4aoq

Cationic trypsin in complex with mutated Spinacia oleracea trypsin inhibitor III (SOTI-III) (F14A)

Method: X-RAY DIFFRACTION Dmax: 98.1 Å Quality: GOOD

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

CATIONIC TRYPSIN

物种未注明

UniProt P00760

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 × 2 PDB 声明:dimeric(2) 与蛋白拷贝数一致 链 A; UniProt 24–246 未记录 TRYPSIN INHIBITOR 3 × 1 (P84781) CA CALCIUM ION × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;292 K;TRYPSIN (SIGMA T1426) WAS DISOLVED IN 1 MM HCL (PH 2.0), 10 MM CACL2, PURIFIED ON A SUPERDEX 75 16/60 COLUMN (BUFFER: 25 MM MES PH 5.5, 50 MM NACL AND 10 MM CACL2). CRYSTALS GREW FROM EQUAL VOLUMES OF TRYPSIN (11.5 MG/ML) INCUBATED WITH LYOPHILIZED SOTI-III F14A (1.5MM) AND PRECIPITANT SOLUTION (0.1M BICINE PH 9, 20% (W/V) PEG 6000) IN HANGING DROP CRYSTALLIZATION PLATES AT 19C. 分辨率 2.00 Å R-free 0.220
2 蛋白异源复合物 异源复合物 蛋白 × 2 PDB 声明:dimeric(2) 与蛋白拷贝数一致 链 B; UniProt 24–246 未记录 TRYPSIN INHIBITOR 3 × 1 (P84781) CA CALCIUM ION × 1 1PE PENTAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;292 K;TRYPSIN (SIGMA T1426) WAS DISOLVED IN 1 MM HCL (PH 2.0), 10 MM CACL2, PURIFIED ON A SUPERDEX 75 16/60 COLUMN (BUFFER: 25 MM MES PH 5.5, 50 MM NACL AND 10 MM CACL2). CRYSTALS GREW FROM EQUAL VOLUMES OF TRYPSIN (11.5 MG/ML) INCUBATED WITH LYOPHILIZED SOTI-III F14A (1.5MM) AND PRECIPITANT SOLUTION (0.1M BICINE PH 9, 20% (W/V) PEG 6000) IN HANGING DROP CRYSTALLIZATION PLATES AT 19C. 分辨率 2.00 Å R-free 0.220
3 蛋白异源复合物 异源复合物 蛋白 × 2 PDB 声明:dimeric(2) 与蛋白拷贝数一致 链 C; UniProt 24–246 未记录 TRYPSIN INHIBITOR 3 × 1 (P84781) CA CALCIUM ION × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;292 K;TRYPSIN (SIGMA T1426) WAS DISOLVED IN 1 MM HCL (PH 2.0), 10 MM CACL2, PURIFIED ON A SUPERDEX 75 16/60 COLUMN (BUFFER: 25 MM MES PH 5.5, 50 MM NACL AND 10 MM CACL2). CRYSTALS GREW FROM EQUAL VOLUMES OF TRYPSIN (11.5 MG/ML) INCUBATED WITH LYOPHILIZED SOTI-III F14A (1.5MM) AND PRECIPITANT SOLUTION (0.1M BICINE PH 9, 20% (W/V) PEG 6000) IN HANGING DROP CRYSTALLIZATION PLATES AT 19C. 分辨率 2.00 Å R-free 0.220

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 608 个其他 PDB 条目、768 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 TRY1_BOVIN
Isoform
PDB实体 1
链与序列区间 作者链 A; PDB构建体 1–223; UniProt 24–246 作者链 B; PDB构建体 1–223; UniProt 24–246 作者链 C; PDB构建体 1–223; UniProt 24–246

TRYPSIN INHIBITOR 3

物种未注明

UniProt P84781

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 × 2 PDB 声明:dimeric(2) 与蛋白拷贝数一致 链 D; UniProt 1–37 突变:YES CATIONIC TRYPSIN × 1 (P00760) CA CALCIUM ION × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;292 K;TRYPSIN (SIGMA T1426) WAS DISOLVED IN 1 MM HCL (PH 2.0), 10 MM CACL2, PURIFIED ON A SUPERDEX 75 16/60 COLUMN (BUFFER: 25 MM MES PH 5.5, 50 MM NACL AND 10 MM CACL2). CRYSTALS GREW FROM EQUAL VOLUMES OF TRYPSIN (11.5 MG/ML) INCUBATED WITH LYOPHILIZED SOTI-III F14A (1.5MM) AND PRECIPITANT SOLUTION (0.1M BICINE PH 9, 20% (W/V) PEG 6000) IN HANGING DROP CRYSTALLIZATION PLATES AT 19C. 分辨率 2.00 Å R-free 0.220
2 蛋白异源复合物 异源复合物 蛋白 × 2 PDB 声明:dimeric(2) 与蛋白拷贝数一致 链 E; UniProt 1–37 突变:YES CATIONIC TRYPSIN × 1 (P00760) CA CALCIUM ION × 1 1PE PENTAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;292 K;TRYPSIN (SIGMA T1426) WAS DISOLVED IN 1 MM HCL (PH 2.0), 10 MM CACL2, PURIFIED ON A SUPERDEX 75 16/60 COLUMN (BUFFER: 25 MM MES PH 5.5, 50 MM NACL AND 10 MM CACL2). CRYSTALS GREW FROM EQUAL VOLUMES OF TRYPSIN (11.5 MG/ML) INCUBATED WITH LYOPHILIZED SOTI-III F14A (1.5MM) AND PRECIPITANT SOLUTION (0.1M BICINE PH 9, 20% (W/V) PEG 6000) IN HANGING DROP CRYSTALLIZATION PLATES AT 19C. 分辨率 2.00 Å R-free 0.220
3 蛋白异源复合物 异源复合物 蛋白 × 2 PDB 声明:dimeric(2) 与蛋白拷贝数一致 链 F; UniProt 1–37 突变:YES CATIONIC TRYPSIN × 1 (P00760) CA CALCIUM ION × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;292 K;TRYPSIN (SIGMA T1426) WAS DISOLVED IN 1 MM HCL (PH 2.0), 10 MM CACL2, PURIFIED ON A SUPERDEX 75 16/60 COLUMN (BUFFER: 25 MM MES PH 5.5, 50 MM NACL AND 10 MM CACL2). CRYSTALS GREW FROM EQUAL VOLUMES OF TRYPSIN (11.5 MG/ML) INCUBATED WITH LYOPHILIZED SOTI-III F14A (1.5MM) AND PRECIPITANT SOLUTION (0.1M BICINE PH 9, 20% (W/V) PEG 6000) IN HANGING DROP CRYSTALLIZATION PLATES AT 19C. 分辨率 2.00 Å R-free 0.220

