8riu

;Crystal structure of the F420-reducing carbon monoxide dehydrogenase component from the ethanotroph Candidatus Ethanoperedens thermophilum ;

Method: X-RAY DIFFRACTION D_max: 128.9 Å Quality: GOOD

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	8riu
沉积日期 deposition_date	2023-12-19
结构标题 title	;Crystal structure of the F420-reducing carbon monoxide dehydrogenase component from the ethanotroph Candidatus Ethanoperedens thermophilum ;
关键词 keywords	;Carbon monoxide dehydrogenase, F420-reductase, acetyl-coenzyme A synthase-decarbonylase complex, anaerobic oxidoreductase, CO2-releasing enzyme, C-cluster, CO, CO2, gas channelling., OXIDOREDUCTASE ;; 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	41.26 Å
回转半径 Rg (电子) rg_electron	40.97 Å
零角强度 I(0) i0	1338050000.00
分子量 molecular_weight	296170.0 kDa
排除体积 excluded_volume	367590 Å³
包络体积 envelope_volume	440640 Å³
水化壳体积 shell_volume	84211 Å³
包络直径 envelope_diameter	136.2 Å
壳层 Rg shell_rg	49.63 Å
包络 Rg envelope_rg	41.50 Å
形状 Rg shape_rg	41.12 Å
总 Rg total_rg	40.82 Å
总原子数 total_atoms	20460
残基数 n_residues	2607
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	128.9 Å
Rg (实空间) rg_real	41.09 Å
Rg 误差 (实空间) rg_real_error	0.61 Å
I(0) (实空间) i0_real	1.3380e+09
I(0) 误差 (实空间) i0_real_error	2.0250e+07
Rg (倒空间) rg_reciprocal	41.26 Å
I(0) (倒空间) i0_reciprocal	1338000000.0000
解质量估计 total_estimate	0.8900
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	50.9 Å
偏度 Skewness skewness	0.167
峰度 Kurtosis kurtosis	-0.507
角度范围 angular_range	— – 0.1900 Å⁻¹
当前正则化参数 α current_alpha	0.0002
最高正则化参数 α highest_alpha	363100000.0000
实空间数据点数 n_real_points	39
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.929; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.802

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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 (12)

Entity 1 polymer

描述 description	Acetyl-CoA decarbonylase/synthase complex subunit alpha
分子量 formula_weight	87549.1 kDa
EC 编号 ec_number	1.2.7.4
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,D
原子数 atom_count	21942

MTKTEKKGNIEIEALKDVVVNIGGIEEEEEEWEPMGPTPMPGIVDLRDWDYKLMDRYKPFYAPYCEMCCFCTFGKCDLTGGKKGACGLDMTAQQARFVTIACLIGCSAHTAHGRHMLNEILHIYGDREIDMGTGINIEAPLTRLITGIKPKRLSDFIPVLDYIEEQIAQVMDSVHTGQEGSNIDYESKAFHVGMLDSLGKEVADIVQIVAFDLPKGDPDAPLVEIGMGCIDETKPMLLVIGHNVVPSVSVIDYMREHDLEDKIEVAGICCTAIDTTRYSDRAKIVGSIGRQLRFVRSGIADVIMVDEQCIRADILEQAKRTHAPLIATNDKALYGLVDRTDDSADDIITILVSGKEPGVVILDPVKAGEVAVRLVQIMHEKRKGLVHLPTDEEFKEYVEMCQNCDANCVIACPQGLPIGEANKAAAAGNIEPLAELFDLCVGCGRCEQVCKKHIPIVDVIHKAALPLVRAEKGMIRVGRGPVLDTEIRNVGAPLVLGTIPGIIAIVGCGNYPNGTKDVYIMAKEFVERKYIVVLTGCGAMDAALYRDEDGKTLYEKYPGDFDGGCIVNIGSCVSNAHIHDAAIKVASIFARRNIRANYAEIADYILNRVGACGMAWGAMSQKAASIASGVNRIGIPVVIGPHGWKYRRAYLGRKDVDRDWMVYDARDGSKVRIEPAPEHLLVAADTLEEAIPLMARLCFRPTDNSMGRQVKLTHYMDLSMKYLGKYPDDWPVFVRTEADLPLAKKEEYLRILKEDYGWDVDLEAKKIISGPIRKFDVSFDATNLEQLIRENK

Entity 2 polymer

描述 description	Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus
分子量 formula_weight	40730.8 kDa
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	B,E

MKFDEKGSIIDLETKVVYSNICCYCGACGAFCTEYISYENGTPVTKQKCFEIHGACFDFCPRTFLPVLEMERELFGEVRSDWELGYYTDIVTARATNPEILEKGQNGGVVTALLTHLIDEGKIDAACITGRSDDEPWKPEPLVATTRDEILKGAGSNYEQCPAIMGVGEALANGSENIAMVGLPCHIQAMRKIQLSKAFDVGASRVKYAIGLLCTETFDRDLLHAKLREMKIKAEDVKKFDIGEGKFKVFTEEGVRTEKIATMKSCMRDGCKVCYDFAAELADISVGSIGSEEGWNTVLIRSKAGKELIDEAEKAKVIEVKPLNEASIQSVKDLASRKKSENMDNIVEIAGATKILHLAVKPQELSLLLG

Entity 3 polymer

描述 description	Acetyl-CoA decarbonylase/synthase complex subunit epsilon
分子量 formula_weight	19058.0 kDa
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	C,F

MNIPFDIGNISGPEMGRIATPEALGRAIKNAKRPLLVVGSEILEDGLIDRAIAIGKKGIPIAATAHSIKGFVDAGYTDNVYMVGLHELANNIKSPDWMGFDGKGGYDLVAVLGGIYYSTSQFLISIKNCATDPLVRAISIDRYYHIAARMTFDNISRKRTDEFKEMLDRVVQSI

Entity 4 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	15

Entity 5 non-polymer

描述 description	1,2-ETHANEDIOL
分子量 formula_weight	62.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	11

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	13

Entity 7 non-polymer

描述 description	FE(4)-NI(1)-S(4) CLUSTER
分子量 formula_weight	410.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 8 non-polymer

描述 description	POTASSIUM ION
分子量 formula_weight	39.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 9 non-polymer

描述 description	FLAVIN-ADENINE DINUCLEOTIDE
分子量 formula_weight	785.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 10 non-polymer

描述 description	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
分子量 formula_weight	354.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 11 non-polymer

描述 description	CHLORIDE ION
分子量 formula_weight	35.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 12 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	1418

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7. 引用文献 (1)

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晶胞边长 a length_a	97.070 Å
晶胞边长 b length_b	159.213 Å
晶胞边长 c length_c	191.444 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 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	1.890 Å
最低分辨率 resolution_low	39.800 Å
R 因子 r_factor	0.1662
R_work r_work	0.1651
R_free r_free	0.1873

fit	/app/data/saxs_computation/ri/8riu/8riu.fit
pddf	/app/data/pr_computation/ri/8riu/8riu.pr.out
profile	/app/data/saxs_computation/ri/8riu/8riu.dat

;Crystal structure of the F420-reducing carbon monoxide dehydrogenase component from the ethanotroph Candidatus Ethanoperedens thermophilum ;

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 (12)

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 non-polymer

Entity 11 non-polymer

Entity 12 water

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)