8xiw

Cryo-EM complex structure between hydroxylase and regulatory component from soluble methane monooxygenase

Method: ELECTRON MICROSCOPY D_max: 130.6 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	8xiw
沉积日期 deposition_date	2023-12-20
最后修订 last_revision	2025-06-25
结构标题 title	Cryo-EM complex structure between hydroxylase and regulatory component from soluble methane monooxygenase
关键词 keywords	soluble methane monooxygenase, hydroxylase, regulatory component, 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	42.11 Å
回转半径 Rg (电子) rg_electron	41.85 Å
零角强度 I(0) i0	969668000.00
分子量 molecular_weight	258450.0 kDa
排除体积 excluded_volume	323160 Å³
包络体积 envelope_volume	405690 Å³
水化壳体积 shell_volume	77173 Å³
包络直径 envelope_diameter	138.7 Å
壳层 Rg shell_rg	49.69 Å
包络 Rg envelope_rg	41.68 Å
形状 Rg shape_rg	41.85 Å
总 Rg total_rg	42.18 Å
总原子数 total_atoms	18303
残基数 n_residues	2266
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	130.6 Å
Rg (实空间) rg_real	42.05 Å
Rg 误差 (实空间) rg_real_error	0.94 Å
I(0) (实空间) i0_real	9.6970e+08
I(0) 误差 (实空间) i0_real_error	1.6440e+07
Rg (倒空间) rg_reciprocal	42.11 Å
I(0) (倒空间) i0_reciprocal	969700000.0000
解质量估计 total_estimate	0.8681
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	45.9 Å
偏度 Skewness skewness	0.286
峰度 Kurtosis kurtosis	-0.516
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	473600000.0000
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: 0.948; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.445

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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	Methane monooxygenase
分子量 formula_weight	59979.2 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,E
原子数 atom_count	18397

MAISLATKAATDALKVNRAPVGVEPQEVHKWLQSFNWDFKENRTKYATKYHMANQTKEQFKVIAKEYARMEAAKDERQFGTLLDGLTRLGAGNKVHPRWGETMKVISNFLEVGEYNAIAASAMLWDSATAAEQKNGYLAQVLDEIRHTHQCAFINHYYSKHYHDPAGHNDARRTRAIGPLWKGMKRVFADGFISGDAVECSVNLQLVGEACFTNPLIVAVTEWASANGDEITPTVFLSVETDELRHMANGYQTVVSIANDPAAAKYLNTDLNNAFWTQQKYFTPALGYLFEYGSKFKVEPWVKTWNRWVYEDWGGIWIGRLGKYGVESPRSLRDAKTDAYWAHHDLALAAYALWPLGFARLALPDEEDQEWFEANYPGWADHYGKIYNEWKKLGYEDPKSGFIPYAWLLANGHDVYIDRVSQVPFIPSLAKGSGSLRVHEFNGKKHSLTDDWGERMWLSEPERYECHNLFEQYEGRELSEVIAEGHGVRSDGKTLIAQPHVRGDNLWTLEDIKRAGCVFPNPLAKF

Entity 2 polymer

描述 description	Methane monooxygenase
分子量 formula_weight	45239.2 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,F

MSQPQSSQVTKRGLTDPERAAIIAAAVPDHALDTQRKYHYFIQPRWKRLSEYEQLSCYAQPNPDWIAGGLDWGDWTQKFHGGRPSWGNESTELRTTDWYRHRDPARRWHAPYVKDKSEEARYTQRFLAAYSSEGSIRTIDAYWRDEILNKYYGALLYNEYGLFNAHSSVGRDCLSDTIRQSATFAGLDKVDNAQMIQMERLFIAKLVPGFDASTDVPKKIWTTDPIYAGARGAVEEIWQGIQDWNEILWAGHAVYDATFGQFARREFFQRLATVYGDTLTPFFTAQSQTYFQTTRGAIEDLFVYCLANDPEFGAHNRTFLNAWTEHYLARSVTALKDFVGIYAKVEKVAGATDRAGVSEALQRVFGDWKVDYADKIGFNIDVDQKVDAVLAGFKN

Entity 3 polymer

描述 description	Methane monooxygenase
分子量 formula_weight	19379.2 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,G

MAKREPIHENSTRTEWEGKIAKLNSVDQATKFIQDFRVAYSSPFRKSYDLDVDYQYIERKIEERLSVLKTEKLSVADLVTKATTGEDAAAVEAAWIAKMKAAESKYAAERIHIEFRQLYKPPVLPVNVFLRTDAALGTILMELRNTDYYATPLEGLRKERGVKVLHLQA

Entity 4 polymer

描述 description	Methane monooxygenase
分子量 formula_weight	14916.9 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	D

MSSAHNAYNAGIMQKTGKAFADEFFAEENQVVHESNAVVLVLMKSDEIDAIIEDMVLKGGKAKNPSIVVEDKAGFWWIKADGAIEIDAAEASDLLGKPFSVYDLLVNVSSTVGRAYTLGTKFTITSELMGLDRALTDI

来源 Source

来源生物 organism	Methylosinus sporium
NCBI 分类编号 ncbi_taxonomy_id	428
宿主生物 host_organism	Escherichia coli

Entity 5 non-polymer

描述 description	FE (III) ION
分子量 formula_weight	55.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 6 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	94

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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	2.85 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	200043

fit	/app/data/saxs_computation/xi/8xiw/8xiw.fit
pddf	/app/data/pr_computation/xi/8xiw/8xiw.pr.out
profile	/app/data/saxs_computation/xi/8xiw/8xiw.dat

Cryo-EM complex structure between hydroxylase and regulatory component from soluble methane monooxygenase

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 (6)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

Entity 4 polymer

聚合体 Polymer

来源 Source

Entity 5 non-polymer

Entity 6 water

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)