SAXSdb — 1bqb

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

PROTEIN (AUREOLYSIN)

物种未注明

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 1–301	未记录	ZN ZINC ION × 1 CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray结晶条件：pH 5.2；0.1 M SODIUM ACETATE PH 5.2 AND 40% PEG 4000	分辨率 1.72 Å R-free 0.239

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 1BQB	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
7SKL Complex between S. aureus aureolysin and IMPI mutant I57I 提交 2021-10-21	构建体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 蛋白异源复合物异源复合物；蛋白 × 3 PDB 声明：trimeric	链 A 209–509（301 aa）	未记录	CA CALCIUM ION × 3 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 5	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；293 K；Best crystals of aureolysin in complex with IMPI mutant I57F were obtained at 20 dgrees with protein solutions consisting of 5 mg/mL of aureolysin and 2.9 mg/mL of IMPI (peptidase:inhibitor molar ratio of 1:2.5) in 50 mM Tris-HCl, 150 mM sodium chloride, 1.6 mM calcium chloride, 8.3 microM zinc chloride, pH 8.0, which was mixed with reservoir solution comprising 0.1 M Bis-Tris, 25% (w/v) PEG 3350, pH 5.5.	分辨率 1.60 Å R-free 0.188
7SKL Complex between S. aureus aureolysin and IMPI mutant I57I 提交 2021-10-21	构建体不同聚集状态不同实验环境不同结构质量不同	Assembly 2 蛋白异源复合物异源复合物；蛋白 × 3 PDB 声明：trimeric	链 C 209–509（301 aa）	未记录	CA CALCIUM ION × 3 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；293 K；Best crystals of aureolysin in complex with IMPI mutant I57F were obtained at 20 dgrees with protein solutions consisting of 5 mg/mL of aureolysin and 2.9 mg/mL of IMPI (peptidase:inhibitor molar ratio of 1:2.5) in 50 mM Tris-HCl, 150 mM sodium chloride, 1.6 mM calcium chloride, 8.3 microM zinc chloride, pH 8.0, which was mixed with reservoir solution comprising 0.1 M Bis-Tris, 25% (w/v) PEG 3350, pH 5.5.	分辨率 1.60 Å R-free 0.188
7SKM Complex between S. aureus aureolysin and wt IMPI. 提交 2021-10-21	构建体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 蛋白异源复合物异源复合物；蛋白 × 3 PDB 声明：trimeric	链 A 209–509（301 aa）	未记录	CA CALCIUM ION × 3 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；Best crystals of aureolysin in complex with either IMPI variant were obtained at 20 degrees with protein solutions consisting of 5 mg/mL of aureolysin and 2.9 mg/mL of IMPI (peptidase:inhibitor molar ratio of 1:2.5) in 50 mM Tris-HCl, 150 mM sodium chloride, 1.6 mM calcium chloride, 8.3 microM zinc chloride, pH 8.0, which was mixed with reservoir solution comprising 0.1 M Bis-Tris, 25% (w/v) PEG 3350, pH 5.5.	分辨率 1.85 Å R-free 0.219
7SKM Complex between S. aureus aureolysin and wt IMPI. 提交 2021-10-21	构建体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 蛋白异源复合物异源复合物；蛋白 × 3 PDB 声明：trimeric	链 C 209–509（301 aa）	未记录	CA CALCIUM ION × 3 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 1 PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；Best crystals of aureolysin in complex with either IMPI variant were obtained at 20 degrees with protein solutions consisting of 5 mg/mL of aureolysin and 2.9 mg/mL of IMPI (peptidase:inhibitor molar ratio of 1:2.5) in 50 mM Tris-HCl, 150 mM sodium chloride, 1.6 mM calcium chloride, 8.3 microM zinc chloride, pH 8.0, which was mixed with reservoir solution comprising 0.1 M Bis-Tris, 25% (w/v) PEG 3350, pH 5.5.	分辨率 1.85 Å R-free 0.219

共 2 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	AURE_STAAU
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 1–301； UniProt 1–301

