1kqg

FORMATE DEHYDROGENASE N FROM E. COLI

Method: X-RAY DIFFRACTION D_max: 151.2 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	1kqg
沉积日期 deposition_date	2002-01-05
结构标题 title	FORMATE DEHYDROGENASE N FROM E. COLI
关键词 keywords	;OXIDOREDUCTASE, SELENIUM, SELENOCYSTEINE, SECYS, MOLYBDENUM, MOLYBDOPTERIN, MPT, MOLYBDOPTERIN GUANINE DINUCLEOTIDE, MGD, IRON SULFUR CLUSTER, FE4S4, FORMATE, DEHYDROGENASE, ANAEROBIC, INTEGRAL MEMBRANE PROTEIN ;; 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)

回转半径 Rg (Guinier) rg_guinier	39.65 Å
回转半径 Rg (电子) rg_electron	41.29 Å
零角强度 I(0) i0	459727000.00
分子量 molecular_weight	172240.0 kDa
排除体积 excluded_volume	213780 Å³
包络体积 envelope_volume	263170 Å³
水化壳体积 shell_volume	55807 Å³
包络直径 envelope_diameter	162.2 Å
壳层 Rg shell_rg	43.41 Å
包络 Rg envelope_rg	43.53 Å
形状 Rg shape_rg	41.41 Å
总 Rg total_rg	40.99 Å
总原子数 total_atoms	12019
残基数 n_residues	1487
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	151.2 Å
Rg (实空间) rg_real	40.59 Å
Rg 误差 (实空间) rg_real_error	1.84 Å
I(0) (实空间) i0_real	4.5970e+08
I(0) 误差 (实空间) i0_real_error	8.9960e+06
Rg (倒空间) rg_reciprocal	40.00 Å
I(0) (倒空间) i0_reciprocal	459400000.0000
解质量估计 total_estimate	0.7155
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	37.8 Å
偏度 Skewness skewness	0.887
峰度 Kurtosis kurtosis	0.437
角度范围 angular_range	— – 0.2000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	104500000.0000
实空间数据点数 n_real_points	41
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.349; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.556; Smooth: 0.694

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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 (10)

Entity 1 polymer

描述 description	FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, MAJOR SUBUNIT
分子量 formula_weight	113088.2 kDa
EC 编号 ec_number	1.2.1.2
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	A
原子数 atom_count	14003

MDVSRRQFFKICAGGMAGTTVAALGFAPKQALAQARNYKLLRAKEIRNTCTYCSVGCGLLMYSLGDGAKNAREAIYHIEGDPDHPVSRGALCPKGAGLLDYVNSENRLRYPEYRAPGSDKWQRISWEEAFSRIAKLMKADRDANFIEKNEQGVTVNRWLSTGMLCASGASNETGMLTQKFARSLGMLAVDNQARVUHGPTVASLAPTFGRGAMTNHWVDIKNANVVMVMGGNAAEAHPVGFRWAMEAKNNNDATLIVVDPRFTRTASVADIYAPIRSGTDITFLSGVLRYLIENNKINAEYVKHYTNASLLVRDDFAFEDGLFSGYDAEKRQYDKSSWNYQLDENGYAKRDETLTHPRCVWNLLKEHVSRYTPDVVENICGTPKADFLKVCEVLASTSAPDRTTTFLYALGWTQHTVGAQNIRTMAMIQLLLGNMGMAGGGVNALRGHSNIQGLTDLGLLSTSLPGYLTLPSEKQVDLQSYLEANTPKATLADQVNYWSNYPKFFVSLMKSFYGDAAQKENNWGYDWLPKWDQTYDVIKYFNMMDEGKVTGYFCQGFNPVASFPDKNKVVSCLSKLKYMVVIDPLVTETSTFWQNHGESNDVDPASIQTEVFRLPSTCFAEEDGSIANSGRWLQWHWKGQDAPGEARNDGEILAGIYHHLRELYQSEGGKGVEPLMKMSWNYKQPHEPQSDEVAKENNGYALEDLYDANGVLIAKKGQLLSSFAHLRDDGTTASSCWIYTGSWTEQGNQMANRDNSDPSGLGNTLGWAWAWPLNRRVLYNRASADINGKPWDPKRMLIQWNGSKWTGNDIPDFGNAAPGTPTGPFIMQPEGMGRLFAINKMAEGPFPEHYEPIETPLGTNPLHPNVVSNPVVRLYEQDALRMGKKEQFPYVGTTYRLTEHFHTWTKHALLNAIAQPEQFVEISETLAAAKGINNGDRVTVSSKRGFIRAVAVVTRRLKPLNVNGQQVETVGIPIHWGFEGVARKGYIANTLTPNVGDANSQTPEYKAFLVNIEKA

