3vdb

E. coli (lacZ) beta-galactosidase (N460T) in complex with galactonolactone

Method: X-RAY DIFFRACTION Dmax: 174.3 Å Quality: GOOD

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

Beta-galactosidase

Escherichia coli

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:N460T 149 D-galactonolactone × 4 MG MAGNESIUM ION × 9 NA SODIUM ION × 14 DMS DIMETHYL SULFOXIDE × 77 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 6.5;288 K;10% PEG8000, 100 mM Bis-Tris, pH 6.5, 200 mM magnesium chloride, 100 mM sodium chloride, 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 288K 分辨率 2.05 Å R-free 0.205

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 38–1052; UniProt 10–1024 作者链 B; PDB构建体 38–1052; UniProt 10–1024 作者链 C; PDB构建体 38–1052; UniProt 10–1024 作者链 D; PDB构建体 38–1052; 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 3vdb

P(r) 距离分布 P(r) Distribution

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

条目编号 entry_id3vdb
沉积日期 deposition_date2012-01-04
结构标题 titleE. coli (lacZ) beta-galactosidase (N460T) in complex with galactonolactone
关键词 keywords;transition state stabilization, substrate binding, 2-stage binding, TIM barrel (alpha/beta barrel), jelly-roll barrel, immunoglobulin, beta supersandwich, 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_guinier52.01
回转半径 Rg (电子) rg_electron51.66
零角强度 I(0) i03277490000.00
分子量 molecular_weight469140.0 kDa
排除体积 excluded_volume581160 ų
包络体积 envelope_volume753530 ų
水化壳体积 shell_volume116460 ų
包络直径 envelope_diameter183.6
壳层 Rg shell_rg58.91
包络 Rg envelope_rg51.11
形状 Rg shape_rg51.65
总 Rg total_rg51.85
总原子数 total_atoms33003
残基数 n_residues4060
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 dmax174.3
Rg (实空间) rg_real51.92
Rg 误差 (实空间) rg_real_error1.43
I(0) (实空间) i0_real3.2770e+09
I(0) 误差 (实空间) i0_real_error6.2610e+07
Rg (倒空间) rg_reciprocal52.08
I(0) (倒空间) i0_reciprocal3278000000.0000
解质量估计 total_estimate0.8688
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks2
主峰位置 r_peak_primary63.9
偏度 Skewness skewness0.307
峰度 Kurtosis kurtosis-0.181
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_alpha515700000.0000
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: 0.832; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.973; Smooth: 0.821

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_idd3vdba1
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.18.1.5 — beta-Galactosidase/glucuronidase, N-terminal domain
结构域编号 domain_idd3vdba2
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.1.4.1 — beta-Galactosidase/glucuronidase domain
结构域编号 domain_idd3vdba3
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.1.8.3 — beta-glycanases
结构域编号 domain_idd3vdba4
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.1.4.1 — beta-Galactosidase/glucuronidase domain
结构域编号 domain_idd3vdba5
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.30.5.1 — beta-Galactosidase, domain 5
结构域编号 domain_idd3vdbb1
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.18.1.5 — beta-Galactosidase/glucuronidase, N-terminal domain
结构域编号 domain_idd3vdbb2
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.1.4.1 — beta-Galactosidase/glucuronidase domain
结构域编号 domain_idd3vdbb3
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.1.8.3 — beta-glycanases
结构域编号 domain_idd3vdbb4
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.1.4.1 — beta-Galactosidase/glucuronidase domain
结构域编号 domain_idd3vdbb5
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.30.5.1 — beta-Galactosidase, domain 5
结构域编号 domain_idd3vdbc1
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.18.1.5 — beta-Galactosidase/glucuronidase, N-terminal domain
结构域编号 domain_idd3vdbc2
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.1.4.1 — beta-Galactosidase/glucuronidase domain
结构域编号 domain_idd3vdbc3
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.1.8.3 — beta-glycanases
结构域编号 domain_idd3vdbc4
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.1.4.1 — beta-Galactosidase/glucuronidase domain
结构域编号 domain_idd3vdbc5
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.30.5.1 — beta-Galactosidase, domain 5
结构域编号 domain_idd3vdbd1
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.18.1.5 — beta-Galactosidase/glucuronidase, N-terminal domain
结构域编号 domain_idd3vdbd2
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.1.4.1 — beta-Galactosidase/glucuronidase domain
结构域编号 domain_idd3vdbd3
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.1.8.3 — beta-glycanases
结构域编号 domain_idd3vdbd4
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.1.4.1 — beta-Galactosidase/glucuronidase domain
结构域编号 domain_idd3vdbd5
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.30.5.1 — beta-Galactosidase, domain 5

CATH v4.4 (20 domains)

结构域编号 domain_id3vdbA01
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_id3vdbA02
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_id3vdbA03
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_id3vdbA04
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_id3vdbA05
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_id3vdbB01
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_id3vdbB02
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_id3vdbB03
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_id3vdbB04
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_id3vdbB05
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_id3vdbC01
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_id3vdbC02
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_id3vdbC03
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_id3vdbC04
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_id3vdbC05
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_id3vdbD01
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_id3vdbD02
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_id3vdbD03
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_id3vdbD04
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_id3vdbD05
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)