SAXSdb — 8v9s

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

Replication protein P

Escherichia phage Lambda

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 105–210	片段：residues 105 to 210 非标准单体：是（mmCIF未提供具体位点）	无其他共同聚合物	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, SITTING DROP；298.15 K；Crystals were prepared using the sitting drop vapor diffusion method by mixing either 0.1, or 0.2, or 0.4 uL of the protein solution and 0.2 uL of a series of commercially available crystallization screens (Qiagen). Optimized crystals for X-ray diffraction were grown at room temperature in a buffer consisting of 3 M to 4 M NaCl with 0.1 M HEPES-NaOH, pH 7 to 8 and required 7 days to form.	分辨率 1.86 Å R-free 0.244

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 8V9S	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
6BBM Mechanisms of Opening and Closing of the Bacterial Replicative Helicase: The DnaB Helicase and Lambda P Helicase Loader Complex 提交 2017-10-18	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验方法不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 11 PDB 声明：undecameric	链 V 1–107（107 aa）链 W 1–107（107 aa）链 X 1–107（107 aa）链 Y 1–107（107 aa）链 Z 1–107（107 aa）	未记录	ADP ADENOSINE-5'-DIPHOSPHATE × 5	ELECTRON MICROSCOPY cryo-EM缓冲液 pH 7.5；Concentrated BP sample (18mg/mL) was diluted with freshly prepared buffer to desired concentration (~1.5 micromolar) for grid preparation. cryo-EM玻璃化条件冷冻剂 ETHANE；3uL of sample was adhered to a fresh plasma cleaned grid and allowed to adsorb for 30 seconds, blotted for 3 seconds with a blot force of 4 and plunge frozen into liquid nitrogen-cooled ethane.	分辨率 4.10 Å
8V9T Ecoli DnaB helicase and Phage Lambda loader P with ADP-Mg in a 6:5 stoichiometry ratio 提交 2023-12-09	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验方法不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 11 PDB 声明：undecameric	链 V 1–233（233 aa）链 W 1–233（233 aa）链 X 1–233（233 aa）链 Y 1–233（233 aa）链 Z 1–233（233 aa）	突变：K2E 突变：K2E 突变：K2E 突变：K2E 突变：K2E	ADP ADENOSINE-5'-DIPHOSPHATE × 5 MG MAGNESIUM ION × 5	ELECTRON MICROSCOPY cryo-EM缓冲液 pH 7.5；20 mM Na-HEPES pH 7.5, 450mM NaCl, 2mM DTT, 0.5mM MgCl2, 0.2mM ATP, 0.25% Glycerol cryo-EM玻璃化条件冷冻剂 ETHANE；Protein BP (1.5 uM) and DNA (1.875 uM) was mixed in a 1.25 molar excess. 3uL of the sample was added to a plasma-cleaned grid at 4 degrees celsius, 100 percent humidity, blot force 4, blot time 4s, wait time 30s, total blots 1, and plunge-frozen into liquid nitrogen-cooled ethane.	分辨率 2.84 Å
9OA1 Ecoli DnaB helicase and Phage Lambda loader P with ADP-Mg in a 6:5 stoichiometry ratio. 提交 2025-04-18	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验方法不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 11 PDB 声明：undecameric	链 V 1–233（233 aa）链 W 1–233（233 aa）链 X 1–233（233 aa）链 Y 1–233（233 aa）链 Z 1–233（233 aa）	突变：K2E 突变：K2E 突变：K2E 突变：K2E 突变：K2E	ADP ADENOSINE-5'-DIPHOSPHATE × 6 MG MAGNESIUM ION × 6	ELECTRON MICROSCOPY cryo-EM缓冲液 pH 7.5；20 mM Na-HEPES pH 7.5, 450mM NaCl, 2mM DTT, 0.5mM MgCl2, 0.2mM ATP, 0.25% Glycerol cryo-EM玻璃化条件冷冻剂 ETHANE；Protein BP (1.5 uM) and DNA (1.875 uM) was mixed in a 1.25 molar excess. 3uL of the sample was added to a plasma-cleaned grid at 4 degrees celsius, 100 percent humidity, blot force 4, blot time 4s, wait time 30s, total blots 1, and plunge-frozen into liquid nitrogen-cooled ethane.	分辨率 2.66 Å
9OA2 Ecoli DnaB helicase and Phage Lambda loader P with ADP-Mg in a 6:6 stoichiometry ratio. 提交 2025-04-18	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验方法不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 12 PDB 声明：dodecameric	链 U 1–233（233 aa）链 V 1–233（233 aa）链 W 1–233（233 aa）链 X 1–233（233 aa）链 Y 1–233（233 aa）链 Z 1–233（233 aa）	突变：K2E 突变：K2E 突变：K2E 突变：K2E 突变：K2E 突变：K2E	ADP ADENOSINE-5'-DIPHOSPHATE × 6 MG MAGNESIUM ION × 6	ELECTRON MICROSCOPY cryo-EM缓冲液 pH 7.5；20 mM Na-HEPES pH 7.5, 450mM NaCl, 2mM DTT, 0.5mM MgCl2, 0.2mM ATP, 0.25% Glycerol cryo-EM玻璃化条件冷冻剂 ETHANE；Protein BP (1.5 uM), ssDNA (1.875 uM), and LO-156-299-NHis (2.25 uM) was mixed at 1.25 and 1.5 molar excess, respectively. 3uL of the sample was added to a plasma-cleaned grid at 4 degrees celsius, 100 percent humidity, blot force 4, blot time 4s, wait time 30s, total blots 1, and plunge-frozen into liquid nitrogen-cooled ethane.	分辨率 3.85 Å

