SAXSdb — 4yx1

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

Surface presentation of antigens protein SpaO

Salmonella typhimurium

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 × 2 PDB 声明：dimeric（2）与蛋白拷贝数一致	链 A； UniProt 232–297 链 B； UniProt 232–297	片段：UNP Residues 232-297 非标准单体：是（mmCIF未提供具体位点）	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, HANGING DROP；293 K；SpaO(232-297) was concentrated to 8mg/mL and crystallized with 35% PEG400, 200mM calcium acetate, 100mM sodium acetate pH=5.0. Crystals were cryoprotected in the mother liquor. 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.	分辨率 1.35 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。

其他 PDB	相对当前条目 4YX1	Assembly / 聚集状态	构建体	突变与修饰	配体、离子与非聚合物	实验方法与环境	结构质量
4YX5 SpaO(SPOA1,2) 提交 2015-03-22	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 145–213（69 aa）片段：UNP Residues 145-213 链 B 232–297（66 aa）片段：UNP Residues 232-297	未记录	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；277 K；SpaO(145-213) + SpaO (232-297) was concentrated to 12mg/mL and crystallized with 25% PEG400, 10% isopropanol, 100mM sodium citrate pH=5.6 at 277K. 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 mother liquor with the PEG400 concentration raised to 37.5%.	分辨率 2.90 Å R-free 0.279
4YX7 Complex of SpaO(SPOA1,2) and OrgB(APAR)::T4lysozyme fusion protein 提交 2015-03-22	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 信息不足异源复合物；蛋白 × 3 PDB 声明：trimeric	链 A 145–213（69 aa）片段：UNP Residues 145-213 链 B 232–297（66 aa）片段：UNP Residues 232-297	未记录	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；293 K；SpaO(145-213) + SpaO (232-297) + OrgB(1-30)::T4 lysozyme was concentrated to 18.5mg/mL 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 30% PEG3350, 10% glycerol, 200mM ammonium acetate, 100mM sodium acetate pH=5.0.	分辨率 2.00 Å R-free 0.210
4YX7 Complex of SpaO(SPOA1,2) and OrgB(APAR)::T4lysozyme fusion protein 提交 2015-03-22	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 2 信息不足异源复合物；蛋白 × 3 PDB 声明：trimeric	链 D 145–213（69 aa）片段：UNP Residues 145-213 链 E 232–297（66 aa）片段：UNP Residues 232-297	未记录	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；293 K；SpaO(145-213) + SpaO (232-297) + OrgB(1-30)::T4 lysozyme was concentrated to 18.5mg/mL 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 30% PEG3350, 10% glycerol, 200mM ammonium acetate, 100mM sodium acetate pH=5.0.	分辨率 2.00 Å R-free 0.210
4YXA Complex of SpaO(SPOA1,2 SeMet) and OrgB(APAR)::T4lysozyme fusion protein 提交 2015-03-22	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 信息不足异源复合物；蛋白 × 3 PDB 声明：trimeric	链 A 145–213（69 aa）片段：UNP Residues 145-213 链 B 232–297（66 aa）片段：UNP Residues 232-297	非标准单体：是（mmCIF未提供具体位点）	未记录非水小分子	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
4YXA Complex of SpaO(SPOA1,2 SeMet) and OrgB(APAR)::T4lysozyme fusion protein 提交 2015-03-22	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 2 信息不足异源复合物；蛋白 × 3 PDB 声明：trimeric	链 D 145–213（69 aa）片段：UNP Residues 145-213 链 E 232–297（66 aa）片段：UNP Residues 232-297	非标准单体：是（mmCIF未提供具体位点）	未记录非水小分子	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

共 3 个其他 PDB 条目、5 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
链与序列区间	作者链 A； PDB构建体 5–70； UniProt 232–297 作者链 B； PDB构建体 5–70； UniProt 232–297

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。

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2. 结构基本信息 2. Structure Basics

条目编号 entry_id	4yx1
沉积日期 deposition_date	2015-03-21
结构标题 title	SpaO(SPOA2)
关键词 keywords	Type III Secretion System, PROTEIN TRANSPORT; PROTEIN TRANSPORT
实验方法 method	X-RAY DIFFRACTION

