9g01

;Structure of carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) from Clostridium autoethanogenum (composite structure, closed and CO-bound state) ;

Method: ELECTRON MICROSCOPY D_max: 191.2 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	9g01
沉积日期 deposition_date	2024-07-06
结构标题 title	;Structure of carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) from Clostridium autoethanogenum (composite structure, closed and CO-bound state) ;
关键词 keywords	anaerobic CO2 fixation, acetyl-CoA synthesis, metalloenzyme, Wood-Ljungdahl pathway., OXIDOREDUCTASE; OXIDOREDUCTASE
实验方法 method	ELECTRON MICROSCOPY

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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	54.27 Å
回转半径 Rg (电子) rg_electron	55.97 Å
零角强度 I(0) i0	856240000.00
分子量 molecular_weight	244830.0 kDa
排除体积 excluded_volume	307240 Å³
包络体积 envelope_volume	404370 Å³
水化壳体积 shell_volume	67531 Å³
包络直径 envelope_diameter	208.0 Å
壳层 Rg shell_rg	49.11 Å
包络 Rg envelope_rg	56.81 Å
形状 Rg shape_rg	56.10 Å
总 Rg total_rg	55.29 Å
总原子数 total_atoms	17029
残基数 n_residues	2254
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	191.2 Å
Rg (实空间) rg_real	55.09 Å
Rg 误差 (实空间) rg_real_error	2.38 Å
I(0) (实空间) i0_real	8.5620e+08
I(0) 误差 (实空间) i0_real_error	1.6830e+07
Rg (倒空间) rg_reciprocal	53.59 Å
I(0) (倒空间) i0_reciprocal	854400000.0000
解质量估计 total_estimate	0.7239
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	39.6 Å
偏度 Skewness skewness	0.700
峰度 Kurtosis kurtosis	-0.066
角度范围 angular_range	— – 0.1450 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	65710000.0000
实空间数据点数 n_real_points	30
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.544; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.632; Smooth: 0.145

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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 (6)

Entity 1 polymer

描述 description	CO-methylating acetyl-CoA synthase
分子量 formula_weight	76991.1 kDa
EC 编号 ec_number	2.3.1.169
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	17029

MNLFQTVFTGSKQALAAAEGIVKQAVDEKGRDYKVAFPDTAYSLPVIFAATGKKITNVGELEGALDIVRSLIVEEEMLDKLLNSGLATAVAAEIIEAAKYVLSDAPYAEPCVGFISDPIIRSLGVPLVTGDIPGVAVILGECPDSETAAKIIKDYQSKGLLTCLVGKVIDQAIEGKVKMGLDLRVIPLGYDVTSVIHVVTIAIRAALIFGGIKGGQLNDILKYTAERVPAFVNAFGPLSELVVSAGAGAIALGFPVLTDQVVPEVPTLLLTQKDYDKMVKTSLEARNIKIKITEIPIPVSFAAAFEGERIRKNDMLAEFGGNKTKAWELVMCADQGEVEDHKIEVIGPDIDTIDKAPGRMPLGMLIKVSGTNMQKDFEPVLERRLHYFLNYIEGVMHVGQRNLTWVRIGKEAFEKGFRLKHFGEVIYAKMLDEFGSVVDKCEVTIITDPGKAEELEGKYAVPRYKERDARLESLVDEKVDTFYSCNLCQSFAPAHVCIVTPERLGLCGAVSWLDAKATLELNPTGPCQAVPKEGVVDENLGIWEKVNETVSKISQGAVTSVTLYSILQDPMTSCGCFECITGIMPEANGVVMVNREFGATTPLGMTFGELASMTGGGVQTPGFMGHGRQFIASKKFMKGEGGLGRIVWMPKELKDFVAEKLNKTAKELYNIDNFADMICDETIATESEEVVKFLEEKGHPALKMDPIM

Entity 2 polymer

描述 description	Carbon monoxide dehydrogenase/acetyl-CoA synthase beta subunit
分子量 formula_weight	67846.3 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	B,C

EEKAKSIDQATLQLLDKAKQDGVETVWDRKADMKVQCGFGSAGVCCRNCSMGPCRVSPVPGKGVERGICGATADVIVSRNFARMVAAGTAAHSDHGRSIALSLYHTSKDGDIKVKDENKLKEVAKSFNVETEGRDIYDIAHDVAKEGLSNYGKQLGEVTLPPSLPEKRKELWRKLGVYPRAVDREIAAVMHSTHIGCNADAEAMIKMSMRCSLTDGWMGSFMGTEFSDIMFGTPHSIDTEANLGVLEKNSVNVVLHGHEPLLSEMVVEAASDPELVELAKSVGADGINLCGMCCTGNEVSMRHGIKIAGNFMQQELAVVTGAVDGLIVDVQCIMPALAKLSKSYHTKFITTSPKAHITDSIYMEFDEENPLDSAKKILKEAILNFKNRDQSKVMIPELKCKAILGYSVEEIINKLDKVVNTQIGPMQTVKPLADVLVSGVLRGAAAVVGCNNPKVVQDSAHIETIKGLIKNDVIVVVTGCAAQAAAKYGLLQKEAAEKYAGPGLATVCKLVDIPPVLHMGSCVDISRILDLVGRVANLLGVDMSDLPVAGVAPEWMSEKAVAIGTYVVTSGIDTWLGVAPPVTGGPEVVDILTNKMEDWVGAKFFIETDPHKAVEQIVNRMNEKRKKLGI

Entity 3 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	4

Entity 4 non-polymer

描述 description	Fe(3)-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 5 non-polymer

描述 description	NICKEL (II) ION
分子量 formula_weight	58.7 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 6 non-polymer

描述 description	CARBON MONOXIDE
分子量 formula_weight	28.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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7. 引用文献 (1)

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晶胞边长 a length_a	1.000 Å
晶胞边长 b length_b	1.000 Å
晶胞边长 c length_c	1.000 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	—

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	2.830 Å
最低分辨率 resolution_low	2.830 Å
R 因子 r_factor	0.3954
R_work r_work	0.3954
R_free r_free	—

分辨率 resolution	2.83 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	649146

fit	/app/data/saxs_computation/g0/9g01/9g01.fit
pddf	/app/data/pr_computation/g0/9g01/9g01.pr.out
profile	/app/data/saxs_computation/g0/9g01/9g01.dat

;Structure of carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) from Clostridium autoethanogenum (composite structure, closed and CO-bound state) ;

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

冷冻电镜 EM 3D

5. 实体与聚合体信息 (6)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)