1o95

Ternary complex between trimethylamine dehydrogenase and electron transferring flavoprotein

Method: X-RAY DIFFRACTION D_max: 175.4 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	1o95
沉积日期 deposition_date	2002-12-11
结构标题 title	Ternary complex between trimethylamine dehydrogenase and electron transferring flavoprotein
关键词 keywords	;ELECTRON TRANSPORT-COMPLEX, PROTEIN COMPLEX, ELECTRON TRANSFER, DEHYDROGENASE, ELECTRON TRANSPORT, FLAVOPROTEIN, OXIDO-REDUCTASE, IRON-SULFUR, FMN ;; 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	48.55 Å
回转半径 Rg (电子) rg_electron	49.98 Å
零角强度 I(0) i0	984962000.00
分子量 molecular_weight	252900.0 kDa
排除体积 excluded_volume	313760 Å³
包络体积 envelope_volume	419240 Å³
水化壳体积 shell_volume	75816 Å³
包络直径 envelope_diameter	185.6 Å
壳层 Rg shell_rg	47.39 Å
包络 Rg envelope_rg	50.81 Å
形状 Rg shape_rg	49.98 Å
总 Rg total_rg	49.86 Å
总原子数 total_atoms	17776
残基数 n_residues	2305
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	175.4 Å
Rg (实空间) rg_real	49.54 Å
Rg 误差 (实空间) rg_real_error	2.48 Å
I(0) (实空间) i0_real	9.8500e+08
I(0) 误差 (实空间) i0_real_error	1.8780e+07
Rg (倒空间) rg_reciprocal	48.56 Å
I(0) (倒空间) i0_reciprocal	983700000.0000
解质量估计 total_estimate	0.7355
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	49.3 Å
偏度 Skewness skewness	0.823
峰度 Kurtosis kurtosis	0.454
角度范围 angular_range	— – 0.1600 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	82640000.0000
实空间数据点数 n_real_points	33
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.555; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.784; Smooth: 0.111

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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	TRIMETHYLAMINE DEHYDROGENASE
分子量 formula_weight	81606.0 kDa
EC 编号 ec_number	1.5.99.7
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
原子数 atom_count	17776

ARDPKHDILFEPIQIGPKTLRNRFYQVPHCIGAGSDKPGFQSAHRSVKAEGGWAALNTEYCSINPESDDTHRLSARIWDEGDVRNLKAMTDEVHKYGALAGVELWYGGAHAPNMESRATPRGPSQYASEFETLSYCKEMDLSDIAQVQQFYVDAAKRSRDAGFDIVYVYGAHSYLPLQFLNPYYNKRTDKYGGSLENRARFWLETLEKVKHAVGSDCAIATRFGVDTVYGPGQIEAEVDGQKFVEMADSLVDMWDITIGDIAEWGEDAGPSRFYQQGHTIPWVKLVKQVSKKPVLGVGRYTDPEKMIEIVTKGYADIIGCARPSIADPFLPQKVEQGRYDDIRVCIGCNVCISRWEIGGPPMICTQNATAGEEYRRGWHPEKFRQTKNKDSVLIVGAGPSGSEAARVLMESGYTVHLTDTAEKIGGHLNQVAALPGLGEWSYHRDYRETQITKLLKKNKESQLALGQKPMTADDVLQYGADKVIIATGARWNTDGTNCLTHDPIPGADASLPDQLTPEQVMDGKKKIGKRVVILNADTYFMAPSLAEKLATAGHEVTIVSGVHLANYMHFTLEYPNMMRRLHELHVEELGDHFCSRIEPGRMEIYNIWGDGSKRTYRGPGVSPRDANTSHRWIEFDSLVLVTGRHSECTLWNELKARESEWAENDIKGIYLIGDAEAPRLIADATFTGHRVAREIEEANPQIAIPYKRETIAWGTPHMPGGNFKIEYKV

Entity 2 polymer

描述 description	ELECTRON TRANSFER FLAVOPROTEIN BETA-SUBUNIT
分子量 formula_weight	28929.8 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	C,E

MKILVAVKQTAALEEDFEIREDGMDVDEDFMMYDLNEWDDFSLEEAMKIKESSDTDVEVVVVSVGPDRVDESLRKCLAKGADRAVRVWDDAAEGSDAIVVGRILTEVIKKEAPDMVFAGVQSSDQAYASTGISVASYLNWPHAAVVADLQYKPGDNKAVIRRELEGGMLQEVEINCPAVLTIQLGINKPRYASLRGIKQAATKPIEEVSLADIGLSANDVGAAQSMSRVRRMYIPEKGRATMIEGTISEQAAKIIQIINEFKGA

来源 Source

来源生物 organism	METHYLOPHILUS METHYLOTROPHUS
NCBI 分类编号 ncbi_taxonomy_id	17
宿主生物 host_organism	ESCHERICHIA COLI

Entity 3 polymer

描述 description	ELECTRON TRANSFER FLAVOPROTEIN ALPHA-SUBUNIT
分子量 formula_weight	33622.9 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	D,F

SKILVIAEHRRNDLRPVSLELIGAANGLKKSGEDKVVVAVIGSQADAFVPALSVNGVDELVVVKGSSIDFDPDVFEASVSALIAAHNPSVVLLPHSVDSLGYASSLASKTGYGFATDVYIVEYQGDELVATRGGYNQKVNVEVDFPGKSTVVLTIRPSVFKPLEGAGSPVVSNVDAPSVQSRSQNKDYVEVGGGNDIDITTVDFIMSIGRGIGEETNVEQFRELADEAGATLCCSRPIADAGWLPKSRQVGQSGKVVGSCKLYVAMGISGSIQHMAGMKHVPTIIAVNTDPGASIFTIAKYGIVADIFDIEEELKAQLAA

来源 Source

来源生物 organism	METHYLOPHILUS METHYLOTROPHUS
NCBI 分类编号 ncbi_taxonomy_id	17
宿主生物 host_organism	ESCHERICHIA COLI

Entity 4 non-polymer

描述 description	FLAVIN MONONUCLEOTIDE
分子量 formula_weight	456.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 5 non-polymer

描述 description	ADENOSINE-5'-DIPHOSPHATE
分子量 formula_weight	427.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 6 non-polymer

描述 description	IRON/SULFUR CLUSTER
分子量 formula_weight	351.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 7 non-polymer

描述 description	ADENOSINE MONOPHOSPHATE
分子量 formula_weight	347.2 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) 20 domains

SCOP 2.08 (10 domains)

结构域编号 domain_id	d1o95a1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.4 — FMN-linked oxidoreductases
家族 Family family	c.1.4.1 — FMN-linked oxidoreductases

结构域编号 domain_id	d1o95a2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.3 — FAD/NAD(P)-binding domain
超家族 Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
家族 Family family	c.3.1.1 — C-terminal domain of adrenodoxin reductase-like

结构域编号 domain_id	d1o95a3
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.4 — Nucleotide-binding domain
超家族 Superfamily superfamily	c.4.1 — Nucleotide-binding domain
家族 Family family	c.4.1.1 — N-terminal domain of adrenodoxin reductase-like

结构域编号 domain_id	d1o95b1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.4 — FMN-linked oxidoreductases
家族 Family family	c.1.4.1 — FMN-linked oxidoreductases

结构域编号 domain_id	d1o95b2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.3 — FAD/NAD(P)-binding domain
超家族 Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
家族 Family family	c.3.1.1 — C-terminal domain of adrenodoxin reductase-like

结构域编号 domain_id	d1o95b3
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.4 — Nucleotide-binding domain
超家族 Superfamily superfamily	c.4.1 — Nucleotide-binding domain
家族 Family family	c.4.1.1 — N-terminal domain of adrenodoxin reductase-like

结构域编号 domain_id	d1o95c_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
超家族 Superfamily superfamily	c.26.2 — Adenine nucleotide alpha hydrolases-like
家族 Family family	c.26.2.3 — ETFP subunits

结构域编号 domain_id	d1o95d_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
超家族 Superfamily superfamily	c.26.2 — Adenine nucleotide alpha hydrolases-like
家族 Family family	c.26.2.3 — ETFP subunits

结构域编号 domain_id	d1o95e_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
超家族 Superfamily superfamily	c.26.2 — Adenine nucleotide alpha hydrolases-like
家族 Family family	c.26.2.3 — ETFP subunits

结构域编号 domain_id	d1o95f_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
超家族 Superfamily superfamily	c.26.2 — Adenine nucleotide alpha hydrolases-like
家族 Family family	c.26.2.3 — ETFP subunits

CATH v4.4 (10 domains)

结构域编号 domain_id	1o95A01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	70 — Aldolase class I

结构域编号 domain_id	1o95A02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	1o95A03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	50 — FAD/NAD(P)-binding domain
同源超家族 H-superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

结构域编号 domain_id	1o95B01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	70 — Aldolase class I

结构域编号 domain_id	1o95B02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	1o95B03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	50 — FAD/NAD(P)-binding domain
同源超家族 H-superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

结构域编号 domain_id	1o95C00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	620 — HUPs

结构域编号 domain_id	1o95D00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	620 — HUPs

结构域编号 domain_id	1o95E00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	620 — HUPs

结构域编号 domain_id	1o95F00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	620 — HUPs

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7. 引用文献 (1)

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晶胞边长 a length_a	102.500 Å
晶胞边长 b length_b	116.513 Å
晶胞边长 c length_c	138.706 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	95.35 °
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	3.700 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.2570
R_work r_work	0.2520
R_free r_free	0.3530

fit	/app/data/saxs_computation/o9/1o95/1o95.fit
pddf	/app/data/pr_computation/o9/1o95/1o95.pr.out
profile	/app/data/saxs_computation/o9/1o95/1o95.dat

Ternary complex between trimethylamine dehydrogenase and electron transferring flavoprotein

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

来源 Source

Entity 3 polymer

聚合体 Polymer

来源 Source

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

6. 折叠分类 (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

CATH v4.4 (10 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)