1q52

Crystal Structure of Mycobacterium tuberculosis MenB, a Key Enzyme in Vitamin K2 Biosynthesis

Method: X-RAY DIFFRACTION D_max: 160.5 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	1q52
沉积日期 deposition_date	2003-08-05
结构标题 title	Crystal Structure of Mycobacterium tuberculosis MenB, a Key Enzyme in Vitamin K2 Biosynthesis
关键词 keywords	LYASE, Structural Genomics, PSI, Protein Structure Initiative, TB Structural Genomics Consortium, TBSGC; 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	47.36 Å
回转半径 Rg (电子) rg_electron	47.11 Å
零角强度 I(0) i0	1930920000.00
分子量 molecular_weight	360870.0 kDa
排除体积 excluded_volume	448790 Å³
包络体积 envelope_volume	551420 Å³
水化壳体积 shell_volume	95281 Å³
包络直径 envelope_diameter	160.4 Å
壳层 Rg shell_rg	52.51 Å
包络 Rg envelope_rg	46.96 Å
形状 Rg shape_rg	47.12 Å
总 Rg total_rg	47.24 Å
总原子数 total_atoms	25503
残基数 n_residues	3240
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	160.5 Å
Rg (实空间) rg_real	47.50 Å
Rg 误差 (实空间) rg_real_error	1.10 Å
I(0) (实空间) i0_real	1.9310e+09
I(0) 误差 (实空间) i0_real_error	3.5810e+07
Rg (倒空间) rg_reciprocal	47.36 Å
I(0) (倒空间) i0_reciprocal	1931000000.0000
解质量估计 total_estimate	0.8528
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	48.6 Å
偏度 Skewness skewness	0.455
峰度 Kurtosis kurtosis	-0.370
角度范围 angular_range	— – 0.1650 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	1017000000.0000
实空间数据点数 n_real_points	34
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.755; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.816

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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) 36 domains

SCOP 2.08 (12 domains)

结构域编号 domain_id	d1q52a_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.14 — ClpP/crotonase
超家族 Superfamily superfamily	c.14.1 — ClpP/crotonase
家族 Family family	c.14.1.3 — Crotonase-like

结构域编号 domain_id	d1q52b_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.14 — ClpP/crotonase
超家族 Superfamily superfamily	c.14.1 — ClpP/crotonase
家族 Family family	c.14.1.3 — Crotonase-like

结构域编号 domain_id	d1q52c_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.14 — ClpP/crotonase
超家族 Superfamily superfamily	c.14.1 — ClpP/crotonase
家族 Family family	c.14.1.3 — Crotonase-like

结构域编号 domain_id	d1q52d_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.14 — ClpP/crotonase
超家族 Superfamily superfamily	c.14.1 — ClpP/crotonase
家族 Family family	c.14.1.3 — Crotonase-like

结构域编号 domain_id	d1q52e_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.14 — ClpP/crotonase
超家族 Superfamily superfamily	c.14.1 — ClpP/crotonase
家族 Family family	c.14.1.3 — Crotonase-like

结构域编号 domain_id	d1q52f_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.14 — ClpP/crotonase
超家族 Superfamily superfamily	c.14.1 — ClpP/crotonase
家族 Family family	c.14.1.3 — Crotonase-like

结构域编号 domain_id	d1q52g_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.14 — ClpP/crotonase
超家族 Superfamily superfamily	c.14.1 — ClpP/crotonase
家族 Family family	c.14.1.3 — Crotonase-like

结构域编号 domain_id	d1q52h_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.14 — ClpP/crotonase
超家族 Superfamily superfamily	c.14.1 — ClpP/crotonase
家族 Family family	c.14.1.3 — Crotonase-like

结构域编号 domain_id	d1q52i_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.14 — ClpP/crotonase
超家族 Superfamily superfamily	c.14.1 — ClpP/crotonase
家族 Family family	c.14.1.3 — Crotonase-like

结构域编号 domain_id	d1q52j_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.14 — ClpP/crotonase
超家族 Superfamily superfamily	c.14.1 — ClpP/crotonase
家族 Family family	c.14.1.3 — Crotonase-like

