4yxa

Complex of SpaO(SPOA1,2 SeMet) and OrgB(APAR)::T4lysozyme fusion protein

Method: X-RAY DIFFRACTION Dmax: 127.7 Å Quality: REASONABLE

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

Surface presentation of antigens protein SpaO

Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)

UniProt P40699

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 信息不足 异源复合物 蛋白 × 3 PDB 声明:trimeric(3) 与蛋白拷贝数一致 链 A; UniProt 145–213 链 B; UniProt 232–297 片段:UNP Residues 145-213 片段:UNP Residues 232-297 非标准单体:是(mmCIF未提供具体位点) Oxygen-regulated invasion protein OrgB,Endolysin × 1 (P0CL45,P00720) X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;293 K;SpaO(145-213, SeMet) + SpaO (232-297, SeMet) + OrgB(1-30)::T4 lysozyme (native) was concentrated to 18mg/mL, supplemented with 50mM maltose, and crystallized with 25% PEG3350, 200mM ammonium formate, 100mM sodium acetate pH=5.0. Microseeding was employed to enhance crystal uniformity and diffraction. Briefly, crystals to be seeded were harvested in precipitant solution and vortexed in a microfuge tube with a small stir bar for ~60 seconds. The slurry of microseeds was serially dilluted (5-10-fold steps) in precipitant solution and 5 selected microseed-precipitant mixtures were mixed with fresh protein as in a normal hanging drop experiment. Crystals were cryoprotected in 25% PEG3350, 10% ethylene glycol, 200mM ammonium formate, 100mM sodium acetate pH=5.0, 50mM maltose. 分辨率 2.35 Å R-free 0.262
2 信息不足 异源复合物 蛋白 × 3 PDB 声明:trimeric(3) 与蛋白拷贝数一致 链 D; UniProt 145–213 链 E; UniProt 232–297 片段:UNP Residues 145-213 片段:UNP Residues 232-297 非标准单体:是(mmCIF未提供具体位点) Oxygen-regulated invasion protein OrgB,Endolysin × 1 (P0CL45,P00720) X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;293 K;SpaO(145-213, SeMet) + SpaO (232-297, SeMet) + OrgB(1-30)::T4 lysozyme (native) was concentrated to 18mg/mL, supplemented with 50mM maltose, and crystallized with 25% PEG3350, 200mM ammonium formate, 100mM sodium acetate pH=5.0. Microseeding was employed to enhance crystal uniformity and diffraction. Briefly, crystals to be seeded were harvested in precipitant solution and vortexed in a microfuge tube with a small stir bar for ~60 seconds. The slurry of microseeds was serially dilluted (5-10-fold steps) in precipitant solution and 5 selected microseed-precipitant mixtures were mixed with fresh protein as in a normal hanging drop experiment. Crystals were cryoprotected in 25% PEG3350, 10% ethylene glycol, 200mM ammonium formate, 100mM sodium acetate pH=5.0, 50mM maltose. 分辨率 2.35 Å R-free 0.262

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 3 个其他 PDB 条目、4 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 SPAO_SALTY
Isoform
PDB实体 1, 2
链与序列区间 作者链 A; PDB构建体 5–73; UniProt 145–213 作者链 D; PDB构建体 5–73; UniProt 145–213 作者链 B; PDB构建体 5–70; UniProt 232–297 作者链 E; PDB构建体 5–70; UniProt 232–297

