SAXSdb — 9ypl

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

Mangotoxin biosynthesis protein MboA

Pseudomonas syringae

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	蛋白单体单体蛋白 × 1 PDB 声明：monomeric（1）与蛋白拷贝数一致	链 A； UniProt 1–225	未记录	SO4 SULFATE ION × 2 CL CHLORIDE ION × 5 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, HANGING DROP；pH 4.8；298 K；MboA crystals were prepared via the hanging drop vapor diffusion method. Hanging drops were prepared by combining equal volumes of MboA (9 mg per mL) protein solution and reservoir solution (0.4 M lithium sulfate and 0.1 M sodium acetate, pH 4.8) for a total drop volume of 2 uL. The substrate bound structure was prepared by incubating apo crystals with 0.3 uL of 100 mM LAR in 0.1 M sodium acetate, pH 4.6 for two hours prior to looping. Crystals were cryoprotected with the addition of 0.75 uL of 40% glycerol in 0.1 M sodium acetate, pH 4.6 and flash frozen in LN2	分辨率 2.20 Å R-free 0.194
2	蛋白单体单体蛋白 × 1 PDB 声明：monomeric（1）与蛋白拷贝数一致	链 B； UniProt 1–225	未记录	SO4 SULFATE ION × 1 CL CHLORIDE ION × 4 GOL GLYCEROL × 1 ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, HANGING DROP；pH 4.8；298 K；MboA crystals were prepared via the hanging drop vapor diffusion method. Hanging drops were prepared by combining equal volumes of MboA (9 mg per mL) protein solution and reservoir solution (0.4 M lithium sulfate and 0.1 M sodium acetate, pH 4.8) for a total drop volume of 2 uL. The substrate bound structure was prepared by incubating apo crystals with 0.3 uL of 100 mM LAR in 0.1 M sodium acetate, pH 4.6 for two hours prior to looping. Crystals were cryoprotected with the addition of 0.75 uL of 40% glycerol in 0.1 M sodium acetate, pH 4.6 and flash frozen in LN2	分辨率 2.20 Å R-free 0.194
3	蛋白单体单体蛋白 × 1 PDB 声明：monomeric（1）与蛋白拷贝数一致	链 C； UniProt 1–225	未记录	CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, HANGING DROP；pH 4.8；298 K；MboA crystals were prepared via the hanging drop vapor diffusion method. Hanging drops were prepared by combining equal volumes of MboA (9 mg per mL) protein solution and reservoir solution (0.4 M lithium sulfate and 0.1 M sodium acetate, pH 4.8) for a total drop volume of 2 uL. The substrate bound structure was prepared by incubating apo crystals with 0.3 uL of 100 mM LAR in 0.1 M sodium acetate, pH 4.6 for two hours prior to looping. Crystals were cryoprotected with the addition of 0.75 uL of 40% glycerol in 0.1 M sodium acetate, pH 4.6 and flash frozen in LN2	分辨率 2.20 Å R-free 0.194
4	蛋白单体单体蛋白 × 1 PDB 声明：monomeric（1）与蛋白拷贝数一致	链 D； UniProt 1–225	未记录	SO4 SULFATE ION × 3 CL CHLORIDE ION × 2 GOL GLYCEROL × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, HANGING DROP；pH 4.8；298 K；MboA crystals were prepared via the hanging drop vapor diffusion method. Hanging drops were prepared by combining equal volumes of MboA (9 mg per mL) protein solution and reservoir solution (0.4 M lithium sulfate and 0.1 M sodium acetate, pH 4.8) for a total drop volume of 2 uL. The substrate bound structure was prepared by incubating apo crystals with 0.3 uL of 100 mM LAR in 0.1 M sodium acetate, pH 4.6 for two hours prior to looping. Crystals were cryoprotected with the addition of 0.75 uL of 40% glycerol in 0.1 M sodium acetate, pH 4.6 and flash frozen in LN2	分辨率 2.20 Å R-free 0.194

