SAXSdb — 2agl

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2agl
沉积日期 deposition_date	2005-07-27
结构标题 title	Crystal structure of the phenylhydrazine adduct of aromatic amine dehydrogenase from Alcaligenes faecalis
关键词 keywords	OXIDOREDUCTASE; 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	30.53 Å
回转半径 Rg (电子) rg_electron	29.98 Å
零角强度 I(0) i0	183340000.00
分子量 molecular_weight	104520.0 kDa
排除体积 excluded_volume	129040 Å³
包络体积 envelope_volume	151660 Å³
水化壳体积 shell_volume	41066 Å³
包络直径 envelope_diameter	103.1 Å
壳层 Rg shell_rg	38.17 Å
包络 Rg envelope_rg	30.17 Å
形状 Rg shape_rg	29.99 Å
总 Rg total_rg	30.61 Å
总原子数 total_atoms	7338
残基数 n_residues	946
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	99.1 Å
Rg (实空间) rg_real	30.52 Å
Rg 误差 (实空间) rg_real_error	0.43 Å
I(0) (实空间) i0_real	1.8330e+08
I(0) 误差 (实空间) i0_real_error	2.3780e+06
Rg (倒空间) rg_reciprocal	30.52 Å
I(0) (倒空间) i0_reciprocal	183300000.0000
解质量估计 total_estimate	0.8906
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	34.3 Å
偏度 Skewness skewness	0.353
峰度 Kurtosis kurtosis	-0.371
角度范围 angular_range	— – 0.2600 Å⁻¹
当前正则化参数 α current_alpha	0.0002
最高正则化参数 α highest_alpha	36430000.0000
实空间数据点数 n_real_points	53
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.886; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.920

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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 (4)

Entity 1 polymer

描述 description	Aromatic amine dehydrogenase
分子量 formula_weight	14516.9 kDa
EC 编号 ec_number	1.4.99.4
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	D,H
原子数 atom_count	8464

AGGGGSSSGADHISLNPDLANEDEVNSCDYWRHCAVDGFLCSCCGGTTTTCPPGSTPSPISWIGTCHNPHDGKDYLISYHDCCGKTACGRCQCNTQTRERPGYEFFLHNDVNWCMANENSTFHCTTSVLVGLAKN

Entity 2 polymer

描述 description	Aromatic amine dehydrogenase
分子量 formula_weight	40016.1 kDa
EC 编号 ec_number	1.4.99.4
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B

REVLTGGHSVSAPQENRIYVMDSVFMHLTESRVHVYDYTNGKFLGMVPTAFNGHVQVSNDGKKIYTMTTYHERITRGKRSDVVEVWDADKLTFEKEISLPPKRVQGLNYDGLFRQTTDGKFIVLQNASPATSIGIVDVAKGDYVEDVTAAAGCWSVIPQPNRPRSFMTICGDGGLLTINLGEDGKVASQSRSKQMFSVKDDPIFIAPALDKDKAHFVSYYGNVYSADFSGDEVKVDGPWSLLNDEDKAKNWVPGGYNLVGLHRASGRMYVFMHPDGKEGTHKFPAAEIWVMDTKTKQRVARIPGRDALSMTIDQQRNLMLTLDGGNVNVYDISQPEPKLLRTIEGAAEASLQVQFHPVGGT

Entity 3 non-polymer

描述 description	1-PHENYLHYDRAZINE
分子量 formula_weight	108.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	1073

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6. 折叠分类 (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d2agld_
类 Class class	g — Small proteins
折叠类型 Fold fold	g.21 — Methylamine dehydrogenase, L chain
超家族 Superfamily superfamily	g.21.1 — Methylamine dehydrogenase, L chain
家族 Family family	g.21.1.0 — automated matches

结构域编号 domain_id	d2aglh_
类 Class class	g — Small proteins
折叠类型 Fold fold	g.21 — Methylamine dehydrogenase, L chain
超家族 Superfamily superfamily	g.21.1 — Methylamine dehydrogenase, L chain
家族 Family family	g.21.1.0 — automated matches

CATH v4.4 (4 domains)

结构域编号 domain_id	2aglA01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	130 — 7 Propeller
拓扑 Topology topology	10 — Methylamine Dehydrogenase; Chain H
同源超家族 H-superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

结构域编号 domain_id	2aglB01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	130 — 7 Propeller
拓扑 Topology topology	10 — Methylamine Dehydrogenase; Chain H
同源超家族 H-superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

结构域编号 domain_id	2aglD00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	30 — Electron Transport Ethylamine Dehydrogenase
同源超家族 H-superfamily homologous superfamily	10 — Methylamine/Aralkylamine dehydrogenase light chain

结构域编号 domain_id	2aglH00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	30 — Electron Transport Ethylamine Dehydrogenase
同源超家族 H-superfamily homologous superfamily	10 — Methylamine/Aralkylamine dehydrogenase light chain

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7. 引用文献 (1)

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晶胞边长 a length_a	70.692 Å
晶胞边长 b length_b	88.667 Å
晶胞边长 c length_c	80.522 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.24 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

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	1.400 Å
最低分辨率 resolution_low	15.000 Å
R 因子 r_factor	0.1720
R_work r_work	0.1700
R_free r_free	0.1960

fit	/app/data/saxs_computation/ag/2agl/2agl.fit
pddf	/app/data/pr_computation/ag/2agl/2agl.pr.out
profile	/app/data/saxs_computation/ag/2agl/2agl.dat

Crystal structure of the phenylhydrazine adduct of aromatic amine dehydrogenase from Alcaligenes faecalis

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 (4)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 non-polymer

Entity 4 water

6. 折叠分类 (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)