4dqk

Crystal structure of the FAD binding domain of cytochrome P450 BM3

Method: X-RAY DIFFRACTION Dmax: 160.5 Å Quality: REASONABLE

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

Bifunctional P-450/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 659–1049 片段:Cytochrome P450 BM3,UNP residues 659-1049 突变:C774A FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 SO4 SULFATE ION × 3 PG4 TETRAETHYLENE GLYCOL × 2 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, SITTING DROP;pH 6.5;293 K;2 microL of mother liquor to 2 microL of 12 mg/ml FAD domain. Crystals were obtained using a well solution of 28% polyethylene glycol 8000, 0.3 M ammonium sulfate, cacodylate buffer pH 6.5. Crystals of dimensions 70 x 70 x 900 M formed after 4-7 days. In order to form a coenzyme complex with NADP+, C773A/C999A FAD domain crystals were soaked in a 10 mM NADP+ solution for 10 minutes., VAPOR DIFFUSION, SITTING DROP, temperature 293K 分辨率 2.40 Å R-free 0.256
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 659–1049 片段:Cytochrome P450 BM3,UNP residues 659-1049 突变:C774A FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 SO4 SULFATE ION × 3 PG4 TETRAETHYLENE GLYCOL × 2 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, SITTING DROP;pH 6.5;293 K;2 microL of mother liquor to 2 microL of 12 mg/ml FAD domain. Crystals were obtained using a well solution of 28% polyethylene glycol 8000, 0.3 M ammonium sulfate, cacodylate buffer pH 6.5. Crystals of dimensions 70 x 70 x 900 M formed after 4-7 days. In order to form a coenzyme complex with NADP+, C773A/C999A FAD domain crystals were soaked in a 10 mM NADP+ solution for 10 minutes., VAPOR DIFFUSION, SITTING DROP, temperature 293K 分辨率 2.40 Å R-free 0.256

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、310 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 1–391; UniProt 659–1049 作者链 B; PDB构建体 1–391; UniProt 659–1049

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 4dqk

P(r) 距离分布 P(r) Distribution

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

条目编号 entry_id4dqk
沉积日期 deposition_date2012-02-16
结构标题 titleCrystal structure of the FAD binding domain of cytochrome P450 BM3
关键词 keywordsRossmann Fold, redox partner to cytochrome P450, FAD and NADP binding, none, 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_guinier46.58
回转半径 Rg (电子) rg_electron47.18
零角强度 I(0) i0111537000.00
分子量 molecular_weight85856.0 kDa
排除体积 excluded_volume106910 ų
包络体积 envelope_volume160130 ų
水化壳体积 shell_volume28976 ų
包络直径 envelope_diameter161.5
壳层 Rg shell_rg50.29
包络 Rg envelope_rg45.54
形状 Rg shape_rg47.16
总 Rg total_rg47.38
总原子数 total_atoms6036
残基数 n_residues762
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 dmax160.5
Rg (实空间) rg_real47.19
Rg 误差 (实空间) rg_real_error2.35
I(0) (实空间) i0_real1.1150e+08
I(0) 误差 (实空间) i0_real_error2.1330e+06
Rg (倒空间) rg_reciprocal46.58
I(0) (倒空间) i0_reciprocal111500000.0000
解质量估计 total_estimate0.6679
解质量评级 solution_quality REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks2
主峰位置 r_peak_primary28.3
偏度 Skewness skewness0.334
峰度 Kurtosis kurtosis-0.937
角度范围 angular_range— – 0.1700 −1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha4601000.0000
实空间数据点数 n_real_points35
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.249; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.262; Smooth: 0.670

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) 10 domains

SCOP 2.08 (4 domains)

结构域编号 domain_idd4dqka1
类 Class classb — All beta proteins
折叠类型 Fold foldb.43 — Reductase/isomerase/elongation factor common domain
超家族 Superfamily superfamilyb.43.4 — Riboflavin synthase domain-like
家族 Family familyb.43.4.0 — automated matches
结构域编号 domain_idd4dqka2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.25 — Ferredoxin reductase-like, C-terminal NADP-linked domain
超家族 Superfamily superfamilyc.25.1 — Ferredoxin reductase-like, C-terminal NADP-linked domain
家族 Family familyc.25.1.0 — automated matches
结构域编号 domain_idd4dqkb1
类 Class classb — All beta proteins
折叠类型 Fold foldb.43 — Reductase/isomerase/elongation factor common domain
超家族 Superfamily superfamilyb.43.4 — Riboflavin synthase domain-like
家族 Family familyb.43.4.0 — automated matches
结构域编号 domain_idd4dqkb2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.25 — Ferredoxin reductase-like, C-terminal NADP-linked domain
超家族 Superfamily superfamilyc.25.1 — Ferredoxin reductase-like, C-terminal NADP-linked domain
家族 Family familyc.25.1.0 — automated matches

CATH v4.4 (6 domains)

结构域编号 domain_id4dqkA01
类 Class class2 — Mainly Beta
架构 Architecture architecture40 — Beta Barrel
拓扑 Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
同源超家族 H-superfamily homologous superfamily10 — Translation factors
结构域编号 domain_id4dqkA02
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology990 — NADPH-cytochrome p450 Reductase; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily10 — NADPH-cytochrome p450 Reductase; Chain A, domain 3
结构域编号 domain_id4dqkA03
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily80 — Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module
结构域编号 domain_id4dqkB01
类 Class class2 — Mainly Beta
架构 Architecture architecture40 — Beta Barrel
拓扑 Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
同源超家族 H-superfamily homologous superfamily10 — Translation factors
结构域编号 domain_id4dqkB02
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology990 — NADPH-cytochrome p450 Reductase; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily10 — NADPH-cytochrome p450 Reductase; Chain A, domain 3
结构域编号 domain_id4dqkB03
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily80 — Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module

8. 引用文献 (1)

9. 文件与曲线 (10)