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 9YPL	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
9YPI MboA HDO apo structure 提交 2025-10-14	配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 1–225（225 aa）	未记录	CL CHLORIDE ION × 5 SO4 SULFATE ION × 1 NA SODIUM ION × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；MboA crystals were prepared via the hanging drop vapor diffusion method. Hanging drops were prepared by combining equal volumes of MboA (18 mg per mL) protein solution and reservoir solution (1.2 M lithium sulfate and 0.1 M sodium acetate, pH 4.6) for a total drop volume of 2 uL. Crystals typically grew in about approximately 1 to 2 weeks. Crystals were cryoprotected with the addition of 0.75 uL of 40% glycerol in 0.1 M sodium acetate, pH 4.6 and flash frozen in LN2	分辨率 2.49 Å R-free 0.221
9YPI MboA HDO apo structure 提交 2025-10-14	配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 B 1–225（225 aa）	未记录	CL CHLORIDE ION × 6 SO4 SULFATE ION × 1 NA SODIUM ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；MboA crystals were prepared via the hanging drop vapor diffusion method. Hanging drops were prepared by combining equal volumes of MboA (18 mg per mL) protein solution and reservoir solution (1.2 M lithium sulfate and 0.1 M sodium acetate, pH 4.6) for a total drop volume of 2 uL. Crystals typically grew in about approximately 1 to 2 weeks. Crystals were cryoprotected with the addition of 0.75 uL of 40% glycerol in 0.1 M sodium acetate, pH 4.6 and flash frozen in LN2	分辨率 2.49 Å R-free 0.221
9YPI MboA HDO apo structure 提交 2025-10-14	配体/离子不同实验环境不同结构质量不同	Assembly 3 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 C 1–225（225 aa）	未记录	CL CHLORIDE ION × 5	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；MboA crystals were prepared via the hanging drop vapor diffusion method. Hanging drops were prepared by combining equal volumes of MboA (18 mg per mL) protein solution and reservoir solution (1.2 M lithium sulfate and 0.1 M sodium acetate, pH 4.6) for a total drop volume of 2 uL. Crystals typically grew in about approximately 1 to 2 weeks. Crystals were cryoprotected with the addition of 0.75 uL of 40% glycerol in 0.1 M sodium acetate, pH 4.6 and flash frozen in LN2	分辨率 2.49 Å R-free 0.221
9YPI MboA HDO apo structure 提交 2025-10-14	配体/离子不同实验环境不同结构质量不同	Assembly 4 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 D 1–225（225 aa）	未记录	CL CHLORIDE ION × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；MboA crystals were prepared via the hanging drop vapor diffusion method. Hanging drops were prepared by combining equal volumes of MboA (18 mg per mL) protein solution and reservoir solution (1.2 M lithium sulfate and 0.1 M sodium acetate, pH 4.6) for a total drop volume of 2 uL. Crystals typically grew in about approximately 1 to 2 weeks. Crystals were cryoprotected with the addition of 0.75 uL of 40% glycerol in 0.1 M sodium acetate, pH 4.6 and flash frozen in LN2	分辨率 2.49 Å R-free 0.221
9YPM MboA with Leu-Ala-Arg peptide substrate and two Fe(II) ions bound 提交 2025-10-14	配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 1–225（225 aa）	未记录	SO4 SULFATE ION × 4 CL CHLORIDE ION × 4 FE2 FE (II) ION × 2 GOL GLYCEROL × 12	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；MboA crystals were prepared via the hanging drop vapor diffusion method in an Coy anaerobic chamber with an atmosphere of < 5 ppm of O2. Hanging drops were prepared by combining equal volumes of MboA (9 mg/mL) protein solution, reservoir solution (0.6 M lithium sulfate and 0.1 M sodium acetate, pH 4.6), and 0.2 uL of a 1:1000 dilution microseed master stock generated from apo crystals for a total drop volume of 2.2 uL. The Fe(II) + substrate bound structure was prepared by incubating apo crystals with 0.4 uL of 100 mM LAR peptide and 100 mM Fe2+ in 0.1 M sodium acetate, pH 4.6 for two hours prior to looping. Crystals were cryoprotected with the addition of 0.75 uL of 40% glycerol in 0.1 M sodium acetate, pH 4.6 and flash frozen in LN2	分辨率 2.45 Å R-free 0.195
