4gam

Complex structure of Methane monooxygenase hydroxylase and regulatory subunit

Method: X-RAY DIFFRACTION Dmax: 161.8 Å Quality: GOOD

1. 蛋白身份与相关结构 Protein Identity & Related Structures

Methane monooxygenase component A beta chain

物种未注明

UniProt P18798

当前结构中的状态

Assembly 聚集状态 构建体 突变与修饰 配体、离子与共同组分 实验方法与环境 结构质量
1 蛋白异源复合物 异源复合物 蛋白 × 8 PDB 声明:octameric(8) 与蛋白拷贝数一致 链 B; UniProt 1–389 链 G; UniProt 1–389 未记录 Methane monooxygenase component A alpha chain × 2 (P22869) Methane monooxygenase component A gamma chain × 2 (P11987) Methane monooxygenase regulatory protein B × 2 (P18797) FE FE (III) ION × 4 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, SITTING DROP;pH 6.5;298 K;0.1 M MES and 15% PEG 20,000 (w/v) ure 298K, pH 6.5, VAPOR DIFFUSION, SITTING DROP 分辨率 2.90 Å R-free 0.258
2 蛋白异源复合物 异源复合物 蛋白 × 8 PDB 声明:octameric(8) 与蛋白拷贝数一致 链 L; UniProt 1–389 链 Q; UniProt 1–389 未记录 Methane monooxygenase component A alpha chain × 2 (P22869) Methane monooxygenase component A gamma chain × 2 (P11987) Methane monooxygenase regulatory protein B × 2 (P18797) FE FE (III) ION × 4 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, SITTING DROP;pH 6.5;298 K;0.1 M MES and 15% PEG 20,000 (w/v) ure 298K, pH 6.5, VAPOR DIFFUSION, SITTING DROP 分辨率 2.90 Å R-free 0.258

数据库中的同蛋白其他状态

以下每一行都是同一 UniProt 蛋白在另一个 PDB 条目中的 biological assembly, “相对当前条目”直接指出证据层面的不同;没有差异标签表示当前已读取字段一致。

共 27 个其他 PDB 条目、27 个 assembly。 打开独立比较页并筛选聚集状态

查看构建体与数据证据
UniProt名称 MEMB_METCA
Isoform
PDB实体 1
链与序列区间 作者链 B; PDB构建体 1–389; UniProt 1–389 作者链 G; PDB构建体 1–389; UniProt 1–389 作者链 L; PDB构建体 1–389; UniProt 1–389 作者链 Q; PDB构建体 1–389; UniProt 1–389

Methane monooxygenase component A alpha chain

物种未注明

UniProt P22869

当前结构中的状态

Assembly 聚集状态 构建体 突变与修饰 配体、离子与共同组分 实验方法与环境 结构质量
1 蛋白异源复合物 异源复合物 蛋白 × 8 PDB 声明:octameric(8) 与蛋白拷贝数一致 链 A; UniProt 1–527 链 F; UniProt 1–527 未记录 Methane monooxygenase component A beta chain × 2 (P18798) Methane monooxygenase component A gamma chain × 2 (P11987) Methane monooxygenase regulatory protein B × 2 (P18797) FE FE (III) ION × 4 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, SITTING DROP;pH 6.5;298 K;0.1 M MES and 15% PEG 20,000 (w/v) ure 298K, pH 6.5, VAPOR DIFFUSION, SITTING DROP 分辨率 2.90 Å R-free 0.258
2 蛋白异源复合物 异源复合物 蛋白 × 8 PDB 声明:octameric(8) 与蛋白拷贝数一致 链 K; UniProt 1–527 链 P; UniProt 1–527 未记录 Methane monooxygenase component A beta chain × 2 (P18798) Methane monooxygenase component A gamma chain × 2 (P11987) Methane monooxygenase regulatory protein B × 2 (P18797) FE FE (III) ION × 4 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, SITTING DROP;pH 6.5;298 K;0.1 M MES and 15% PEG 20,000 (w/v) ure 298K, pH 6.5, VAPOR DIFFUSION, SITTING DROP 分辨率 2.90 Å R-free 0.258

数据库中的同蛋白其他状态

以下每一行都是同一 UniProt 蛋白在另一个 PDB 条目中的 biological assembly, “相对当前条目”直接指出证据层面的不同;没有差异标签表示当前已读取字段一致。