Entity 2 polymer

描述 description	FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, IRON-SULFUR SUBUNIT
分子量 formula_weight	32279.7 kDa
EC 编号 ec_number	1.2.1.2
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	B

MAMETQDIIKRSATNSITPPSQVRDYKAEVAKLIDVSTCIGCKACQVACSEWNDIRDEVGHCVGVYDNPADLSAKSWTVMRFSETEQNGKLEWLIRKDGCMHCEDPGCLKACPSAGAIIQYANGIVDFQSENCIGCGYCIAGCPFNIPRLNKEDNRVYKCTLCVDRVSVGQEPACVKTCPTGAIHFGTKKEMLELAEQRVAKLKARGYEHAGVYNPEGVGGTHVMYVLHHADQPELYHGLPKDPKIDTSVSLWKGALKPLAAAGFIATFAGLIFHYIGIGPNKEVDDDEEDHHE

Entity 3 polymer

描述 description	FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, CYTOCHROME B556(FDN) SUBUNIT
分子量 formula_weight	25405.5 kDa
EC 编号 ec_number	1.2.1.2
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

MSKSKMIVRTKFIDRACHWTVVICFFLVALSGISFFFPTLQWLTQTFGTPQMGRILHPFFGIAIFVALMFMFVRFVHHNIPDKKDIPWLLNIVEVLKGNEHKVADVGKYNAGQKMMFWSIMSMIFVLLVTGVIIWRPYFAQYFPMQVVRYSLLIHAAAGIILIHAILIHMYMAFWVKGSIKGMIEGKVSRRWAKKHHPRWYREIEKAEAKKESEEGI

Entity 4 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	5

Entity 5 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	2

Entity 6 non-polymer

描述 description	MOLYBDENUM(VI) ION
分子量 formula_weight	95.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 7 non-polymer

描述 description	CARDIOLIPIN
分子量 formula_weight	1464.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 8 non-polymer

描述 description	PROTOPORPHYRIN IX CONTAINING FE
分子量 formula_weight	616.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 9 non-polymer

描述 description	2-HEPTYL-4-HYDROXY QUINOLINE N-OXIDE
分子量 formula_weight	259.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 10 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	1984

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6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (5 domains)

结构域编号 domain_id	d1kqga1
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	d1kqga2
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

结构域编号 domain_id	d1kqgb1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.1 — 4Fe-4S ferredoxins
家族 Family family	d.58.1.5 — Ferredoxin domains from multidomain proteins

结构域编号 domain_id	d1kqgb2
类 Class class	f — Membrane and cell surface proteins and peptides
折叠类型 Fold fold	f.23 — Single transmembrane helix
超家族 Superfamily superfamily	f.23.22 — Iron-sulfur subunit of formate dehydrogenase N, transmembrane anchor
家族 Family family	f.23.22.1 — Iron-sulfur subunit of formate dehydrogenase N, transmembrane anchor

结构域编号 domain_id	d1kqgc_
类 Class class	f — Membrane and cell surface proteins and peptides
折叠类型 Fold fold	f.21 — Heme-binding four-helical bundle
超家族 Superfamily superfamily	f.21.1 — Transmembrane di-heme cytochromes
家族 Family family	f.21.1.1 — Formate dehydrogenase N, cytochrome (gamma) subunit

CATH v4.4 (7 domains)

结构域编号 domain_id	1kqgA02
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	1kqgA03
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	1kqgA04
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 —

结构域编号 domain_id	1kqgB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1kqgB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1kqgB03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	480 — Single helix bin

结构域编号 domain_id	1kqgC00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	950 — Fumarate Reductase Cytochrome B subunit
同源超家族 H-superfamily homologous superfamily	20 — Transmembrane di-heme cytochromes, Chain C

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7. 引用文献 (1)

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晶胞边长 a length_a	203.000 Å
晶胞边长 b length_b	203.000 Å
晶胞边长 c length_c	203.000 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	12

空间群 space_group	P 21 3
空间群编号 int_tables_number	198
晶系 crystal_system	—

分辨率 resolution	2.800 Å
最低分辨率 resolution_low	40.000 Å
R 因子 r_factor	0.1980
R_work r_work	0.1980
R_free r_free	0.2390

fit	/app/data/saxs_computation/kq/1kqg/1kqg.fit
pddf	/app/data/pr_computation/kq/1kqg/1kqg.pr.out
profile	/app/data/saxs_computation/kq/1kqg/1kqg.dat

FORMATE DEHYDROGENASE N FROM E. COLI

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 (10)

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 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 water

6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (5 domains)

CATH v4.4 (7 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)