9YPM MboA with Leu-Ala-Arg peptide substrate and two Fe(II) ions bound 提交 2025-10-14	配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 B 1–225（225 aa）	未记录	SO4 SULFATE ION × 5 CL CHLORIDE ION × 4 FE2 FE (II) ION × 2 GOL GLYCEROL × 7 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；MboA crystals were prepared via the hanging drop vapor diffusion method in an Coy anaerobic chamber with an atmosphere of < 5 ppm of O2. Hanging drops were prepared by combining equal volumes of MboA (9 mg/mL) protein solution, reservoir solution (0.6 M lithium sulfate and 0.1 M sodium acetate, pH 4.6), and 0.2 uL of a 1:1000 dilution microseed master stock generated from apo crystals for a total drop volume of 2.2 uL. The Fe(II) + substrate bound structure was prepared by incubating apo crystals with 0.4 uL of 100 mM LAR peptide and 100 mM Fe2+ in 0.1 M sodium acetate, pH 4.6 for two hours prior to looping. Crystals were cryoprotected with the addition of 0.75 uL of 40% glycerol in 0.1 M sodium acetate, pH 4.6 and flash frozen in LN2	分辨率 2.45 Å R-free 0.195
9YPM MboA with Leu-Ala-Arg peptide substrate and two Fe(II) ions bound 提交 2025-10-14	配体/离子不同实验环境不同结构质量不同	Assembly 3 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 C 1–225（225 aa）	未记录	SO4 SULFATE ION × 3 CL CHLORIDE ION × 2 FE2 FE (II) ION × 2 GOL GLYCEROL × 10 ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；MboA crystals were prepared via the hanging drop vapor diffusion method in an Coy anaerobic chamber with an atmosphere of < 5 ppm of O2. Hanging drops were prepared by combining equal volumes of MboA (9 mg/mL) protein solution, reservoir solution (0.6 M lithium sulfate and 0.1 M sodium acetate, pH 4.6), and 0.2 uL of a 1:1000 dilution microseed master stock generated from apo crystals for a total drop volume of 2.2 uL. The Fe(II) + substrate bound structure was prepared by incubating apo crystals with 0.4 uL of 100 mM LAR peptide and 100 mM Fe2+ in 0.1 M sodium acetate, pH 4.6 for two hours prior to looping. Crystals were cryoprotected with the addition of 0.75 uL of 40% glycerol in 0.1 M sodium acetate, pH 4.6 and flash frozen in LN2	分辨率 2.45 Å R-free 0.195
9YPM MboA with Leu-Ala-Arg peptide substrate and two Fe(II) ions bound 提交 2025-10-14	配体/离子不同实验环境不同结构质量不同	Assembly 4 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 D 1–225（225 aa）	未记录	SO4 SULFATE ION × 3 CL CHLORIDE ION × 2 FE2 FE (II) ION × 2 GOL GLYCEROL × 7	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；MboA crystals were prepared via the hanging drop vapor diffusion method in an Coy anaerobic chamber with an atmosphere of < 5 ppm of O2. Hanging drops were prepared by combining equal volumes of MboA (9 mg/mL) protein solution, reservoir solution (0.6 M lithium sulfate and 0.1 M sodium acetate, pH 4.6), and 0.2 uL of a 1:1000 dilution microseed master stock generated from apo crystals for a total drop volume of 2.2 uL. The Fe(II) + substrate bound structure was prepared by incubating apo crystals with 0.4 uL of 100 mM LAR peptide and 100 mM Fe2+ in 0.1 M sodium acetate, pH 4.6 for two hours prior to looping. Crystals were cryoprotected with the addition of 0.75 uL of 40% glycerol in 0.1 M sodium acetate, pH 4.6 and flash frozen in LN2	分辨率 2.45 Å R-free 0.195

