SAXSdb — 2iv2

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2iv2
沉积日期 deposition_date	2006-06-08
结构标题 title	Reinterpretation of reduced form of formate dehydrogenase H from E. coli
关键词 keywords	;OXIDOREDUCTASE, 4FE-4S, NAEROBIC, DEHYDROGENASE, FE4S4, FORMATE, IRON, IRON SULFUR CLUSTER, IRON-SULFUR, METAL-BINDING, MGD, MOLYBDENUM, MOLYBDOPTERIN, MOLYBDOPTERIN GUANINE DINUCLEOTIDE, MPT, NAD, SECYS, SELENIUM, SELENOCYSTEINE ;; 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)

该条目暂无 SAXS 数据。

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3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

该条目暂无 P(r) 分析数据。

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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	Formate dehydrogenase H
分子量 formula_weight	79465.7 kDa
EC 编号 ec_number	1.17.1.9,1.17.99.7
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	X
原子数 atom_count	5817

MKKVVTVCPYCASGCKINLVVDNGKIVRAEAAQGKTNQGTLCLKGYYGWDFINDTQILTPRLKTPMIRRQRGGKLEPVSWDEALNYVAERLSAIKEKYGPDAIQTTGSSRGTGNETNYVMQKFARAVIGTNNVDCCARVUHGPSVAGLHQSVGNGAMSNAINEIDNTDLVFVFGYNPADSHPIVANHVINAKRNGAKIIVCDPRKIETARIADMHIALKNGSNIALLNAMGHVIIEENLYDKAFVASRTEGFEEYRKIVEGYTPESVEDITGVSASEIRQAARMYAQAKSAAILWGMGVTQFYQGVETVRSLTSLAMLTGNLGKPHAGVNPVRGQNNVQGACDMGALPDTYPGYQYVKDPANREKFAKAWGVESLPAHTGYRISELPHRAAHGEVRAAYIMGEDPLQTDAELSAVRKAFEDLELVIVQDIFMTKTASAADVILPSTSWGEHEGVFTAADRGFQRFFKAVEPKWDLKTDWQIISEIATRMGYPMHYNNTQEIWDELRHLCPDFYGATYEKMGELGFIQWPCRDTSDADQGTSYLFKEKFDTPNGLAQFFTCDWVAPIDKLTDEYPMVLSTVREVGHYSCRSMTGNCAALAALADEPGYAQINTEDAKRLGIEDEALVWVHSRKGKIITRAQVSDRPNKGAIYMTYQWWIGACNELVTENLSPITKTPEYKYCAVRVEPIADQRAAEQYVIDEYNKLKTRLREAALA

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 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	1

Entity 3 non-polymer

描述 description	;GUANYLATE-O'-PHOSPHORIC ACID MONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,5,6,7,8A,9,10,10A-OCTAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL) ESTER ;
分子量 formula_weight	742.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
分子量 formula_weight	740.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 non-polymer

描述 description	MOLYBDENUM ATOM
分子量 formula_weight	95.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 6 non-polymer

描述 description	UNKNOWN ATOM OR ION
来源方法 src_method	syn
拷贝数 entity_count	1

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	267

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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	d2iv2x1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.52 — Double psi beta-barrel
超家族 Superfamily superfamily	b.52.2 — ADC-like
家族 Family family	b.52.2.2 — Formate dehydrogenase/DMSO reductase, C-terminal domain

结构域编号 domain_id	d2iv2x2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.81 — Formate dehydrogenase/DMSO reductase, domains 1-3
超家族 Superfamily superfamily	c.81.1 — Formate dehydrogenase/DMSO reductase, domains 1-3
家族 Family family	c.81.1.1 — Formate dehydrogenase/DMSO reductase, domains 1-3

CATH v4.4 (4 domains)

结构域编号 domain_id	2iv2X01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	20 — Single Sheet
拓扑 Topology topology	25 — N-terminal domain of TfIIb
同源超家族 H-superfamily homologous superfamily	90 — ADC-like domains

结构域编号 domain_id	2iv2X02
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	740 —

结构域编号 domain_id	2iv2X03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	228 — Dimethylsulfoxide Reductase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Dimethylsulfoxide Reductase, domain 2

结构域编号 domain_id	2iv2X04
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	40 — Barwin-like endoglucanases
同源超家族 H-superfamily homologous superfamily	20 —

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7. 引用文献 (2)

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晶胞边长 a length_a	146.400 Å
晶胞边长 b length_b	146.400 Å
晶胞边长 c length_c	81.270 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 41 21 2
空间群编号 int_tables_number	92
晶系 crystal_system	—

分辨率 resolution	2.270 Å
最低分辨率 resolution_low	34.500 Å
R 因子 r_factor	0.1780
R_work r_work	0.1750
R_free r_free	0.2260

Reinterpretation of reduced form of formate dehydrogenase H from E. coli

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution