3dyo

E. coli (lacZ) beta-galactosidase (H418N) in complex with IPTG

Method: X-RAY DIFFRACTION Dmax: 172.5 Å Quality: GOOD

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

Beta-galactosidase

Escherichia coli K12

UniProt P00722

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 蛋白同源多聚体 同源多聚体 蛋白 × 4 PDB 声明:tetrameric(4) 与蛋白拷贝数一致 链 A; UniProt 10–1024 链 B; UniProt 10–1024 链 C; UniProt 10–1024 链 D; UniProt 10–1024 突变:H418N MG MAGNESIUM ION × 14 NA SODIUM ION × 18 IPT 1-methylethyl 1-thio-beta-D-galactopyranoside × 12 DMS DIMETHYL SULFOXIDE × 97 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 6.5;288 K;pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K 分辨率 1.80 Å R-free 0.241

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 67 个其他 PDB 条目、83 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 BGAL_ECOLI
Isoform
PDB实体 1
链与序列区间 作者链 A; PDB构建体 9–1023; UniProt 10–1024 作者链 B; PDB构建体 9–1023; UniProt 10–1024 作者链 C; PDB构建体 9–1023; UniProt 10–1024 作者链 D; PDB构建体 9–1023; UniProt 10–1024

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 3dyo

P(r) 距离分布 P(r) Distribution

P(r) distribution for 3dyo
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2. 结构基本信息 2. Structure Basics

条目编号 entry_id3dyo
沉积日期 deposition_date2008-07-28
结构标题 titleE. coli (lacZ) beta-galactosidase (H418N) in complex with IPTG
关键词 keywordsbeta-galactosidase, Glycosidase, Hydrolase; HYDROLASE
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_guinier51.94
回转半径 Rg (电子) rg_electron51.59
零角强度 I(0) i03309230000.00
分子量 molecular_weight471190.0 kDa
排除体积 excluded_volume583610 ų
包络体积 envelope_volume750410 ų
水化壳体积 shell_volume116230 ų
包络直径 envelope_diameter183.9
壳层 Rg shell_rg58.79
包络 Rg envelope_rg51.01
形状 Rg shape_rg51.59
总 Rg total_rg51.75
总原子数 total_atoms33092
残基数 n_residues4044
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 dmax172.5
Rg (实空间) rg_real51.85
Rg 误差 (实空间) rg_real_error1.47
I(0) (实空间) i0_real3.3090e+09
I(0) 误差 (实空间) i0_real_error5.9800e+07
Rg (倒空间) rg_reciprocal52.01
I(0) (倒空间) i0_reciprocal3310000000.0000
解质量估计 total_estimate0.8654
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks2
主峰位置 r_peak_primary63.2
偏度 Skewness skewness0.306
峰度 Kurtosis kurtosis-0.183
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_alpha492700000.0000
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: 0.844; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.744

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) 40 domains

SCOP 2.08 (20 domains)

结构域编号 domain_idd3dyoa1
类 Class classb — All beta proteins
折叠类型 Fold foldb.18 — Galactose-binding domain-like
超家族 Superfamily superfamilyb.18.1 — Galactose-binding domain-like
家族 Family familyb.18.1.0 — automated matches
结构域编号 domain_idd3dyoa2
类 Class classb — All beta proteins
折叠类型 Fold foldb.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamilyb.1.4 — beta-Galactosidase/glucuronidase domain
家族 Family familyb.1.4.0 — automated matches
结构域编号 domain_idd3dyoa3
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamilyc.1.8 — (Trans)glycosidases
家族 Family familyc.1.8.0 — automated matches
结构域编号 domain_idd3dyoa4
类 Class classb — All beta proteins
折叠类型 Fold foldb.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamilyb.1.4 — beta-Galactosidase/glucuronidase domain
家族 Family familyb.1.4.0 — automated matches
结构域编号 domain_idd3dyoa5
类 Class classb — All beta proteins
折叠类型 Fold foldb.30 — Supersandwich
超家族 Superfamily superfamilyb.30.5 — Galactose mutarotase-like
家族 Family familyb.30.5.0 — automated matches
结构域编号 domain_idd3dyob1
类 Class classb — All beta proteins
折叠类型 Fold foldb.18 — Galactose-binding domain-like
超家族 Superfamily superfamilyb.18.1 — Galactose-binding domain-like
家族 Family familyb.18.1.0 — automated matches
结构域编号 domain_idd3dyob2
类 Class classb — All beta proteins
折叠类型 Fold foldb.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamilyb.1.4 — beta-Galactosidase/glucuronidase domain
家族 Family familyb.1.4.0 — automated matches
结构域编号 domain_idd3dyob3
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamilyc.1.8 — (Trans)glycosidases
家族 Family familyc.1.8.0 — automated matches
结构域编号 domain_idd3dyob4
类 Class classb — All beta proteins
折叠类型 Fold foldb.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamilyb.1.4 — beta-Galactosidase/glucuronidase domain
家族 Family familyb.1.4.0 — automated matches
结构域编号 domain_idd3dyob5
类 Class classb — All beta proteins
折叠类型 Fold foldb.30 — Supersandwich
超家族 Superfamily superfamilyb.30.5 — Galactose mutarotase-like
家族 Family familyb.30.5.0 — automated matches
结构域编号 domain_idd3dyoc1
类 Class classb — All beta proteins
折叠类型 Fold foldb.18 — Galactose-binding domain-like
超家族 Superfamily superfamilyb.18.1 — Galactose-binding domain-like
家族 Family familyb.18.1.0 — automated matches
结构域编号 domain_idd3dyoc2
类 Class classb — All beta proteins
折叠类型 Fold foldb.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamilyb.1.4 — beta-Galactosidase/glucuronidase domain
家族 Family familyb.1.4.0 — automated matches
结构域编号 domain_idd3dyoc3
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamilyc.1.8 — (Trans)glycosidases
家族 Family familyc.1.8.0 — automated matches
结构域编号 domain_idd3dyoc4
类 Class classb — All beta proteins
折叠类型 Fold foldb.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamilyb.1.4 — beta-Galactosidase/glucuronidase domain
家族 Family familyb.1.4.0 — automated matches
结构域编号 domain_idd3dyoc5
类 Class classb — All beta proteins
折叠类型 Fold foldb.30 — Supersandwich
超家族 Superfamily superfamilyb.30.5 — Galactose mutarotase-like
家族 Family familyb.30.5.0 — automated matches
结构域编号 domain_idd3dyod1
类 Class classb — All beta proteins
折叠类型 Fold foldb.18 — Galactose-binding domain-like
超家族 Superfamily superfamilyb.18.1 — Galactose-binding domain-like
家族 Family familyb.18.1.0 — automated matches
结构域编号 domain_idd3dyod2
类 Class classb — All beta proteins
折叠类型 Fold foldb.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamilyb.1.4 — beta-Galactosidase/glucuronidase domain
家族 Family familyb.1.4.0 — automated matches
结构域编号 domain_idd3dyod3
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamilyc.1.8 — (Trans)glycosidases
家族 Family familyc.1.8.0 — automated matches
结构域编号 domain_idd3dyod4
类 Class classb — All beta proteins
折叠类型 Fold foldb.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamilyb.1.4 — beta-Galactosidase/glucuronidase domain
家族 Family familyb.1.4.0 — automated matches
结构域编号 domain_idd3dyod5
类 Class classb — All beta proteins
折叠类型 Fold foldb.30 — Supersandwich
超家族 Superfamily superfamilyb.30.5 — Galactose mutarotase-like
家族 Family familyb.30.5.0 — automated matches

