2gc7

Substrate reduced, copper free complex of methylamine dehydrogenase, amicyanin and cytochrome c551i from Paracoccus denitrificans.

Method: X-RAY DIFFRACTION D_max: 194.2 Å Quality: REASONABLE

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	2gc7
沉积日期 deposition_date	2006-03-13
结构标题 title	Substrate reduced, copper free complex of methylamine dehydrogenase, amicyanin and cytochrome c551i from Paracoccus denitrificans.
关键词 keywords	Electron transfer, Methylamine dehydrogenase, Cytochrome, amicyanin, Oxidoreductase, Electron transport; 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	57.96 Å
回转半径 Rg (电子) rg_electron	57.81 Å
零角强度 I(0) i0	1656950000.00
分子量 molecular_weight	336210.0 kDa
排除体积 excluded_volume	416700 Å³
包络体积 envelope_volume	606780 Å³
水化壳体积 shell_volume	84904 Å³
包络直径 envelope_diameter	213.0 Å
壳层 Rg shell_rg	64.42 Å
包络 Rg envelope_rg	56.09 Å
形状 Rg shape_rg	57.81 Å
总 Rg total_rg	57.92 Å
总原子数 total_atoms	23676
残基数 n_residues	3032
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	194.2 Å
Rg (实空间) rg_real	57.92 Å
Rg 误差 (实空间) rg_real_error	1.97 Å
I(0) (实空间) i0_real	1.6570e+09
I(0) 误差 (实空间) i0_real_error	3.4770e+07
Rg (倒空间) rg_reciprocal	57.95 Å
I(0) (倒空间) i0_reciprocal	1657000000.0000
解质量估计 total_estimate	0.6225
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	86.3 Å
偏度 Skewness skewness	0.159
峰度 Kurtosis kurtosis	-0.582
角度范围 angular_range	— – 0.1350 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	152900000.0000
实空间数据点数 n_real_points	28
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.763; Stabil: 1.000; Sysdev: 0.009; Positv: 1.000; Valcen: 0.957; Smooth: 0.813

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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 (7)

Entity 1 polymer

描述 description	Methylamine dehydrogenase heavy chain
分子量 formula_weight	42449.3 kDa
EC 编号 ec_number	1.4.99.3
来源方法 src_method	nat
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,E,I,M
原子数 atom_count	24910

QDAPEAETQAQETQGQAAARAAAADLAAGQDDEPRILEAPAPDARRVYVNDPAHFAAVTQQFVIDGEAGRVIGMIDGGFLPNPVVADDGSFIAHASTVFSRIARGERTDYVEVFDPVTLLPTADIELPDAPRFLVGTYPWMTSLTPDGKTLLFYQFSPAPAVGVVDLEGKAFKRMLDVPDCYHIFPTAPDTFFMHCRDGSLAKVAFGTEGTPEITHTEVFHPEDEFLINHPAYSQKAGRLVWPTYTGKIHQIDLSSGDAKFLPAVEALTEAERADGWRPGGWQQVAYHRALDRIYLLVDQRDEWRHKTASRFVVVLDAKTGERLAKFEMGHEIDSINVSQDEKPLLYALSTGDKTLYIHDAESGEELRSVNQLGHGPQVITTADMG

Entity 2 polymer

描述 description	Methylamine dehydrogenase light chain
分子量 formula_weight	14210.7 kDa
EC 编号 ec_number	1.4.99.3
来源方法 src_method	nat
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B,F,J,N

ADAPAGTDPRAKWVPQDNDIQACDYWRHCSIDGNICDCSGGSLTNCPPGTKLATASWVASCYNPTDGQSYLIAYRDCCGYNVSGRCPCLNTEGELPVYRPEFANDIIWCFGAEDDAMTYHCTISPIVGKAS

Entity 3 polymer

描述 description	Amicyanin
分子量 formula_weight	11505.2 kDa
来源方法 src_method	nat
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C,G,K,O

