2c2x

Three dimensional structure of bifunctional methylenetetrahydrofolate dehydrogenase-cyclohydrolase from Mycobacterium tuberculosis

Method: X-RAY DIFFRACTION D_max: 76.3 Å Quality: EXCELLENT

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	2c2x
沉积日期 deposition_date	2005-09-30
结构标题 title	Three dimensional structure of bifunctional methylenetetrahydrofolate dehydrogenase-cyclohydrolase from Mycobacterium tuberculosis
关键词 keywords	;TETRAHYDROFOLATE, NADP, METHYLENETETRAHYDROFOLATE DEHYDROGENASE, CYCLOHYDROLASE, HYDROLASE, OXIDOREDUCTASE, PSI, PROTEIN STRUCTURE INITIATIVE, TB STRUCTURAL GENOMICS CONSORTIUM, TBSGC ;; OXIDOREDUCTASE
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	25.89 Å
回转半径 Rg (电子) rg_electron	24.66 Å
零角强度 I(0) i0	58897500.00
分子量 molecular_weight	58661.0 kDa
排除体积 excluded_volume	73229 Å³
包络体积 envelope_volume	88235 Å³
水化壳体积 shell_volume	29483 Å³
包络直径 envelope_diameter	77.3 Å
壳层 Rg shell_rg	32.05 Å
包络 Rg envelope_rg	24.53 Å
形状 Rg shape_rg	24.68 Å
总 Rg total_rg	25.41 Å
总原子数 total_atoms	4124
残基数 n_residues	560
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	76.3 Å
Rg (实空间) rg_real	25.74 Å
Rg 误差 (实空间) rg_real_error	0.49 Å
I(0) (实空间) i0_real	5.8900e+07
I(0) 误差 (实空间) i0_real_error	8.2850e+05
Rg (倒空间) rg_reciprocal	25.79 Å
I(0) (倒空间) i0_reciprocal	58900000.0000
解质量估计 total_estimate	0.9160
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	32.5 Å
偏度 Skewness skewness	0.096
峰度 Kurtosis kurtosis	-0.627
角度范围 angular_range	— – 0.3050 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	7182000.0000
实空间数据点数 n_real_points	62
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.981; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.969

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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	d2c2xa1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.58 — Aminoacid dehydrogenase-like, N-terminal domain
超家族 Superfamily superfamily	c.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
家族 Family family	c.58.1.0 — automated matches

结构域编号 domain_id	d2c2xa2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family family	c.2.1.0 — automated matches

结构域编号 domain_id	d2c2xb1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.58 — Aminoacid dehydrogenase-like, N-terminal domain
超家族 Superfamily superfamily	c.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
家族 Family family	c.58.1.0 — automated matches

结构域编号 domain_id	d2c2xb2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family family	c.2.1.0 — automated matches

CATH v4.4 (4 domains)

结构域编号 domain_id	2c2xA01
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	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	2c2xA02
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	10860 — Leucine Dehydrogenase, chain A, domain 1

结构域编号 domain_id	2c2xB01
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	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	2c2xB02
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	10860 — Leucine Dehydrogenase, chain A, domain 1

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7. 引用文献 (1)

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晶胞边长 a length_a	59.511 Å
晶胞边长 b length_b	86.760 Å
晶胞边长 c length_c	111.539 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	8

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	2.000 Å
最低分辨率 resolution_low	111.800 Å
R 因子 r_factor	0.2080
R_work r_work	0.2060
R_free r_free	0.2480

描述 description	METHYLENETETRAHYDROFOLATE DEHYDROGENASE-METHENYLTETRAHYDROFOLATE CYCLOHYDROLASE
分子量 formula_weight	29488.7 kDa
EC 编号 ec_number	1.5.1.5, 3.5.4.9
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	4384

Three dimensional structure of bifunctional methylenetetrahydrofolate dehydrogenase-cyclohydrolase from Mycobacterium tuberculosis

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) 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	MYCOBACTERIUM TUBERCULOSIS
NCBI 分类编号 ncbi_taxonomy_id	83332
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	260

fit	/app/data/saxs_computation/c2/2c2x/2c2x.fit
pddf	/app/data/pr_computation/c2/2c2x/2c2x.pr.out
profile	/app/data/saxs_computation/c2/2c2x/2c2x.dat