共 31 个其他 PDB 条目、46 个 assembly。 打开独立比较页并筛选聚集状态

查看构建体与数据证据
UniProt名称 MEMA_METCA
Isoform
PDB实体 2
链与序列区间 作者链 A; PDB构建体 1–527; UniProt 1–527 作者链 F; PDB构建体 1–527; UniProt 1–527 作者链 K; PDB构建体 1–527; UniProt 1–527 作者链 P; PDB构建体 1–527; UniProt 1–527

Methane monooxygenase component A gamma chain

物种未注明

UniProt P11987

当前结构中的状态

Assembly 聚集状态 构建体 突变与修饰 配体、离子与共同组分 实验方法与环境 结构质量
1 蛋白异源复合物 异源复合物 蛋白 × 8 PDB 声明:octameric(8) 与蛋白拷贝数一致 链 C; UniProt 1–170 链 H; UniProt 1–170 未记录 Methane monooxygenase component A beta chain × 2 (P18798) Methane monooxygenase component A alpha chain × 2 (P22869) Methane monooxygenase regulatory protein B × 2 (P18797) FE FE (III) ION × 4 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, SITTING DROP;pH 6.5;298 K;0.1 M MES and 15% PEG 20,000 (w/v) ure 298K, pH 6.5, VAPOR DIFFUSION, SITTING DROP 分辨率 2.90 Å R-free 0.258
2 蛋白异源复合物 异源复合物 蛋白 × 8 PDB 声明:octameric(8) 与蛋白拷贝数一致 链 M; UniProt 1–170 链 R; UniProt 1–170 未记录 Methane monooxygenase component A beta chain × 2 (P18798) Methane monooxygenase component A alpha chain × 2 (P22869) Methane monooxygenase regulatory protein B × 2 (P18797) FE FE (III) ION × 4 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, SITTING DROP;pH 6.5;298 K;0.1 M MES and 15% PEG 20,000 (w/v) ure 298K, pH 6.5, VAPOR DIFFUSION, SITTING DROP 分辨率 2.90 Å R-free 0.258

数据库中的同蛋白其他状态

以下每一行都是同一 UniProt 蛋白在另一个 PDB 条目中的 biological assembly, “相对当前条目”直接指出证据层面的不同;没有差异标签表示当前已读取字段一致。

共 28 个其他 PDB 条目、28 个 assembly。 打开独立比较页并筛选聚集状态

查看构建体与数据证据
UniProt名称 MEMG_METCA
Isoform
PDB实体 3
链与序列区间 作者链 C; PDB构建体 1–170; UniProt 1–170 作者链 H; PDB构建体 1–170; UniProt 1–170 作者链 M; PDB构建体 1–170; UniProt 1–170 作者链 R; PDB构建体 1–170; UniProt 1–170

Methane monooxygenase regulatory protein B

Methylococcus capsulatus

UniProt P18797

当前结构中的状态

Assembly 聚集状态 构建体 突变与修饰 配体、离子与共同组分 实验方法与环境 结构质量
1 蛋白异源复合物 异源复合物 蛋白 × 8 PDB 声明:octameric(8) 与蛋白拷贝数一致 链 D; UniProt 1–141 链 I; UniProt 1–141 未记录 Methane monooxygenase component A beta chain × 2 (P18798) Methane monooxygenase component A alpha chain × 2 (P22869) Methane monooxygenase component A gamma chain × 2 (P11987) FE FE (III) ION × 4 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, SITTING DROP;pH 6.5;298 K;0.1 M MES and 15% PEG 20,000 (w/v) ure 298K, pH 6.5, VAPOR DIFFUSION, SITTING DROP 分辨率 2.90 Å R-free 0.258
2 蛋白异源复合物 异源复合物 蛋白 × 8 PDB 声明:octameric(8) 与蛋白拷贝数一致 链 N; UniProt 1–141 链 S; UniProt 1–141 未记录 Methane monooxygenase component A beta chain × 2 (P18798) Methane monooxygenase component A alpha chain × 2 (P22869) Methane monooxygenase component A gamma chain × 2 (P11987) FE FE (III) ION × 4 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, SITTING DROP;pH 6.5;298 K;0.1 M MES and 15% PEG 20,000 (w/v) ure 298K, pH 6.5, VAPOR DIFFUSION, SITTING DROP 分辨率 2.90 Å R-free 0.258

