SAXSdb — 2iaa

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2iaa
沉积日期 deposition_date	2006-09-07
结构标题 title	;Crystal Structure of an Electron Transfer Complex Between Aromatic Amine Dephydrogenase and Azurin from Alcaligenes Faecalis (Form 2) ;
关键词 keywords	Quinoprotein, tryptophan tryptophylquinone, cupredoxin, electron transfer, OXIDOREDUCTASE-electron transport COMPLEX; OXIDOREDUCTASE/electron transport
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	32.63 Å
回转半径 Rg (电子) rg_electron	32.27 Å
零角强度 I(0) i0	232703000.00
分子量 molecular_weight	118370.0 kDa
排除体积 excluded_volume	146170 Å³
包络体积 envelope_volume	176690 Å³
水化壳体积 shell_volume	44981 Å³
包络直径 envelope_diameter	115.3 Å
壳层 Rg shell_rg	39.65 Å
包络 Rg envelope_rg	32.61 Å
形状 Rg shape_rg	32.26 Å
总 Rg total_rg	32.82 Å
总原子数 total_atoms	8302
残基数 n_residues	1070
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	106.8 Å
Rg (实空间) rg_real	32.66 Å
Rg 误差 (实空间) rg_real_error	0.83 Å
I(0) (实空间) i0_real	2.3270e+08
I(0) 误差 (实空间) i0_real_error	3.7700e+06
Rg (倒空间) rg_reciprocal	32.65 Å
I(0) (倒空间) i0_reciprocal	232700000.0000
解质量估计 total_estimate	0.8824
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	37.1 Å
偏度 Skewness skewness	0.392
峰度 Kurtosis kurtosis	-0.321
角度范围 angular_range	— – 0.2450 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	44730000.0000
实空间数据点数 n_real_points	50
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.871; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.859

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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 (5)

Entity 1 polymer

描述 description	Aromatic Amine Dehydrogenase
分子量 formula_weight	42978.8 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,D
原子数 atom_count	9307

MKSKFKLTTAAAMLGLMVLAGGAQAQDKPREVLTGGHSVSAPQENRIYVMDSVFMHLTESRVHVYDYTNGKFLGMVPTAFNGHVQVSNDGKKIYTMTTYHERITRGKRSDVVEVWDADKLTFEKEISLPPKRVQGLNYDGLFRQTTDGKFIVLQNASPATSIGIVDVAKGDYVEDVTAAAGCWSVIPQPNRPRSFMTICGDGGLLTINLGEDGKVASQSRSKQMFSVKDDPIFIAPALDKDKAHFVSYYGNVYSADFSGDEVKVDGPWSLLNDEDKAKNWVPGGYNLVGLHRASGRMYVFMHPDGKEGTHKFPAAEIWVMDTKTKQRVARIPGRDALSMTIDQQRNLMLTLDGGNVNVYDISQPEPKLLRTIEGAAEASLQVQFHPVGGV

Entity 2 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	B,E

AGGGGSSSGADHISLNPDLANEDEVNSCDYWRHCAVDGFLCSCCGGTTTTCPPGSTPSPISWIGTCHNPHDGKDYLISYHDCCGKTACGRCQCNTQTRERPGYEFFLHNDVNWCMANENSTFHCTTSVLVGLAKN

Entity 3 polymer

描述 description	Azurin
分子量 formula_weight	13711.4 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C

ACDVSIEGNDSMQFNTKSIVVDKTCKEFTINLKHTGKLPKAAMGHNVVVSKKSDESAVATDGMKAGLNNDYVKAGDERVIAHTSVIGGGETDSVTFDVSKLKEGEDYAFFCSFPGHWSIMKGTIELGS

Entity 4 non-polymer

描述 description	COPPER (II) ION
分子量 formula_weight	63.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 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	989

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (3 domains)

结构域编号 domain_id	d2iaab_
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	d2iaac_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.6 — Cupredoxin-like
超家族 Superfamily superfamily	b.6.1 — Cupredoxins
家族 Family family	b.6.1.1 — Plastocyanin/azurin-like

结构域编号 domain_id	d2iaae_
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 (5 domains)

结构域编号 domain_id	2iaaA01
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	2iaaB00
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	2iaaC00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

结构域编号 domain_id	2iaaD01
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	2iaaE00
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 (2)

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晶胞边长 a length_a	67.216 Å
晶胞边长 b length_b	131.722 Å
晶胞边长 c length_c	133.204 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	1.950 Å
最低分辨率 resolution_low	47.040 Å
R 因子 r_factor	0.1740
R_work r_work	0.1740
R_free r_free	0.2050

fit	/app/data/saxs_computation/ia/2iaa/2iaa.fit
pddf	/app/data/pr_computation/ia/2iaa/2iaa.pr.out
profile	/app/data/saxs_computation/ia/2iaa/2iaa.dat

;Crystal Structure of an Electron Transfer Complex Between Aromatic Amine Dephydrogenase and Azurin from Alcaligenes Faecalis (Form 2) ;

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 (5)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

Entity 4 non-polymer

Entity 5 water

6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (3 domains)

CATH v4.4 (5 domains)

7. 引用文献 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)