结构域编号 domain_id	d1q52k_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.14 — ClpP/crotonase
超家族 Superfamily superfamily	c.14.1 — ClpP/crotonase
家族 Family family	c.14.1.3 — Crotonase-like

结构域编号 domain_id	d1q52l_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.14 — ClpP/crotonase
超家族 Superfamily superfamily	c.14.1 — ClpP/crotonase
家族 Family family	c.14.1.3 — Crotonase-like

CATH v4.4 (24 domains)

结构域编号 domain_id	1q52A01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

结构域编号 domain_id	1q52A02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	12 — Lyase 2-enoyl-coa Hydratase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Lyase 2-enoyl-coa Hydratase, Chain A, domain 2

结构域编号 domain_id	1q52B01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

结构域编号 domain_id	1q52B02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	12 — Lyase 2-enoyl-coa Hydratase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Lyase 2-enoyl-coa Hydratase, Chain A, domain 2

结构域编号 domain_id	1q52C01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

结构域编号 domain_id	1q52C02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	12 — Lyase 2-enoyl-coa Hydratase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Lyase 2-enoyl-coa Hydratase, Chain A, domain 2

结构域编号 domain_id	1q52D01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

结构域编号 domain_id	1q52D02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	12 — Lyase 2-enoyl-coa Hydratase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Lyase 2-enoyl-coa Hydratase, Chain A, domain 2

结构域编号 domain_id	1q52E01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

结构域编号 domain_id	1q52E02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	12 — Lyase 2-enoyl-coa Hydratase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Lyase 2-enoyl-coa Hydratase, Chain A, domain 2

结构域编号 domain_id	1q52F01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

结构域编号 domain_id	1q52F02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	12 — Lyase 2-enoyl-coa Hydratase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Lyase 2-enoyl-coa Hydratase, Chain A, domain 2

结构域编号 domain_id	1q52G01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

结构域编号 domain_id	1q52G02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	12 — Lyase 2-enoyl-coa Hydratase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Lyase 2-enoyl-coa Hydratase, Chain A, domain 2

结构域编号 domain_id	1q52H01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

结构域编号 domain_id	1q52H02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	12 — Lyase 2-enoyl-coa Hydratase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Lyase 2-enoyl-coa Hydratase, Chain A, domain 2

结构域编号 domain_id	1q52I01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

结构域编号 domain_id	1q52I02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	12 — Lyase 2-enoyl-coa Hydratase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Lyase 2-enoyl-coa Hydratase, Chain A, domain 2

结构域编号 domain_id	1q52J01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

结构域编号 domain_id	1q52J02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	12 — Lyase 2-enoyl-coa Hydratase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Lyase 2-enoyl-coa Hydratase, Chain A, domain 2

结构域编号 domain_id	1q52K01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

结构域编号 domain_id	1q52K02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	12 — Lyase 2-enoyl-coa Hydratase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Lyase 2-enoyl-coa Hydratase, Chain A, domain 2

结构域编号 domain_id	1q52L01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

结构域编号 domain_id	1q52L02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	12 — Lyase 2-enoyl-coa Hydratase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Lyase 2-enoyl-coa Hydratase, Chain A, domain 2

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7. 引用文献 (1)

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晶胞边长 a length_a	90.375 Å
晶胞边长 b length_b	139.432 Å
晶胞边长 c length_c	142.027 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	97.29 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	24

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	1.800 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	0.1975
R_work r_work	0.1954
R_free r_free	0.2186

描述 description	menB
分子量 formula_weight	34731.9 kDa
EC 编号 ec_number	4.1.3.36
来源方法 src_method	man
拷贝数 entity_count	12

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H,I,J,K,L
原子数 atom_count	28487

Crystal Structure of Mycobacterium tuberculosis MenB, a Key Enzyme in Vitamin K2 Biosynthesis

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) 36 domains

SCOP 2.08 (12 domains)

CATH v4.4 (24 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)

来源生物 organism	Mycobacterium tuberculosis
NCBI 分类编号 ncbi_taxonomy_id	83332
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	2984

fit	/app/data/saxs_computation/q5/1q52/1q52.fit
pddf	/app/data/pr_computation/q5/1q52/1q52.pr.out
profile	/app/data/saxs_computation/q5/1q52/1q52.dat