数据库中的同蛋白其他状态

以下每一行都是同一 UniProt 蛋白在另一个 PDB 条目中的 biological assembly, “相对当前条目”直接指出证据层面的不同;没有差异标签表示当前已读取字段一致。

共 1 个其他 PDB 条目、1 个 assembly。 打开独立比较页并筛选聚集状态

查看构建体与数据证据
UniProt名称 MMOB_METCA
Isoform
PDB实体 4
链与序列区间 作者链 D; PDB构建体 1–141; UniProt 1–141 作者链 I; PDB构建体 1–141; UniProt 1–141 作者链 N; PDB构建体 1–141; UniProt 1–141 作者链 S; PDB构建体 1–141; UniProt 1–141

页面优先展示蛋白身份、当前 assembly、共同组分、聚集状态和跨 PDB 结构链接。 链映射与序列区间收在“数据证据”中;数据库内部编号、导入时间和 assembly 操作表达式仅用于维护,因此不在读者页面展示。

SAXS 散射曲线 SAXS Profile

SAXS profile for 4gam

P(r) 距离分布 P(r) Distribution

P(r) distribution for 4gam
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2. 结构基本信息 2. Structure Basics

条目编号 entry_id4gam
沉积日期 deposition_date2012-07-25
结构标题 titleComplex structure of Methane monooxygenase hydroxylase and regulatory subunit
关键词 keywordsMethane Monooxygenase, hydroxylase, regulatory subunit B, OXIDOREDUCTASE; OXIDOREDUCTASE
实验方法 methodX-RAY DIFFRACTION

3. SAXS 参数 (CRYSOL 理论计算) 3. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier51.76
回转半径 Rg (电子) rg_electron51.29
零角强度 I(0) i04287900000.00
分子量 molecular_weight552830.0 kDa
排除体积 excluded_volume690620 ų
包络体积 envelope_volume836630 ų
水化壳体积 shell_volume126430 ų
包络直径 envelope_diameter172.0
壳层 Rg shell_rg61.60
包络 Rg envelope_rg50.79
形状 Rg shape_rg51.28
总 Rg total_rg51.57
总原子数 total_atoms39100
残基数 n_residues4788
球谐函数阶数 n_harmonics20
q 范围 q_range— – 0.5000 −1
数据点数 n_points101
壳层类型 shell_typedirectional
溶剂电子密度 solvent_density0.3340 e/ų
壳层衬度 contrast_shell0.0300 e/ų
CRYSOL 版本 crysol_version4.1.3

4. P(r) 距离分布 (GNOM 反演) 4. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax161.8
Rg (实空间) rg_real51.55
Rg 误差 (实空间) rg_real_error0.98
I(0) (实空间) i0_real4.2880e+09
I(0) 误差 (实空间) i0_real_error8.1160e+07
Rg (倒空间) rg_reciprocal51.93
I(0) (倒空间) i0_reciprocal4290000000.0000
解质量估计 total_estimate0.8766
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks1
主峰位置 r_peak_primary70.1
偏度 Skewness skewness0.137
峰度 Kurtosis kurtosis-0.460
角度范围 angular_range— – 0.1500 −1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha1742000000.0000
实空间数据点数 n_real_points31
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.915; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.960; Smooth: 0.686

5. 晶体学与实验 5. Crystallography & Experiment

6. 实体与聚合物信息 Entities & Polymers (6)

7. 折叠分类 (SCOP + CATH) 36 domains

SCOP 2.08 (16 domains)