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3. SAXS 参数 (CRYSOL 理论计算) 3. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	16.17 Å
回转半径 Rg (电子) rg_electron	14.98 Å
零角强度 I(0) i0	4741750.00
分子量 molecular_weight	15502.0 kDa
排除体积 excluded_volume	19321 Å³
包络体积 envelope_volume	22411 Å³
水化壳体积 shell_volume	12885 Å³
包络直径 envelope_diameter	51.0 Å
壳层 Rg shell_rg	20.43 Å
包络 Rg envelope_rg	15.31 Å
形状 Rg shape_rg	15.00 Å
总 Rg total_rg	16.01 Å
总原子数 total_atoms	1064
残基数 n_residues	131
球谐函数阶数 n_harmonics	20
q 范围 q_range	— – 0.5000 Å⁻¹
数据点数 n_points	101
壳层类型 shell_type	directional
溶剂电子密度 solvent_density	0.3340 e/Å³
壳层衬度 contrast_shell	0.0300 e/Å³
CRYSOL 版本 crysol_version	4.1.3

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4. P(r) 距离分布 (GNOM 反演) 4. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	52.2 Å
Rg (实空间) rg_real	16.08 Å
Rg 误差 (实空间) rg_real_error	0.29 Å
I(0) (实空间) i0_real	4.7420e+06
I(0) 误差 (实空间) i0_real_error	6.2030e+04
Rg (倒空间) rg_reciprocal	16.09 Å
I(0) (倒空间) i0_reciprocal	4742000.0000
解质量估计 total_estimate	0.6592
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	20.7 Å
偏度 Skewness skewness	0.186
峰度 Kurtosis kurtosis	-0.299
角度范围 angular_range	— – 0.4900 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	634200.0000
实空间数据点数 n_real_points	79
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.838; Stabil: 1.000; Sysdev: 0.353; Positv: 1.000; Valcen: 0.993; Smooth: 0.000

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

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6. 实体与聚合物信息 Entities & Polymers (3)

实体 1 Entity 1 polymer

描述 description	Surface presentation of antigens protein SpaO
分子量 formula_weight	7851.5 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	1286

GPVDVKLEFVLYRKNVTLAELEAMGQQQLLSLPTNAELNVEIMANGVLLGNGELVQMNDTLGVEIHEWLS

来源 Source

来源生物 organism	Salmonella typhimurium
NCBI 分类编号 ncbi_taxonomy_id	99287
宿主生物 host_organism	Escherichia coli

实体 2 Entity 2 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

实体 3 Entity 3 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	222

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7. 折叠分类 (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

结构域编号 domain_id	4yx1A00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	330 — Surface presentation of antigens (SPOA)
同源超家族 H-superfamily homologous superfamily	10 — SpoA-like

结构域编号 domain_id	4yx1B00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	330 — Surface presentation of antigens (SPOA)
同源超家族 H-superfamily homologous superfamily	10 — SpoA-like

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8. 引用文献 (1)

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晶胞边长 a length_a	35.000 Å
晶胞边长 b length_b	41.270 Å
晶胞边长 c length_c	48.000 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	103.92 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	1.350 Å
最低分辨率 resolution_low	31.262 Å
R 因子 r_factor	0.1747
R_work r_work	0.1724
R_free r_free	0.2053

fit	/app/data/saxs_computation/yx/4yx1/4yx1.fit
pddf	/app/data/pr_computation/yx/4yx1/4yx1.pr.out
profile	/app/data/saxs_computation/yx/4yx1/4yx1.dat

SpaO(SPOA2)

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

Surface presentation of antigens protein SpaO

当前结构中的状态

数据库中的同蛋白其他状态

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

2. 结构基本信息 2. Structure Basics

3. SAXS 参数 (CRYSOL 理论计算) 3. SAXS Parameters (CRYSOL)

4. P(r) 距离分布 (GNOM 反演) 4. P(r) Analysis (GNOM)

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

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

衍射实验 Diffraction