CATH v4.4 (20 domains)

结构域编号 domain_id3dyoA01
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily260 — Galactose-binding domain-like
结构域编号 domain_id3dyoA02
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily10 — Immunoglobulins
结构域编号 domain_id3dyoA03
类 Class class3 — Alpha Beta
架构 Architecture architecture20 — Alpha-Beta Barrel
拓扑 Topology topology20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily80 — Glycosidases
结构域编号 domain_id3dyoA04
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily10 — Immunoglobulins
结构域编号 domain_id3dyoA05
类 Class class2 — Mainly Beta
架构 Architecture architecture70 — Distorted Sandwich
拓扑 Topology topology98 — Beta-galactosidase; Chain A, domain 5
同源超家族 H-superfamily homologous superfamily10
结构域编号 domain_id3dyoB01
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily260 — Galactose-binding domain-like
结构域编号 domain_id3dyoB02
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily10 — Immunoglobulins
结构域编号 domain_id3dyoB03
类 Class class3 — Alpha Beta
架构 Architecture architecture20 — Alpha-Beta Barrel
拓扑 Topology topology20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily80 — Glycosidases
结构域编号 domain_id3dyoB04
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily10 — Immunoglobulins
结构域编号 domain_id3dyoB05
类 Class class2 — Mainly Beta
架构 Architecture architecture70 — Distorted Sandwich
拓扑 Topology topology98 — Beta-galactosidase; Chain A, domain 5
同源超家族 H-superfamily homologous superfamily10
结构域编号 domain_id3dyoC01
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily260 — Galactose-binding domain-like
结构域编号 domain_id3dyoC02
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily10 — Immunoglobulins
结构域编号 domain_id3dyoC03
类 Class class3 — Alpha Beta
架构 Architecture architecture20 — Alpha-Beta Barrel
拓扑 Topology topology20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily80 — Glycosidases
结构域编号 domain_id3dyoC04
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily10 — Immunoglobulins
结构域编号 domain_id3dyoC05
类 Class class2 — Mainly Beta
架构 Architecture architecture70 — Distorted Sandwich
拓扑 Topology topology98 — Beta-galactosidase; Chain A, domain 5
同源超家族 H-superfamily homologous superfamily10
结构域编号 domain_id3dyoD01
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily260 — Galactose-binding domain-like
结构域编号 domain_id3dyoD02
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily10 — Immunoglobulins
结构域编号 domain_id3dyoD03
类 Class class3 — Alpha Beta
架构 Architecture architecture20 — Alpha-Beta Barrel
拓扑 Topology topology20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily80 — Glycosidases
结构域编号 domain_id3dyoD04
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily10 — Immunoglobulins
结构域编号 domain_id3dyoD05
类 Class class2 — Mainly Beta
架构 Architecture architecture70 — Distorted Sandwich
拓扑 Topology topology98 — Beta-galactosidase; Chain A, domain 5
同源超家族 H-superfamily homologous superfamily10

8. 引用文献 (1)

9. 文件与曲线 (10)