SAXSdb — 1mda

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1mda
沉积日期 deposition_date	1992-03-02
结构标题 title	CRYSTAL STRUCTURE OF AN ELECTRON-TRANSFER COMPLEX BETWEEN METHYLAMINE DEHYDROGENASE AND AMICYANIN
关键词 keywords	ELECTRON TRANSPORT; 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	32.64 Å
回转半径 Rg (电子) rg_electron	32.13 Å
零角强度 I(0) i0	259952000.00
分子量 molecular_weight	122370.0 kDa
排除体积 excluded_volume	150040 Å³
包络体积 envelope_volume	190920 Å³
水化壳体积 shell_volume	48306 Å³
包络直径 envelope_diameter	112.8 Å
壳层 Rg shell_rg	40.00 Å
包络 Rg envelope_rg	32.15 Å
形状 Rg shape_rg	32.11 Å
总 Rg total_rg	32.76 Å
总原子数 total_atoms	8567
残基数 n_residues	1182
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	102.0 Å
Rg (实空间) rg_real	32.52 Å
Rg 误差 (实空间) rg_real_error	0.49 Å
I(0) (实空间) i0_real	2.6000e+08
I(0) 误差 (实空间) i0_real_error	3.6760e+06
Rg (倒空间) rg_reciprocal	32.57 Å
I(0) (倒空间) i0_reciprocal	260000000.0000
解质量估计 total_estimate	0.9028
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	39.5 Å
偏度 Skewness skewness	0.244
峰度 Kurtosis kurtosis	-0.463
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	42670000.0000
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: 0.934; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.933

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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	METHYLAMINE DEHYDROGENASE (HEAVY SUBUNIT)
分子量 formula_weight	36866.6 kDa
EC 编号 ec_number	1.4.99.3
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	H,J
原子数 atom_count	8567

EKSKVAGSAAAASAAAASDGSSCDHGPGAISRRSHITLPAYFAGTTENWVSCAGCGVTLGHSLGAFLSLAVAGHSGSDFALASTSFARSAKGKRTDYVEVFDPVTFLPIADIELPDAPRFSVGPRVHIIGNCASSACLLFFLFGSSAAAGLSVPGASDDQLTKSASCFHIHPGAAATHYLGSCPASLAASDLAAAPAAAGIVGAQCTGAQNCSSQAAQANYPGMLVWAVASSILQGDIPAAGATMKAAIDGNESGRKADNFRSAGFQMVAKLKNTDGIMILTVEHSRSCLAAAENTSSVTASVGQTSGPISNGHDSDAIIAAQDGASDNYANSAGTEVLDIYDAASDQDQSSVELDKGPESLSVQNEA

来源 Source

来源生物 organism	Paracoccus denitrificans
NCBI 分类编号 ncbi_taxonomy_id	266

Entity 2 polymer

描述 description	METHYLAMINE DEHYDROGENASE (LIGHT SUBUNIT)
分子量 formula_weight	13080.4 kDa
EC 编号 ec_number	1.4.99.3
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

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

VDPRAKWQPQDNDIQACDYWRHCSIAGNICDCSAGSLTSCPPGTLVASGSWVGSCYNPPDPNKYITAYRDCCGYNVSGRCACLNTEGELPVYNKDANDIIWCFGGEDGMTYHCSISPVSGA

来源 Source

来源生物 organism	Paracoccus denitrificans
NCBI 分类编号 ncbi_taxonomy_id	266

Entity 3 polymer

描述 description	AMICYANIN
分子量 formula_weight	11260.9 kDa
来源方法 src_method	man
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

ATIPSESPFAAAEVADGAIVVDIAKMKYETPELHVKVGDTVTWINREAMPHNVHFVAGVLGEAALKGPMMKKEQAYSLTFTEAGTYDYHCTPHPFMRGKVVVE

来源 Source

来源生物 organism	Paracoccus denitrificans
NCBI 分类编号 ncbi_taxonomy_id	266

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	2

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6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d1mdaa_
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	d1mdab_
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	d1mdah_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.69 — 7-bladed beta-propeller
超家族 Superfamily superfamily	b.69.2 — YVTN repeat-like/Quinoprotein amine dehydrogenase
家族 Family family	b.69.2.1 — Methylamine dehydrogenase, H-chain

结构域编号 domain_id	d1mdaj_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.69 — 7-bladed beta-propeller
超家族 Superfamily superfamily	b.69.2 — YVTN repeat-like/Quinoprotein amine dehydrogenase
家族 Family family	b.69.2.1 — Methylamine dehydrogenase, H-chain

结构域编号 domain_id	d1mdal_
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.21.1.1 — Methylamine dehydrogenase, L chain

结构域编号 domain_id	d1mdam_
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.21.1.1 — Methylamine dehydrogenase, L chain

CATH v4.4 (6 domains)

结构域编号 domain_id	1mdaA00
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	1mdaB00
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	1mdaH00
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	1mdaJ00
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	1mdaL00
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	1mdaM00
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 (5)

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晶胞边长 a length_a	124.700 Å
晶胞边长 b length_b	124.700 Å
晶胞边长 c length_c	247.400 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	16

空间群 space_group	P 41 21 2
空间群编号 int_tables_number	92
晶系 crystal_system	—

分辨率 resolution	2.500 Å
最低分辨率 resolution_low	— Å
R 因子 r_factor	0.2850
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/md/1mda/1mda.fit
pddf	/app/data/pr_computation/md/1mda/1mda.pr.out
profile	/app/data/saxs_computation/md/1mda/1mda.dat

CRYSTAL STRUCTURE OF AN ELECTRON-TRANSFER COMPLEX BETWEEN METHYLAMINE DEHYDROGENASE AND AMICYANIN

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

5. 实体与聚合体信息 (4)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 polymer

聚合体 Polymer

来源 Source

Entity 4 non-polymer

6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. 引用文献 (5)

8. 文件与曲线 (10)

Files (7)

Curves (3)