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	1bqb
沉积日期 deposition_date	1998-07-14
结构标题 title	AUREOLYSIN, STAPHYLOCOCCUS AUREUS METALLOPROTEINASE
关键词 keywords	HYDROLASE, METALLOPROTEINASE; HYDROLASE
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	20.39 Å
回转半径 Rg (电子) rg_electron	19.51 Å
零角强度 I(0) i0	21654500.00
分子量 molecular_weight	33489.0 kDa
排除体积 excluded_volume	40880 Å³
包络体积 envelope_volume	46524 Å³
水化壳体积 shell_volume	20043 Å³
包络直径 envelope_diameter	67.5 Å
壳层 Rg shell_rg	25.77 Å
包络 Rg envelope_rg	19.81 Å
形状 Rg shape_rg	19.51 Å
总 Rg total_rg	20.29 Å
总原子数 total_atoms	2358
残基数 n_residues	301
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	67.7 Å
Rg (实空间) rg_real	20.35 Å
Rg 误差 (实空间) rg_real_error	0.41 Å
I(0) (实空间) i0_real	2.1650e+07
I(0) 误差 (实空间) i0_real_error	2.9180e+05
Rg (倒空间) rg_reciprocal	20.36 Å
I(0) (倒空间) i0_reciprocal	21650000.0000
解质量估计 total_estimate	0.7223
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	24.2 Å
偏度 Skewness skewness	0.337
峰度 Kurtosis kurtosis	-0.252
角度范围 angular_range	— – 0.3900 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	4014000.0000
实空间数据点数 n_real_points	71
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.819; Stabil: 1.000; Sysdev: 0.319; Positv: 1.000; Valcen: 0.999; Smooth: 0.971

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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 (4)

实体 1 Entity 1 polymer

描述 description	PROTEIN (AUREOLYSIN)
分子量 formula_weight	33358.8 kDa
EC 编号 ec_number	3.4.24.27
来源方法 src_method	nat
拷贝数 entity_count	1

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	2518

AAATGTGKGVLGDTKDININSIDGGFSLEDLTHQGKLSAYNFNDQTGQATLITNEDENFVKDDQRAGVDANYYAKQTYDYYKNTFGRESYDNHGSPIVSLTHVNHYGGQDNRNNAAWIGDKMIYGDGDGRTFTNLSGANDVVAHEITHGVTQQTANLEYKDQSGALNESFSDVFGYFVDDEDFLMGEDVYTPGKEGDALRSMSNPEQFGQPSHMKDYVYTEKDNGGVHTNSGIPNKAAYNVIQAIGKSKSEQIYYRALTEYLTSNSNFKDLKDALYQAAKDLYEQQTAEQVYEAWNEVGVE

实体 2 Entity 2 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

实体 3 Entity 3 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	3

实体 4 Entity 4 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	160

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7. 折叠分类 (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

结构域编号 domain_id	d1bqba_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.92 — Zincin-like
超家族 Superfamily superfamily	d.92.1 — Metalloproteases ('zincins'), catalytic domain
家族 Family family	d.92.1.2 — Thermolysin-like

CATH v4.4 (2 domains)

结构域编号 domain_id	1bqbA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	170 — Elastase; domain 1
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1bqbA02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	390 — Neutral Protease; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Neutral Protease Domain 2

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8. 引用文献 (1)

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晶胞边长 a length_a	33.700 Å
晶胞边长 b length_b	79.500 Å
晶胞边长 c length_c	100.100 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	4

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	1.720 Å
最低分辨率 resolution_low	8.000 Å
R 因子 r_factor	0.1760
R_work r_work	0.1760
R_free r_free	0.2390

fit	/app/data/saxs_computation/bq/1bqb/1bqb.fit
pddf	/app/data/pr_computation/bq/1bqb/1bqb.pr.out
profile	/app/data/saxs_computation/bq/1bqb/1bqb.dat

AUREOLYSIN, STAPHYLOCOCCUS AUREUS METALLOPROTEINASE

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

PROTEIN (AUREOLYSIN)

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