共 2 个其他 PDB 条目、8 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	A0A244EXR3_PSESX
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 26–250； UniProt 1–225 作者链 B； PDB构建体 26–250； UniProt 1–225 作者链 C； PDB构建体 26–250； UniProt 1–225 作者链 D； PDB构建体 26–250； UniProt 1–225

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	9ypl
沉积日期 deposition_date	2025-10-14
结构标题 title	MboA with Leu-Ala-Arg peptide substrate bound
关键词 keywords	Heme-oxygenase like domain containing enzyme, HDO, Di-iron oxidase, alkynase, BIOSYNTHETIC PROTEIN; BIOSYNTHETIC PROTEIN
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	32.87 Å
回转半径 Rg (电子) rg_electron	32.28 Å
零角强度 I(0) i0	179015000.00
分子量 molecular_weight	107010.0 kDa
排除体积 excluded_volume	133430 Å³
包络体积 envelope_volume	164810 Å³
水化壳体积 shell_volume	42738 Å³
包络直径 envelope_diameter	118.8 Å
壳层 Rg shell_rg	39.03 Å
包络 Rg envelope_rg	32.18 Å
形状 Rg shape_rg	32.27 Å
总 Rg total_rg	32.83 Å
总原子数 total_atoms	7497
残基数 n_residues	938
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	109.2 Å
Rg (实空间) rg_real	32.78 Å
Rg 误差 (实空间) rg_real_error	0.78 Å
I(0) (实空间) i0_real	1.7900e+08
I(0) 误差 (实空间) i0_real_error	2.6880e+06
Rg (倒空间) rg_reciprocal	32.82 Å
I(0) (倒空间) i0_reciprocal	179000000.0000
解质量估计 total_estimate	0.8938
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	43.2 Å
偏度 Skewness skewness	0.249
峰度 Kurtosis kurtosis	-0.406
角度范围 angular_range	— – 0.2400 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	50750000.0000
实空间数据点数 n_real_points	49
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.879; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.984

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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 (7)

实体 1 Entity 1 polymer

描述 description	Mangotoxin biosynthesis protein MboA
分子量 formula_weight	28433.1 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	8203

MGHHHHHHHHHHSSGHLEVLFQGPHMISTAEMLKTLETTVDTCLEAEFKKDTVMGEFHKGDWFNESYYKRHILECVIRIHMNNELDARAVQVAAIDNISAAKQLSYYLYDEFGHDEMFGQDLITYGYSASDIKAEFAFPETWKLMGYLNFCVSKFGPLSSITWDWFLEYYGDKYSSFITQKASASMGQPAVSGAASHVAFDEAEDHSGMMNNMLSSVIKDEKDLAKAVVHIKAFVPMVGEYFQALRAATL

来源 Source

来源生物 organism	Pseudomonas syringae
NCBI 分类编号 ncbi_taxonomy_id	317
宿主生物 host_organism	Escherichia coli BL21(DE3)

实体 2 Entity 2 polymer

描述 description	LEU-ALA-ARG peptide substrate
分子量 formula_weight	359.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	E,J,K,L

LAR

实体 3 Entity 3 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

实体 4 Entity 4 non-polymer

描述 description	CHLORIDE ION
分子量 formula_weight	35.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	14

实体 5 Entity 5 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

实体 6 Entity 6 non-polymer

描述 description	ACETATE ION
分子量 formula_weight	59.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

实体 7 Entity 7 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	595

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8. 引用文献 (1)

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晶胞边长 a length_a	157.741 Å
晶胞边长 b length_b	157.741 Å
晶胞边长 c length_c	157.014 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	32

空间群 space_group	P 43 21 2
空间群编号 int_tables_number	96
晶系 crystal_system	tetragonal

分辨率 resolution	2.200 Å
最低分辨率 resolution_low	43.750 Å
R 因子 r_factor	0.1720
R_work r_work	0.1713
R_free r_free	0.1936

fit	/app/data/saxs_computation/yp/9ypl/9ypl.fit
pddf	/app/data/pr_computation/yp/9ypl/9ypl.pr.out
profile	/app/data/saxs_computation/yp/9ypl/9ypl.dat

MboA with Leu-Ala-Arg peptide substrate bound

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

Mangotoxin biosynthesis protein MboA

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

6. 实体与聚合物信息 Entities & Polymers (7)

实体 1 Entity 1 polymer

聚合物 Polymer

来源 Source

实体 2 Entity 2 polymer

聚合物 Polymer

实体 3 Entity 3 non-polymer

实体 4 Entity 4 non-polymer

实体 5 Entity 5 non-polymer

实体 6 Entity 6 non-polymer

实体 7 Entity 7 water

8. 引用文献 (1)

9. 文件与曲线 (10)

Files (7)

Curves (3)