1yew

Crystal structure of particulate methane monooxygenase

Method: X-RAY DIFFRACTION D_max: 124.0 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	1yew
沉积日期 deposition_date	2004-12-28
结构标题 title	Crystal structure of particulate methane monooxygenase
关键词 keywords	membrane protein, methane, beta barrel, OXIDOREDUCTASE; OXIDOREDUCTASE, MEMBRANE PROTEIN
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	41.66 Å
回转半径 Rg (电子) rg_electron	40.80 Å
零角强度 I(0) i0	1001440000.00
分子量 molecular_weight	279540.0 kDa
排除体积 excluded_volume	356120 Å³
包络体积 envelope_volume	453210 Å³
水化壳体积 shell_volume	87613 Å³
包络直径 envelope_diameter	129.8 Å
壳层 Rg shell_rg	50.35 Å
包络 Rg envelope_rg	39.85 Å
形状 Rg shape_rg	40.77 Å
总 Rg total_rg	41.36 Å
总原子数 total_atoms	19772
残基数 n_residues	2424
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	124.0 Å
Rg (实空间) rg_real	41.37 Å
Rg 误差 (实空间) rg_real_error	0.81 Å
I(0) (实空间) i0_real	1.0010e+09
I(0) 误差 (实空间) i0_real_error	1.6650e+07
Rg (倒空间) rg_reciprocal	41.66 Å
I(0) (倒空间) i0_reciprocal	1002000000.0000
解质量估计 total_estimate	0.8839
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	58.7 Å
偏度 Skewness skewness	0.016
峰度 Kurtosis kurtosis	-0.425
角度范围 angular_range	— – 0.1900 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	188900000.0000
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: 0.896; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.953; Smooth: 0.847

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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	particulate methane monooxygenase, B subunit
分子量 formula_weight	42832.9 kDa
来源方法 src_method	nat
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,E,I
原子数 atom_count	19772

HGEKSQAAFMRMRTIHWYDLSWSKEKVKINETVEIKGKFHVFEGWPETVDEPDVAFLNVGMPGPVFIRKESYIGGQLVPRSVRLEIGKTYDFRVVLKARRPGDWHVHTMMNVQGGGPIIGPGKWITVEGSMSEFRNPVTTLTGQTVDLENYNEGNTYFWHAFWFAIGVAWIGYWSRRPIFIPRLLMVDAGRADELVSATDRKVAMGFLAATILIVVMAMSSANSKYPITIPLQAGTMRGMKPLELPAPTVSVKVEDATYRVPGRAMRMKLTITNHGNSPIRLGEFYTASVRFLDSDVYKDTTGYPEDLLAEDGLSVSDNSPLAPGETRTVDVTASDAAWEVYRLSDIIYDPDSRFAGLLFFFDATGNRQVVQIDAPLIPSFM

Entity 2 polymer

描述 description	particulate methane monooxygenase, A subunit
分子量 formula_weight	28445.1 kDa
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B,F,J

MSAAQSAVRSHAEAVQVSRTIDWMALFVVFFVIVGSYHIHAMLTMGDWDFWSDWKDRRLWVTVTPIVLVTFPAAVQSYLWERYRLPWGATVCVLGLLLGEWINRYFNFWGWTYFPINFVFPASLVPGAIILDTVLMLSGSYLFTAIVGAMGWGLIFYPGNWPIIAPLHVPVEYNGMLMSIADIQGYNYVRTGTPEYIRMVEKGTLRTFGKDVAPVSAFFSAFMSILIYFMWHFIGRWFSNERFLQST

来源 Source

来源生物 organism	Methylococcus capsulatus
NCBI 分类编号 ncbi_taxonomy_id	243233
宿主生物 host_organism	Escherichia coli

Entity 3 polymer

描述 description	particulate methane monooxygenase subunit C2
分子量 formula_weight	33214.2 kDa
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C,G,K

