5e9z

Cytochrome P450 BM3 mutant M11

Method: X-RAY DIFFRACTION Dmax: 170.7 Å Quality: GOOD

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

Bifunctional cytochrome P450/NADPH--P450 reductase

Bacillus megaterium

UniProt P14779

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 蛋白单体 单体 蛋白 × 1 PDB 声明:monomeric(1) 与蛋白拷贝数一致 链 A; UniProt 1–468 片段:UNP residues 1-468 突变:R47L, E64G, F81I, F87V, E143G, L188Q, Y198C, E267V, H285Y, G415S FE2 FE (II) ION × 1 PP9 PROTOPORPHYRIN IX × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 8;295 K;Prior to the crystallization setup, 3mM of DTT was added to the concentrated M11 protein sample. Crystals were grown using hanging drops mixing 0.5 uL of M11 with 0.5 uL of the reservoir solution containing 10-15% PEG 3350, 0.1M Tris pH8.0, 0.1-0.2 M MgCl2 or MgSO4, and 10 mM DTT 分辨率 2.23 Å R-free 0.225
2 蛋白单体 单体 蛋白 × 1 PDB 声明:monomeric(1) 与蛋白拷贝数一致 链 B; UniProt 1–468 片段:UNP residues 1-468 突变:R47L, E64G, F81I, F87V, E143G, L188Q, Y198C, E267V, H285Y, G415S FE2 FE (II) ION × 1 PP9 PROTOPORPHYRIN IX × 1 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 8;295 K;Prior to the crystallization setup, 3mM of DTT was added to the concentrated M11 protein sample. Crystals were grown using hanging drops mixing 0.5 uL of M11 with 0.5 uL of the reservoir solution containing 10-15% PEG 3350, 0.1M Tris pH8.0, 0.1-0.2 M MgCl2 or MgSO4, and 10 mM DTT 分辨率 2.23 Å R-free 0.225
3 蛋白单体 单体 蛋白 × 1 PDB 声明:monomeric(1) 与蛋白拷贝数一致 链 C; UniProt 1–468 片段:UNP residues 1-468 突变:R47L, E64G, F81I, F87V, E143G, L188Q, Y198C, E267V, H285Y, G415S FE2 FE (II) ION × 1 PP9 PROTOPORPHYRIN IX × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 8;295 K;Prior to the crystallization setup, 3mM of DTT was added to the concentrated M11 protein sample. Crystals were grown using hanging drops mixing 0.5 uL of M11 with 0.5 uL of the reservoir solution containing 10-15% PEG 3350, 0.1M Tris pH8.0, 0.1-0.2 M MgCl2 or MgSO4, and 10 mM DTT 分辨率 2.23 Å R-free 0.225
4 蛋白单体 单体 蛋白 × 1 PDB 声明:monomeric(1) 与蛋白拷贝数一致 链 D; UniProt 1–468 片段:UNP residues 1-468 突变:R47L, E64G, F81I, F87V, E143G, L188Q, Y198C, E267V, H285Y, G415S FE2 FE (II) ION × 1 PP9 PROTOPORPHYRIN IX × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 8;295 K;Prior to the crystallization setup, 3mM of DTT was added to the concentrated M11 protein sample. Crystals were grown using hanging drops mixing 0.5 uL of M11 with 0.5 uL of the reservoir solution containing 10-15% PEG 3350, 0.1M Tris pH8.0, 0.1-0.2 M MgCl2 or MgSO4, and 10 mM DTT 分辨率 2.23 Å R-free 0.225

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 168 个其他 PDB 条目、308 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 CPXB_BACME
Isoform
PDB实体 1
链与序列区间 作者链 A; PDB构建体 2–469; UniProt 1–468 作者链 B; PDB构建体 2–469; UniProt 1–468 作者链 C; PDB构建体 2–469; UniProt 1–468 作者链 D; PDB构建体 2–469; UniProt 1–468

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 5e9z

P(r) 距离分布 P(r) Distribution

P(r) distribution for 5e9z
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2. 结构基本信息 2. Structure Basics

条目编号 entry_id5e9z
沉积日期 deposition_date2015-10-15
结构标题 titleCytochrome P450 BM3 mutant M11
关键词 keywordsmetabolism, molecular dynamics, free energy calculations, thermodynamic integration, 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_guinier49.62
回转半径 Rg (电子) rg_electron49.97
零角强度 I(0) i0571963000.00
分子量 molecular_weight202930.0 kDa
排除体积 excluded_volume255940 ų
包络体积 envelope_volume361480 ų
水化壳体积 shell_volume64369 ų
包络直径 envelope_diameter178.7
壳层 Rg shell_rg48.82
包络 Rg envelope_rg49.03
形状 Rg shape_rg49.98
总 Rg total_rg49.88
总原子数 total_atoms14432
残基数 n_residues1792
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 dmax170.7
Rg (实空间) rg_real50.02
Rg 误差 (实空间) rg_real_error1.87
I(0) (实空间) i0_real5.7200e+08
I(0) 误差 (实空间) i0_real_error1.1540e+07
Rg (倒空间) rg_reciprocal49.62
I(0) (倒空间) i0_reciprocal571700000.0000
解质量估计 total_estimate0.7998
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks1
主峰位置 r_peak_primary69.4
偏度 Skewness skewness0.465
峰度 Kurtosis kurtosis-0.201
角度范围 angular_range— – 0.1600 −1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha121900000.0000
实空间数据点数 n_real_points33
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.692; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.897; Smooth: 0.418

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

6. 实体与聚合物信息 Entities & Polymers (5)

7. 折叠分类 (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

结构域编号 domain_idd5e9za_
类 Class classa — All alpha proteins
折叠类型 Fold folda.104 — Cytochrome P450
超家族 Superfamily superfamilya.104.1 — Cytochrome P450
家族 Family familya.104.1.1 — Cytochrome P450
结构域编号 domain_idd5e9zb_
类 Class classa — All alpha proteins
折叠类型 Fold folda.104 — Cytochrome P450
超家族 Superfamily superfamilya.104.1 — Cytochrome P450
家族 Family familya.104.1.1 — Cytochrome P450
结构域编号 domain_idd5e9zc1
类 Class classa — All alpha proteins
折叠类型 Fold folda.104 — Cytochrome P450
超家族 Superfamily superfamilya.104.1 — Cytochrome P450
家族 Family familya.104.1.1 — Cytochrome P450
结构域编号 domain_idd5e9zc2
类 Class classl — Artifacts
折叠类型 Fold foldl.1 — Tags
超家族 Superfamily superfamilyl.1.1 — Tags
家族 Family familyl.1.1.1 — Tags
结构域编号 domain_idd5e9zd_
类 Class classa — All alpha proteins
折叠类型 Fold folda.104 — Cytochrome P450
超家族 Superfamily superfamilya.104.1 — Cytochrome P450
家族 Family familya.104.1.1 — Cytochrome P450

CATH v4.4 (4 domains)

结构域编号 domain_id5e9zA00
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology630 — Cytochrome p450
同源超家族 H-superfamily homologous superfamily10 — Cytochrome P450
结构域编号 domain_id5e9zB00
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology630 — Cytochrome p450
同源超家族 H-superfamily homologous superfamily10 — Cytochrome P450
结构域编号 domain_id5e9zC00
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology630 — Cytochrome p450
同源超家族 H-superfamily homologous superfamily10 — Cytochrome P450
结构域编号 domain_id5e9zD00
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology630 — Cytochrome p450
同源超家族 H-superfamily homologous superfamily10 — Cytochrome P450

8. 引用文献 (1)

9. 文件与曲线 (10)