8uem

The CryoEM structure of the high affinity Carbon monoxide dehydrogenase from Mycobacterium smegmatis

Method: ELECTRON MICROSCOPY D_max: 146.4 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	8uem
沉积日期 deposition_date	2023-10-02
结构标题 title	The CryoEM structure of the high affinity Carbon monoxide dehydrogenase from Mycobacterium smegmatis
关键词 keywords	Carbon monoxide dehydrogenase, MoCu, Mycobacterium smegmatis, High affinity, trace gas scavenging, 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	43.19 Å
回转半径 Rg (电子) rg_electron	43.19 Å
零角强度 I(0) i0	1112350000.00
分子量 molecular_weight	267300.0 kDa
排除体积 excluded_volume	330690 Å³
包络体积 envelope_volume	381670 Å³
水化壳体积 shell_volume	72935 Å³
包络直径 envelope_diameter	151.0 Å
壳层 Rg shell_rg	48.35 Å
包络 Rg envelope_rg	43.39 Å
形状 Rg shape_rg	43.23 Å
总 Rg total_rg	43.23 Å
总原子数 total_atoms	18672
残基数 n_residues	2450
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	146.4 Å
Rg (实空间) rg_real	43.32 Å
Rg 误差 (实空间) rg_real_error	1.77 Å
I(0) (实空间) i0_real	1.1120e+09
I(0) 误差 (实空间) i0_real_error	2.3260e+07
Rg (倒空间) rg_reciprocal	43.20 Å
I(0) (倒空间) i0_reciprocal	1112000000.0000
解质量估计 total_estimate	0.8623
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	43.5 Å
偏度 Skewness skewness	0.442
峰度 Kurtosis kurtosis	-0.327
角度范围 angular_range	— – 0.1850 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	140500000.0000
实空间数据点数 n_real_points	38
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.812; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.781

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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 (8)

Entity 1 polymer

描述 description	Carbon monoxide dehydrogenase (Large chain), CoxL
分子量 formula_weight	85957.8 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	A,D
原子数 atom_count	19599

MTTLENPVERPEDTAVNDAKPCGHGRMLRKEDPRFIRGRGNYVDDVKLPGMLHLAILRSPYAHATINSIDVTAAQAHPKVKAVVTGADLAAKGLAWMPTLSNDVQAVLATDKVRFQGQEVAFVVAEDRYSARDALELIDVDYEPLDPVIDARHALDPGAPVIRTDLDGKTDNHCFDWETGDAAATDAVFAKADVVVKQEMVYPRVHPAPMETCGAVADLDPVTRKLTLWSTTQAPHAHRTLYALVAGLPEHKIRVISPDIGGGFGNKVPIYPGYVCAIVGSLLLGKPVKWMEDRSENLTSTGFARDYIMVGEIAATRDGKILAIRSNVLADHGAFNGTAAPVKYPAGFFGVFTGSYDIEAAYCHMTAVYTNKAPGGVAYACSFRITEAVYFVERLVDCLAYELKMDPAQLRLQNLLKAEQFPYTSKTGWVYDSGDYEKTMRLAMEMVDYEGLRAEQAEKRKRGELMGIGMSFFTEAVGAGPRKDMDILGLGMADGCELRVHPTGKAVVRLSVQSQGQGHETTFAQIVAEELGIPPEDIDVVHGDTDQTPFGLGTYGSRSTPVSGAAAALVARKVRDKAKIIAAGMLEASIADLEWDKGSFHIKGDPSASVTIADIAMRAHGAGDLPEGLEGGLDAQICYNPSNLTYPYGAYFCVVDIDPGTAVVKVRRFVAVDDCGTRINPMIIEGQIHGGLVDGIGMALMEMIAFDEDGNCLGGSLMDYLIPTAMEVPHFETGHTVTPSPHHPIGAKGIGESATVGSPPAVVNAVVDALAPYGVRHADMPLTPSRVWEAMQGRATPPI

Entity 2 polymer

描述 description	Carbon monoxide dehydrogenase medium chain
分子量 formula_weight	31710.1 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

MQVPGPFEYERATSVDHAVGLLDRLGEDARIVAGGHSLLPMMKLRIANPEYLVDINDLAVELGYVITDPTLVRIGAMARHRQVLESDPLAAVCPIFRDAERVIADPVVRNRGTLGGSLCQADPAEDLTTVCTILGAVCLARGPGGEREIGIDDFLVGPYETALAHNEMLVEVRIPVRHRTSSAYAKVERRVGDWAVTAAGAQVTLDGDSIVAARVGLTAVNPDPDALRALADDLIGKPATEETFAAAGELAVQACEPVTDTRGSADYKRHLARELTIRTMRTAVERVRTAPAPEGN

Entity 3 polymer

描述 description	[2Fe-2S] binding domain protein
分子量 formula_weight	17148.6 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

MQVTMTVNGEAVTADVEPRMLLVHFLRDQLGLTGTHWGCDTSNCGTCVVEVDGEPVKSCTMLAAMASGHSVNTVEGMEVDGKLDPVQEGFMQCHGLQCGFCTPGMMITARALLRQNPDPTEEEIREAISGQICRCTGYTTIVRSVQWAARHAREEAKA

Entity 4 non-polymer

描述 description	CU(I)-S-MO(IV)(=O)OH CLUSTER
分子量 formula_weight	224.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 5 non-polymer

描述 description	PTERIN CYTOSINE DINUCLEOTIDE
分子量 formula_weight	696.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 6 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 7 non-polymer

描述 description	FE2/S2 (INORGANIC) CLUSTER
分子量 formula_weight	175.8 kDa
来源方法 src_method	nat
拷贝数 entity_count	4

Entity 8 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	899

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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	1.85 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	290597

fit	/app/data/saxs_computation/ue/8uem/8uem.fit
pddf	/app/data/pr_computation/ue/8uem/8uem.pr.out
profile	/app/data/saxs_computation/ue/8uem/8uem.dat

The CryoEM structure of the high affinity Carbon monoxide dehydrogenase from Mycobacterium smegmatis

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

冷冻电镜 EM 3D

5. 实体与聚合体信息 (8)

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 water

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)