MHETKQGGEKRFTGAICRCSHRYNSMEVKMAATTIGGAAAAEAPLLDKKWLTFALAIYTVFYLWVRWYEGVYGWSAGLDSFAPEFETYWMNFLYTEIVLEIVTASILWGYLWKTRDRNLAALTPREELRRNFTHLVWLVAYAWAIYWGASYFTEQDGTWHQTIVRDTDFTPSHIIEFYLSYPIYIITGFAAFIYAKTRLPFFAKGISLPYLVLVVGPFMILPNVGLNEWGHTFWFMEELFVAPLHYGFVIFGWLALAVMGTLTQTFYSFAQGGLGQSLCEAVDEGLIAK

来源 Source

来源生物 organism	Methylococcus capsulatus
NCBI 分类编号 ncbi_taxonomy_id	414
宿主生物 host_organism	Escherichia coli

Entity 4 non-polymer

描述 description	COPPER (II) ION
分子量 formula_weight	63.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 5 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

Entity 6 non-polymer

描述 description	DINUCLEAR COPPER ION
分子量 formula_weight	127.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

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6. 折叠分类 (SCOP + CATH) 15 domains

CATH v4.4 (15 domains)

结构域编号 domain_id	1yewA01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	570 — Particulate methane monooxygenase, b subunit. Chain: A, domain 1

结构域编号 domain_id	1yewA02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	710 — Helix hairpin bin

结构域编号 domain_id	1yewA03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	1580 — Particulate methane monooxygenase, b subunit. Chain: A, domain 3

结构域编号 domain_id	1yewB00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1450 — particulate methane monooxygenase, chain B
同源超家族 H-superfamily homologous superfamily	10 — Ammonia/particulate methane monooxygenase, subunit A

结构域编号 domain_id	1yewC00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	50 — Particulate methane monooxygenase subunit c2. Chain: C

结构域编号 domain_id	1yewE01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	570 — Particulate methane monooxygenase, b subunit. Chain: A, domain 1

结构域编号 domain_id	1yewE02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	710 — Helix hairpin bin

结构域编号 domain_id	1yewE03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	1580 — Particulate methane monooxygenase, b subunit. Chain: A, domain 3

结构域编号 domain_id	1yewF00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1450 — particulate methane monooxygenase, chain B
同源超家族 H-superfamily homologous superfamily	10 — Ammonia/particulate methane monooxygenase, subunit A

结构域编号 domain_id	1yewG00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	50 — Particulate methane monooxygenase subunit c2. Chain: C

结构域编号 domain_id	1yewI01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	570 — Particulate methane monooxygenase, b subunit. Chain: A, domain 1

结构域编号 domain_id	1yewI02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	710 — Helix hairpin bin

结构域编号 domain_id	1yewI03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	1580 — Particulate methane monooxygenase, b subunit. Chain: A, domain 3

结构域编号 domain_id	1yewJ00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1450 — particulate methane monooxygenase, chain B
同源超家族 H-superfamily homologous superfamily	10 — Ammonia/particulate methane monooxygenase, subunit A

结构域编号 domain_id	1yewK00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	50 — Particulate methane monooxygenase subunit c2. Chain: C

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7. 引用文献 (1)

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晶胞边长 a length_a	264.140 Å
晶胞边长 b length_b	264.140 Å
晶胞边长 c length_c	150.005 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	24

空间群 space_group	P 42 21 2
空间群编号 int_tables_number	94
晶系 crystal_system	—

分辨率 resolution	2.801 Å
最低分辨率 resolution_low	29.550 Å
R 因子 r_factor	0.2730
R_work r_work	0.2715
R_free r_free	0.3016

fit	/app/data/saxs_computation/ye/1yew/1yew.fit
pddf	/app/data/pr_computation/ye/1yew/1yew.pr.out
profile	/app/data/saxs_computation/ye/1yew/1yew.dat

Crystal structure of particulate 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

精修参数 Refinement

衍射实验 Diffraction

5. 实体与聚合体信息 (6)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 polymer

聚合体 Polymer

来源 Source

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

6. 折叠分类 (SCOP + CATH) 15 domains

CATH v4.4 (15 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)