2aag

;Crystal Structures of the Wild-type, Mutant-P1A and Inactivated Malonate Semialdehyde Decarboxylase: A Structural Basis for the Decarboxylase and Hydratase Activities ;

Method: X-RAY DIFFRACTION D_max: 87.5 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	2aag
沉积日期 deposition_date	2005-07-13
结构标题 title	;Crystal Structures of the Wild-type, Mutant-P1A and Inactivated Malonate Semialdehyde Decarboxylase: A Structural Basis for the Decarboxylase and Hydratase Activities ;
关键词 keywords	tautomerase superfamily; beta-alpha-beta; homotrimeric, LYASE; 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	28.65 Å
回转半径 Rg (电子) rg_electron	27.50 Å
零角强度 I(0) i0	117697000.00
分子量 molecular_weight	84513.0 kDa
排除体积 excluded_volume	105420 Å³
包络体积 envelope_volume	122440 Å³
水化壳体积 shell_volume	36536 Å³
包络直径 envelope_diameter	88.9 Å
壳层 Rg shell_rg	35.50 Å
包络 Rg envelope_rg	27.31 Å
形状 Rg shape_rg	27.50 Å
总 Rg total_rg	28.28 Å
总原子数 total_atoms	5952
残基数 n_residues	775
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	87.5 Å
Rg (实空间) rg_real	28.55 Å
Rg 误差 (实空间) rg_real_error	0.64 Å
I(0) (实空间) i0_real	1.1770e+08
I(0) 误差 (实空间) i0_real_error	1.6610e+06
Rg (倒空间) rg_reciprocal	28.59 Å
I(0) (倒空间) i0_reciprocal	117700000.0000
解质量估计 total_estimate	0.9053
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	35.0 Å
偏度 Skewness skewness	0.205
峰度 Kurtosis kurtosis	-0.569
角度范围 angular_range	— – 0.2750 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	35230000.0000
实空间数据点数 n_real_points	56
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.937; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.956

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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) 13 domains

SCOP 2.08 (7 domains)

结构域编号 domain_id	d2aaga_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.80 — Tautomerase/MIF
超家族 Superfamily superfamily	d.80.1 — Tautomerase/MIF
家族 Family family	d.80.1.6 — MSAD-like

结构域编号 domain_id	d2aagb2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.80 — Tautomerase/MIF
超家族 Superfamily superfamily	d.80.1 — Tautomerase/MIF
家族 Family family	d.80.1.6 — MSAD-like

结构域编号 domain_id	d2aagb3
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	d2aagc_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.80 — Tautomerase/MIF
超家族 Superfamily superfamily	d.80.1 — Tautomerase/MIF
家族 Family family	d.80.1.6 — MSAD-like

结构域编号 domain_id	d2aagd_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.80 — Tautomerase/MIF
超家族 Superfamily superfamily	d.80.1 — Tautomerase/MIF
家族 Family family	d.80.1.6 — MSAD-like

结构域编号 domain_id	d2aage_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.80 — Tautomerase/MIF
超家族 Superfamily superfamily	d.80.1 — Tautomerase/MIF
家族 Family family	d.80.1.6 — MSAD-like

结构域编号 domain_id	d2aagf_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.80 — Tautomerase/MIF
超家族 Superfamily superfamily	d.80.1 — Tautomerase/MIF
家族 Family family	d.80.1.6 — MSAD-like

CATH v4.4 (6 domains)

结构域编号 domain_id	2aagA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	429 — Macrophage Migration Inhibitory Factor
同源超家族 H-superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

结构域编号 domain_id	2aagB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	429 — Macrophage Migration Inhibitory Factor
同源超家族 H-superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

结构域编号 domain_id	2aagC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	429 — Macrophage Migration Inhibitory Factor
同源超家族 H-superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

结构域编号 domain_id	2aagD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	429 — Macrophage Migration Inhibitory Factor
同源超家族 H-superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

结构域编号 domain_id	2aagE00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	429 — Macrophage Migration Inhibitory Factor
同源超家族 H-superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

结构域编号 domain_id	2aagF00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	429 — Macrophage Migration Inhibitory Factor
同源超家族 H-superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

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7. 引用文献 (1)

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晶胞边长 a length_a	57.709 Å
晶胞边长 b length_b	82.105 Å
晶胞边长 c length_c	77.603 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	101.15 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	12

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	1.850 Å
最低分辨率 resolution_low	19.210 Å
R 因子 r_factor	0.1810
R_work r_work	0.1783
R_free r_free	0.2318

描述 description	Malonate Semialdehyde Decarboxylase
分子量 formula_weight	14181.0 kDa
EC 编号 ec_number	4.1.1.-
来源方法 src_method	man
拷贝数 entity_count	6

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F
原子数 atom_count	6770

;Crystal Structures of the Wild-type, Mutant-P1A and Inactivated Malonate Semialdehyde Decarboxylase: A Structural Basis for the Decarboxylase and Hydratase Activities ;

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) 13 domains

SCOP 2.08 (7 domains)

CATH v4.4 (6 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)

来源生物 organism	Pseudomonas pavonaceae
NCBI 分类编号 ncbi_taxonomy_id	47881
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	807

fit	/app/data/saxs_computation/aa/2aag/2aag.fit
pddf	/app/data/pr_computation/aa/2aag/2aag.pr.out
profile	/app/data/saxs_computation/aa/2aag/2aag.dat