Oxygen-regulated invasion protein OrgB,Endolysin

Enterobacteria phage T4

UniProt P00720

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 信息不足 异源复合物 蛋白 × 3 PDB 声明:trimeric(3) 与蛋白拷贝数一致 链 C; UniProt 2–164 片段:UNP Residues 1-30,UNP Residues 1-30 突变:D20N, C54T, C97A,D20N, C54T, C97A Surface presentation of antigens protein SpaO × 1 (P40699) Surface presentation of antigens protein SpaO × 1 (P40699) X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;293 K;SpaO(145-213, SeMet) + SpaO (232-297, SeMet) + OrgB(1-30)::T4 lysozyme (native) was concentrated to 18mg/mL, supplemented with 50mM maltose, and crystallized with 25% PEG3350, 200mM ammonium formate, 100mM sodium acetate pH=5.0. Microseeding was employed to enhance crystal uniformity and diffraction. Briefly, crystals to be seeded were harvested in precipitant solution and vortexed in a microfuge tube with a small stir bar for ~60 seconds. The slurry of microseeds was serially dilluted (5-10-fold steps) in precipitant solution and 5 selected microseed-precipitant mixtures were mixed with fresh protein as in a normal hanging drop experiment. Crystals were cryoprotected in 25% PEG3350, 10% ethylene glycol, 200mM ammonium formate, 100mM sodium acetate pH=5.0, 50mM maltose. 分辨率 2.35 Å R-free 0.262
2 信息不足 异源复合物 蛋白 × 3 PDB 声明:trimeric(3) 与蛋白拷贝数一致 链 F; UniProt 2–164 片段:UNP Residues 1-30,UNP Residues 1-30 突变:D20N, C54T, C97A,D20N, C54T, C97A Surface presentation of antigens protein SpaO × 1 (P40699) Surface presentation of antigens protein SpaO × 1 (P40699) X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;293 K;SpaO(145-213, SeMet) + SpaO (232-297, SeMet) + OrgB(1-30)::T4 lysozyme (native) was concentrated to 18mg/mL, supplemented with 50mM maltose, and crystallized with 25% PEG3350, 200mM ammonium formate, 100mM sodium acetate pH=5.0. Microseeding was employed to enhance crystal uniformity and diffraction. Briefly, crystals to be seeded were harvested in precipitant solution and vortexed in a microfuge tube with a small stir bar for ~60 seconds. The slurry of microseeds was serially dilluted (5-10-fold steps) in precipitant solution and 5 selected microseed-precipitant mixtures were mixed with fresh protein as in a normal hanging drop experiment. Crystals were cryoprotected in 25% PEG3350, 10% ethylene glycol, 200mM ammonium formate, 100mM sodium acetate pH=5.0, 50mM maltose. 分辨率 2.35 Å R-free 0.262

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 721 个其他 PDB 条目、845 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 ENLYS_BPT4
Isoform
PDB实体 3
链与序列区间 作者链 C; PDB构建体 35–197; UniProt 2–164 作者链 F; PDB构建体 35–197; UniProt 2–164

Oxygen-regulated invasion protein OrgB,Endolysin

Enterobacteria phage T4

UniProt P0CL45

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 信息不足 异源复合物 蛋白 × 3 PDB 声明:trimeric(3) 与蛋白拷贝数一致 链 C; UniProt 1–30 片段:UNP Residues 1-30,UNP Residues 1-30 突变:D20N, C54T, C97A,D20N, C54T, C97A Surface presentation of antigens protein SpaO × 1 (P40699) Surface presentation of antigens protein SpaO × 1 (P40699) X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;293 K;SpaO(145-213, SeMet) + SpaO (232-297, SeMet) + OrgB(1-30)::T4 lysozyme (native) was concentrated to 18mg/mL, supplemented with 50mM maltose, and crystallized with 25% PEG3350, 200mM ammonium formate, 100mM sodium acetate pH=5.0. Microseeding was employed to enhance crystal uniformity and diffraction. Briefly, crystals to be seeded were harvested in precipitant solution and vortexed in a microfuge tube with a small stir bar for ~60 seconds. The slurry of microseeds was serially dilluted (5-10-fold steps) in precipitant solution and 5 selected microseed-precipitant mixtures were mixed with fresh protein as in a normal hanging drop experiment. Crystals were cryoprotected in 25% PEG3350, 10% ethylene glycol, 200mM ammonium formate, 100mM sodium acetate pH=5.0, 50mM maltose. 分辨率 2.35 Å R-free 0.262
2 信息不足 异源复合物 蛋白 × 3 PDB 声明:trimeric(3) 与蛋白拷贝数一致 链 F; UniProt 1–30 片段:UNP Residues 1-30,UNP Residues 1-30 突变:D20N, C54T, C97A,D20N, C54T, C97A Surface presentation of antigens protein SpaO × 1 (P40699) Surface presentation of antigens protein SpaO × 1 (P40699) X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;293 K;SpaO(145-213, SeMet) + SpaO (232-297, SeMet) + OrgB(1-30)::T4 lysozyme (native) was concentrated to 18mg/mL, supplemented with 50mM maltose, and crystallized with 25% PEG3350, 200mM ammonium formate, 100mM sodium acetate pH=5.0. Microseeding was employed to enhance crystal uniformity and diffraction. Briefly, crystals to be seeded were harvested in precipitant solution and vortexed in a microfuge tube with a small stir bar for ~60 seconds. The slurry of microseeds was serially dilluted (5-10-fold steps) in precipitant solution and 5 selected microseed-precipitant mixtures were mixed with fresh protein as in a normal hanging drop experiment. Crystals were cryoprotected in 25% PEG3350, 10% ethylene glycol, 200mM ammonium formate, 100mM sodium acetate pH=5.0, 50mM maltose. 分辨率 2.35 Å R-free 0.262