DKATIPSESPFAAAEVADGAIVVDIAKMKYETPELHVKVGDTVTWINREAMPHNVHFVAGVLGEAALKGPMMKKEQAYSLTFTEAGTYDYHCTPHPFMRGKVVVE

Entity 4 polymer

描述 description	Cytochrome c-L
分子量 formula_weight	16274.9 kDa
来源方法 src_method	nat
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	D,H,L,P

APQFFNIIDGSPLNFDDAMEEGRDTEAVKHFLETGENVYNEDPEILPEAEELYAGMCSGCHGHYAEGKIGPGLNDAYWTYPGNETDVGLFSTLYGGATGQMGPMWGSLTLDEMLRTMAWVRHLYTGDPKDASWLTDEQKAGFTPFQP

Entity 5 non-polymer

描述 description	SODIUM ION
分子量 formula_weight	23.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 6 non-polymer

描述 description	HEME C
分子量 formula_weight	618.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 7 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	1234

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6. 折叠分类 (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

结构域编号 domain_id	d2gc7a_
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.69.2.0 — automated matches

结构域编号 domain_id	d2gc7b_
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	d2gc7c_
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	d2gc7d_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.3 — Cytochrome c
超家族 Superfamily superfamily	a.3.1 — Cytochrome c
家族 Family family	a.3.1.1 — monodomain cytochrome c

结构域编号 domain_id	d2gc7e_
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.69.2.0 — automated matches

结构域编号 domain_id	d2gc7f_
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	d2gc7g_
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	d2gc7h_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.3 — Cytochrome c
超家族 Superfamily superfamily	a.3.1 — Cytochrome c
家族 Family family	a.3.1.1 — monodomain cytochrome c

结构域编号 domain_id	d2gc7i_
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.69.2.0 — automated matches

结构域编号 domain_id	d2gc7j_
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	d2gc7k_
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	d2gc7l_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.3 — Cytochrome c
超家族 Superfamily superfamily	a.3.1 — Cytochrome c
家族 Family family	a.3.1.1 — monodomain cytochrome c

结构域编号 domain_id	d2gc7m_
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.69.2.0 — automated matches

结构域编号 domain_id	d2gc7n_
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	d2gc7o_
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	d2gc7p_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.3 — Cytochrome c
超家族 Superfamily superfamily	a.3.1 — Cytochrome c
家族 Family family	a.3.1.1 — monodomain cytochrome c

CATH v4.4 (16 domains)

结构域编号 domain_id	2gc7A00
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	2gc7B00
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	2gc7C00
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	2gc7D00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	760 — Cytochrome Bc1 Complex; Chain D, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Cytochrome c-like domain

结构域编号 domain_id	2gc7E00
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	2gc7F00
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	2gc7G00
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	2gc7H00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	760 — Cytochrome Bc1 Complex; Chain D, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Cytochrome c-like domain

结构域编号 domain_id	2gc7I00
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	2gc7J00
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	2gc7K00
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	2gc7L00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	760 — Cytochrome Bc1 Complex; Chain D, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Cytochrome c-like domain

结构域编号 domain_id	2gc7M00
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	2gc7N00
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	2gc7O00
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	2gc7P00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	760 — Cytochrome Bc1 Complex; Chain D, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Cytochrome c-like domain

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7. 引用文献 (2)

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晶胞边长 a length_a	81.323 Å
晶胞边长 b length_b	189.127 Å
晶胞边长 c length_c	128.906 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	99.75 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

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	1.900 Å
最低分辨率 resolution_low	29.940 Å
R 因子 r_factor	—
R_work r_work	0.1710
R_free r_free	0.1980

fit	/app/data/saxs_computation/gc/2gc7/2gc7.fit
pddf	/app/data/pr_computation/gc/2gc7/2gc7.pr.out
profile	/app/data/saxs_computation/gc/2gc7/2gc7.dat

Substrate reduced, copper free complex of methylamine dehydrogenase, amicyanin and cytochrome c551i from Paracoccus denitrificans.

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 (7)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

Entity 4 polymer

聚合体 Polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 water

6. 折叠分类 (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

CATH v4.4 (16 domains)

7. 引用文献 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)