9g03

Structure of carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) in complex with ferredoxin (Clostridium autoethanogenum)

Method: ELECTRON MICROSCOPY D_max: 170.7 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

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9g03
沉积日期 deposition_date	2024-07-06
结构标题 title	Structure of carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) in complex with ferredoxin (Clostridium autoethanogenum)
关键词 keywords	anaerobic CO2 fixation, acetyl-CoA synthesis, metalloenzyme, Wood-Ljungdahl pathway., OXIDOREDUCTASE; OXIDOREDUCTASE
实验方法 method	ELECTRON MICROSCOPY

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	44.69 Å
回转半径 Rg (电子) rg_electron	46.53 Å
零角强度 I(0) i0	616329000.00
分子量 molecular_weight	204330.0 kDa
排除体积 excluded_volume	256010 Å³
包络体积 envelope_volume	315150 Å³
水化壳体积 shell_volume	61798 Å³
包络直径 envelope_diameter	183.0 Å
壳层 Rg shell_rg	44.89 Å
包络 Rg envelope_rg	47.66 Å
形状 Rg shape_rg	46.71 Å
总 Rg total_rg	45.85 Å
总原子数 total_atoms	14176
残基数 n_residues	1890
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

▼

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

最大尺寸 Dmax dmax	170.7 Å
Rg (实空间) rg_real	45.42 Å
Rg 误差 (实空间) rg_real_error	2.30 Å
I(0) (实空间) i0_real	6.1630e+08
I(0) 误差 (实空间) i0_real_error	1.2130e+07
Rg (倒空间) rg_reciprocal	44.70 Å
I(0) (倒空间) i0_reciprocal	615800000.0000
解质量估计 total_estimate	0.7377
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	39.0 Å
偏度 Skewness skewness	0.805
峰度 Kurtosis kurtosis	0.558
角度范围 angular_range	— – 0.1750 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	108500000.0000
实空间数据点数 n_real_points	36
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.496; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.469; Smooth: 0.628

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (5)

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	14176

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 polymer

描述 description	Ferredoxin
分子量 formula_weight	5877.5 kDa
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	E

MAYKITEDCVSCGSCASECPADAISQGDSQFVIDPEKCIECGNCANVCPVGAPVEES

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	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

▶

7. 引用文献 (1)

▶

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	2.100 Å
最低分辨率 resolution_low	183.960 Å
R 因子 r_factor	0.3335
R_work r_work	0.3335
R_free r_free	—

分辨率 resolution	2.10 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	896132

fit	/app/data/saxs_computation/g0/9g03/9g03.fit
pddf	/app/data/pr_computation/g0/9g03/9g03.pr.out
profile	/app/data/saxs_computation/g0/9g03/9g03.dat

Structure of carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) in complex with ferredoxin (Clostridium autoethanogenum)

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 (5)

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

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)