结构域编号 domain_idd4gama_
类 Class classa — All alpha proteins
折叠类型 Fold folda.25 — Ferritin-like
超家族 Superfamily superfamilya.25.1 — Ferritin-like
家族 Family familya.25.1.2 — Ribonucleotide reductase-like
结构域编号 domain_idd4gamb_
类 Class classa — All alpha proteins
折叠类型 Fold folda.25 — Ferritin-like
超家族 Superfamily superfamilya.25.1 — Ferritin-like
家族 Family familya.25.1.2 — Ribonucleotide reductase-like
结构域编号 domain_idd4gamc_
类 Class classa — All alpha proteins
折叠类型 Fold folda.23 — Open three-helical up-and-down bundle
超家族 Superfamily superfamilya.23.3 — Methane monooxygenase hydrolase, gamma subunit
家族 Family familya.23.3.1 — Methane monooxygenase hydrolase, gamma subunit
结构域编号 domain_idd4gamd_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.137 — Monooxygenase (hydroxylase) regulatory protein
超家族 Superfamily superfamilyd.137.1 — Monooxygenase (hydroxylase) regulatory protein
家族 Family familyd.137.1.1 — Monooxygenase (hydroxylase) regulatory protein
结构域编号 domain_idd4gamf_
类 Class classa — All alpha proteins
折叠类型 Fold folda.25 — Ferritin-like
超家族 Superfamily superfamilya.25.1 — Ferritin-like
家族 Family familya.25.1.2 — Ribonucleotide reductase-like
结构域编号 domain_idd4gamg_
类 Class classa — All alpha proteins
折叠类型 Fold folda.25 — Ferritin-like
超家族 Superfamily superfamilya.25.1 — Ferritin-like
家族 Family familya.25.1.2 — Ribonucleotide reductase-like
结构域编号 domain_idd4gamh_
类 Class classa — All alpha proteins
折叠类型 Fold folda.23 — Open three-helical up-and-down bundle
超家族 Superfamily superfamilya.23.3 — Methane monooxygenase hydrolase, gamma subunit
家族 Family familya.23.3.1 — Methane monooxygenase hydrolase, gamma subunit
结构域编号 domain_idd4gami_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.137 — Monooxygenase (hydroxylase) regulatory protein
超家族 Superfamily superfamilyd.137.1 — Monooxygenase (hydroxylase) regulatory protein
家族 Family familyd.137.1.1 — Monooxygenase (hydroxylase) regulatory protein
结构域编号 domain_idd4gamk_
类 Class classa — All alpha proteins
折叠类型 Fold folda.25 — Ferritin-like
超家族 Superfamily superfamilya.25.1 — Ferritin-like
家族 Family familya.25.1.2 — Ribonucleotide reductase-like
结构域编号 domain_idd4gaml_
类 Class classa — All alpha proteins
折叠类型 Fold folda.25 — Ferritin-like
超家族 Superfamily superfamilya.25.1 — Ferritin-like
家族 Family familya.25.1.2 — Ribonucleotide reductase-like
结构域编号 domain_idd4gamm_
类 Class classa — All alpha proteins
折叠类型 Fold folda.23 — Open three-helical up-and-down bundle
超家族 Superfamily superfamilya.23.3 — Methane monooxygenase hydrolase, gamma subunit
家族 Family familya.23.3.1 — Methane monooxygenase hydrolase, gamma subunit
结构域编号 domain_idd4gamn_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.137 — Monooxygenase (hydroxylase) regulatory protein
超家族 Superfamily superfamilyd.137.1 — Monooxygenase (hydroxylase) regulatory protein
家族 Family familyd.137.1.1 — Monooxygenase (hydroxylase) regulatory protein
结构域编号 domain_idd4gamp_
类 Class classa — All alpha proteins
折叠类型 Fold folda.25 — Ferritin-like
超家族 Superfamily superfamilya.25.1 — Ferritin-like
家族 Family familya.25.1.2 — Ribonucleotide reductase-like
结构域编号 domain_idd4gamq_
类 Class classa — All alpha proteins
折叠类型 Fold folda.25 — Ferritin-like
超家族 Superfamily superfamilya.25.1 — Ferritin-like
家族 Family familya.25.1.2 — Ribonucleotide reductase-like
结构域编号 domain_idd4gamr_
类 Class classa — All alpha proteins
折叠类型 Fold folda.23 — Open three-helical up-and-down bundle
超家族 Superfamily superfamilya.23.3 — Methane monooxygenase hydrolase, gamma subunit
家族 Family familya.23.3.1 — Methane monooxygenase hydrolase, gamma subunit
结构域编号 domain_idd4gams_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.137 — Monooxygenase (hydroxylase) regulatory protein
超家族 Superfamily superfamilyd.137.1 — Monooxygenase (hydroxylase) regulatory protein
家族 Family familyd.137.1.1 — Monooxygenase (hydroxylase) regulatory protein

CATH v4.4 (20 domains)