共 4 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	VRPP_LAMBD
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 9–114； UniProt 105–210

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	8v9s
沉积日期 deposition_date	2023-12-09
结构标题 title	Distinct Quaternary States, Intermediates, and Autoinhibition During Loading of the DnaB-Replicative Helicase by the Phage Lambda P Helicase Loader
关键词 keywords	hexameric DnaB helicase, replicative loader, Phage Lambda P helicase loader, bacterial DNA replication initiation, REPLICATION; REPLICATION
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	13.37 Å
回转半径 Rg (电子) rg_electron	12.09 Å
零角强度 I(0) i0	1857290.00
分子量 molecular_weight	8775.0 kDa
排除体积 excluded_volume	10727 Å³
包络体积 envelope_volume	12147 Å³
水化壳体积 shell_volume	8920 Å³
包络直径 envelope_diameter	45.2 Å
壳层 Rg shell_rg	17.16 Å
包络 Rg envelope_rg	12.53 Å
形状 Rg shape_rg	12.11 Å
总 Rg total_rg	13.27 Å
总原子数 total_atoms	607
残基数 n_residues	71
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	44.8 Å
Rg (实空间) rg_real	13.32 Å
Rg 误差 (实空间) rg_real_error	0.30 Å
I(0) (实空间) i0_real	1.8570e+06
I(0) 误差 (实空间) i0_real_error	1.9270e+04
Rg (倒空间) rg_reciprocal	13.33 Å
I(0) (倒空间) i0_reciprocal	1857000.0000
解质量估计 total_estimate	0.7958
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	15.9 Å
偏度 Skewness skewness	0.225
峰度 Kurtosis kurtosis	-0.244
角度范围 angular_range	— – 0.5000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	353900.0000
实空间数据点数 n_real_points	80
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.781; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; 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 (2)

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8. 引用文献 (2)

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晶胞边长 a length_a	49.731 Å
晶胞边长 b length_b	49.731 Å
晶胞边长 c length_c	70.772 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	120.00 °
晶胞分子数 Z z_pdb	6

空间群 space_group	P 31 2 1
空间群编号 int_tables_number	152
晶系 crystal_system	trigonal

分辨率 resolution	1.860 Å
最低分辨率 resolution_low	43.070 Å
R 因子 r_factor	0.2276
R_work r_work	0.2258
R_free r_free	0.2436

描述 description	Replication protein P
分子量 formula_weight	13405.5 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合物类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	683

Distinct Quaternary States, Intermediates, and Autoinhibition During Loading of the DnaB-Replicative Helicase by the Phage Lambda P Helicase Loader

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

Replication protein P

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 (2)

实体 1 Entity 1 polymer

聚合物 Polymer

来源 Source

实体 2 Entity 2 water

8. 引用文献 (2)

9. 文件与曲线 (10)

Files (7)

Curves (3)

来源生物 organism	Escherichia phage Lambda
NCBI 分类编号 ncbi_taxonomy_id	2681611
宿主生物 host_organism	Escherichia coli BL21(DE3)

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	76

fit	/app/data/saxs_computation/v9/8v9s/8v9s.fit
pddf	/app/data/pr_computation/v9/8v9s/8v9s.pr.out
profile	/app/data/saxs_computation/v9/8v9s/8v9s.dat