶胞边长 c length_c	109.250 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	94.69 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

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	2.300 Å
最低分辨率 resolution_low	500.000 Å
R 因子 r_factor	0.2270
R_work r_work	0.2214
R_free r_free	0.2773

描述 description	conserved protein MT0001
分子量 formula_weight	30235.0 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	4278

Crystal Structure of the Methyltransferase with a Knot from Methanobacterium thermoautotrophicum

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

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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 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 BL21(DE3)

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	120

fit	/app/data/saxs_computation/k3/1k3r/1k3r.fit
pddf	/app/data/pr_computation/k3/1k3r/1k3r.pr.out
profile	/app/data/saxs_computation/k3/1k3r/1k3r.dat