结构域编号 domain_id4gamA00
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology620 — Ribonucleotide Reductase, subunit A
同源超家族 H-superfamily homologous superfamily20 — Ribonucleotide Reductase, subunit A
结构域编号 domain_id4gamB00
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology620 — Ribonucleotide Reductase, subunit A
同源超家族 H-superfamily homologous superfamily20 — Ribonucleotide Reductase, subunit A
结构域编号 domain_id4gamC01
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology1280 — Monooxygenase
同源超家族 H-superfamily homologous superfamily10 — Methane monooxygenase, gamma chain, domain 1
结构域编号 domain_id4gamC02
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology1280 — Monooxygenase
同源超家族 H-superfamily homologous superfamily30 — Methane monooxygenase, gamma chain, domain 2
结构域编号 domain_id4gamD00
类 Class class3 — Alpha Beta
架构 Architecture architecture90 — Alpha-Beta Complex
拓扑 Topology topology56 — Phenol Hydroxylase P2 Protein
同源超家族 H-superfamily homologous superfamily10 — Monooxygenase component MmoB/DmpM
结构域编号 domain_id4gamF00
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology620 — Ribonucleotide Reductase, subunit A
同源超家族 H-superfamily homologous superfamily20 — Ribonucleotide Reductase, subunit A
结构域编号 domain_id4gamG00
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology620 — Ribonucleotide Reductase, subunit A
同源超家族 H-superfamily homologous superfamily20 — Ribonucleotide Reductase, subunit A
结构域编号 domain_id4gamH01
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology1280 — Monooxygenase
同源超家族 H-superfamily homologous superfamily10 — Methane monooxygenase, gamma chain, domain 1
结构域编号 domain_id4gamH02
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology1280 — Monooxygenase
同源超家族 H-superfamily homologous superfamily30 — Methane monooxygenase, gamma chain, domain 2
结构域编号 domain_id4gamI00
类 Class class3 — Alpha Beta
架构 Architecture architecture90 — Alpha-Beta Complex
拓扑 Topology topology56 — Phenol Hydroxylase P2 Protein
同源超家族 H-superfamily homologous superfamily10 — Monooxygenase component MmoB/DmpM
结构域编号 domain_id4gamK00
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology620 — Ribonucleotide Reductase, subunit A
同源超家族 H-superfamily homologous superfamily20 — Ribonucleotide Reductase, subunit A
结构域编号 domain_id4gamL00
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology620 — Ribonucleotide Reductase, subunit A
同源超家族 H-superfamily homologous superfamily20 — Ribonucleotide Reductase, subunit A
结构域编号 domain_id4gamM01
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology1280 — Monooxygenase
同源超家族 H-superfamily homologous superfamily10 — Methane monooxygenase, gamma chain, domain 1
结构域编号 domain_id4gamM02
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology1280 — Monooxygenase
同源超家族 H-superfamily homologous superfamily30 — Methane monooxygenase, gamma chain, domain 2
结构域编号 domain_id4gamN00
类 Class class3 — Alpha Beta
架构 Architecture architecture90 — Alpha-Beta Complex
拓扑 Topology topology56 — Phenol Hydroxylase P2 Protein
同源超家族 H-superfamily homologous superfamily10 — Monooxygenase component MmoB/DmpM
结构域编号 domain_id4gamP00
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology620 — Ribonucleotide Reductase, subunit A
同源超家族 H-superfamily homologous superfamily20 — Ribonucleotide Reductase, subunit A
结构域编号 domain_id4gamQ00
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology620 — Ribonucleotide Reductase, subunit A
同源超家族 H-superfamily homologous superfamily20 — Ribonucleotide Reductase, subunit A
结构域编号 domain_id4gamR01
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology1280 — Monooxygenase
同源超家族 H-superfamily homologous superfamily10 — Methane monooxygenase, gamma chain, domain 1
结构域编号 domain_id4gamR02
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology1280 — Monooxygenase
同源超家族 H-superfamily homologous superfamily30 — Methane monooxygenase, gamma chain, domain 2
结构域编号 domain_id4gamS00
类 Class class3 — Alpha Beta
架构 Architecture architecture90 — Alpha-Beta Complex
拓扑 Topology topology56 — Phenol Hydroxylase P2 Protein
同源超家族 H-superfamily homologous superfamily10 — Monooxygenase component MmoB/DmpM

8. 引用文献 (1)

9. 文件与曲线 (10)