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、2 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 ORGB_SALTY
Isoform
PDB实体 3
链与序列区间 作者链 C; PDB构建体 5–34; UniProt 1–30 作者链 F; PDB构建体 5–34; UniProt 1–30

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 4yxa

P(r) 距离分布 P(r) Distribution

P(r) distribution for 4yxa
下载 Download

2. 结构基本信息 2. Structure Basics

条目编号 entry_id4yxa
沉积日期 deposition_date2015-03-22
结构标题 titleComplex of SpaO(SPOA1,2 SeMet) and OrgB(APAR)::T4lysozyme fusion protein
关键词 keywordsType III Secretion System, PROTEIN TRANSPORT; PROTEIN TRANSPORT
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_guinier36.33
回转半径 Rg (电子) rg_electron36.44
零角强度 I(0) i071088800.00
分子量 molecular_weight68577.0 kDa
排除体积 excluded_volume86477 ų
包络体积 envelope_volume115510 ų
水化壳体积 shell_volume29720 ų
包络直径 envelope_diameter127.5
壳层 Rg shell_rg37.27
包络 Rg envelope_rg36.29
形状 Rg shape_rg36.48
总 Rg total_rg36.37
总原子数 total_atoms4810
残基数 n_residues612
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 dmax127.7
Rg (实空间) rg_real38.11
Rg 误差 (实空间) rg_real_error0.53
I(0) (实空间) i0_real7.1280e+07
I(0) 误差 (实空间) i0_real_error1.0790e+06
Rg (倒空间) rg_reciprocal36.54
I(0) (倒空间) i0_reciprocal71070000.0000
解质量估计 total_estimate0.5826
解质量评级 solution_quality REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks1
主峰位置 r_peak_primary29.0
偏度 Skewness skewness0.564
峰度 Kurtosis kurtosis-0.481
角度范围 angular_range— – 0.2200 −1
当前正则化参数 α current_alpha2.7090
最高正则化参数 α highest_alpha7087000.0000
实空间数据点数 n_real_points45
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.658; Stabil: 0.916; Sysdev: 0.000; Positv: 1.000; Valcen: 0.407; Smooth: 0.469

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

6. 实体与聚合物信息 Entities & Polymers (4)

7. 折叠分类 (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

结构域编号 domain_id4yxaB00
类 Class class2 — Mainly Beta
架构 Architecture architecture30 — Roll
拓扑 Topology topology330 — Surface presentation of antigens (SPOA)
同源超家族 H-superfamily homologous superfamily10 — SpoA-like
结构域编号 domain_id4yxaC00
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology530 — Lysozyme
同源超家族 H-superfamily homologous superfamily40
结构域编号 domain_id4yxaE00
类 Class class2 — Mainly Beta
架构 Architecture architecture30 — Roll
拓扑 Topology topology330 — Surface presentation of antigens (SPOA)
同源超家族 H-superfamily homologous superfamily10 — SpoA-like
结构域编号 domain_id4yxaF00
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology530 — Lysozyme
同源超家族 H-superfamily homologous superfamily40

8. 引用文献 (1)

9. 文件与曲线 (10)