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、3 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 ITR3_SPIOL
Isoform
PDB实体 2
链与序列区间 作者链 D; PDB构建体 1–37; UniProt 1–37 作者链 E; PDB构建体 1–37; UniProt 1–37 作者链 F; PDB构建体 1–37; UniProt 1–37

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 4aoq

P(r) 距离分布 P(r) Distribution

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

条目编号 entry_id4aoq
沉积日期 deposition_date2012-03-29
结构标题 titleCationic trypsin in complex with mutated Spinacia oleracea trypsin inhibitor III (SOTI-III) (F14A)
关键词 keywordsHYDROLASE-INHIBITOR COMPLEX, MINIPROTEIN SCAFFOLD, KNOTTINS, SERINE PROTEASE INHIBITOR; HYDROLASE/INHIBITOR
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_guinier30.19
回转半径 Rg (电子) rg_electron29.74
零角强度 I(0) i0112146000.00
分子量 molecular_weight80718.0 kDa
排除体积 excluded_volume99714 ų
包络体积 envelope_volume120310 ų
水化壳体积 shell_volume34111 ų
包络直径 envelope_diameter100.1
壳层 Rg shell_rg36.43
包络 Rg envelope_rg29.52
形状 Rg shape_rg29.73
总 Rg total_rg30.34
总原子数 total_atoms5620
残基数 n_residues773
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 dmax98.1
Rg (实空间) rg_real30.17
Rg 误差 (实空间) rg_real_error0.77
I(0) (实空间) i0_real1.1210e+08
I(0) 误差 (实空间) i0_real_error1.7980e+06
Rg (倒空间) rg_reciprocal30.19
I(0) (倒空间) i0_reciprocal112100000.0000
解质量估计 total_estimate0.8945
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks2
主峰位置 r_peak_primary30.2
偏度 Skewness skewness0.261
峰度 Kurtosis kurtosis-0.570
角度范围 angular_range— – 0.2600 −1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha22860000.0000
实空间数据点数 n_real_points53
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.911; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.973; Smooth: 0.918

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) 6 domains

CATH v4.4 (6 domains)

结构域编号 domain_id4aoqA01
类 Class class2 — Mainly Beta
架构 Architecture architecture40 — Beta Barrel
拓扑 Topology topology10 — Thrombin, subunit H
同源超家族 H-superfamily homologous superfamily10 — Trypsin-like serine proteases
结构域编号 domain_id4aoqA02
类 Class class2 — Mainly Beta
架构 Architecture architecture40 — Beta Barrel
拓扑 Topology topology10 — Thrombin, subunit H
同源超家族 H-superfamily homologous superfamily10 — Trypsin-like serine proteases
结构域编号 domain_id4aoqB01
类 Class class2 — Mainly Beta
架构 Architecture architecture40 — Beta Barrel
拓扑 Topology topology10 — Thrombin, subunit H
同源超家族 H-superfamily homologous superfamily10 — Trypsin-like serine proteases
结构域编号 domain_id4aoqB02
类 Class class2 — Mainly Beta
架构 Architecture architecture40 — Beta Barrel
拓扑 Topology topology10 — Thrombin, subunit H
同源超家族 H-superfamily homologous superfamily10 — Trypsin-like serine proteases
结构域编号 domain_id4aoqC01
类 Class class2 — Mainly Beta
架构 Architecture architecture40 — Beta Barrel
拓扑 Topology topology10 — Thrombin, subunit H
同源超家族 H-superfamily homologous superfamily10 — Trypsin-like serine proteases
结构域编号 domain_id4aoqC02
类 Class class2 — Mainly Beta
架构 Architecture architecture40 — Beta Barrel
拓扑 Topology topology10 — Thrombin, subunit H
同源超家族 H-superfamily homologous superfamily10 — Trypsin-like serine proteases

8. 引用文献 (1)

9. 文件与曲线 (10)