SAXSdb — 3bh4

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

Alpha-amylase

Bacillus amyloliquefaciens

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 32–514	未记录	CA CALCIUM ION × 4 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；100mM Tris-HCl, pH7.5, 24% PEG3350, 3.5mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K	分辨率 1.40 Å R-free 0.219
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 32–514	未记录	CA CALCIUM ION × 4 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；100mM Tris-HCl, pH7.5, 24% PEG3350, 3.5mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K	分辨率 1.40 Å R-free 0.219

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 3BH4	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
1E3X Native structure of chimaeric amylase from B. amyloliquefaciens and B. licheniformis at 1.92A 提交 2000-06-26	构建体不同聚集状态不同实验环境不同结构质量不同	Assembly 1 信息不足单体；蛋白 × 1 PDB 声明：monomeric	链 A 32–331（300 aa）	未记录	CA CALCIUM ION × 4 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；CRYSTALS WERE GROWN AT 18C USING THE HANGING DROP METHOD WITH 8-13% MONOMETHYL ETHER POLYETHYLENE GLYCOL 2000 OR 5000 AS PRECIPITANT. DROPS WERE BUFFERED WITH 0.1M TRIS/HCL PH 7.5 CONTAINING 5MM CACL2 AND THE PROTEIN CONCENTRATION WAS 30-35MG/ML.	分辨率 1.90 Å R-free 0.200
1E3Z Acarbose complex of chimaeric amylase from B. amyloliquefaciens and B. licheniformis at 1.93A 提交 2000-06-27	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 信息不足单体；蛋白 × 1 PDB 声明：monomeric	链 A 32–331（300 aa）	未记录	CA CALCIUM ION × 4 NA SODIUM ION × 1 ACI 6-AMINO-4-HYDROXYMETHYL-CYCLOHEX-4-ENE-1,2,3-TRIOL × 3	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；CRYSTALS WERE GROWN AT 18C USING THE HANGING DROP METHOD WITH 8-13% MONOMETHYL ETHER POLYETHYLENE GLYCOL 2000 OR 5000 AS PRECIPITANT. DROPS WERE BUFFERED WITH 0.1M TRIS/HCL PH 7.5 CONTAINING 5MM CACL2 AND THE PROTEIN CONCENTRATION WAS 30-35MG/ML. CRYSTALS WERE THEN SOAKED IN 10MM ACARBOSE SOLUTION TO OBTAIN THE COMPLEX.	分辨率 1.93 Å R-free 0.200
1E40 Tris/maltotriose complex of chimaeric amylase from B. amyloliquefaciens and B. licheniformis at 2.2A 提交 2000-06-27	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 信息不足单体；蛋白 × 1 PDB 声明：monomeric	链 A 32–331（300 aa）	未记录	CA CALCIUM ION × 4 NA SODIUM ION × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；CRYSTALS WERE GROWN AT 18C USING THE HANGING DROP METHOD WITH 8-13% MONOMETHYL ETHER POLYETHYLENE GLYCOL 2000 OR 5000 AS PRECIPITANT. DROPS WERE BUFFERED WITH 0.1M TRIS/HCL PH 7.5 CONTAINING 5MM CACL2 AND THE PROTEIN CONCENTRATION WAS 30-35MG/ML. CRYSTALS WERE THEN SOAKED IN 10MM MALTOTRIOSE SOLUTION TO OBTAIN THE COMPLEX.	分辨率 2.20 Å R-free 0.210
1E43 Native structure of chimaeric amylase from B. amyloliquefaciens and B. licheniformis at 1.7A 提交 2000-06-27	构建体不同聚集状态不同实验环境不同结构质量不同	Assembly 1 信息不足单体；蛋白 × 1 PDB 声明：monomeric	链 A 32–331（300 aa）	未记录	CA CALCIUM ION × 4 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 10；291 K；CRYSTALS WERE GROWN AT 18C USING THE HANGING DROP METHOD WITH 8-13% MONOMETHYL ETHER POLYETHYLENE GLYCOL 2000 OR 5000 AS PRECIPITANT. DROPS WERE BUFFERED WITH 0.1M TRIS/HCL PH 7.5 CONTAINING 5MM CACL2 AND THE PROTEIN CONCENTRATION WAS 30-35MG/ML.	分辨率 1.70 Å R-free 0.185

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	AMY_BACAM
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 1–483； UniProt 32–514 作者链 B； PDB构建体 1–483； UniProt 32–514

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	3bh4
沉积日期 deposition_date	2007-11-28
结构标题 title	High resolution crystal structure of Bacillus amyloliquefaciens alpha-amylase
关键词 keywords	crystal structure alpha-amylase, Calcium, Carbohydrate metabolism, Glycosidase, Hydrolase, Metal-binding, Secreted; 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	34.83 Å
回转半径 Rg (电子) rg_electron	34.24 Å
零角强度 I(0) i0	192801000.00
分子量 molecular_weight	110010.0 kDa
排除体积 excluded_volume	136420 Å³
包络体积 envelope_volume	160540 Å³
水化壳体积 shell_volume	39865 Å³
包络直径 envelope_diameter	125.7 Å
壳层 Rg shell_rg	39.61 Å
包络 Rg envelope_rg	34.12 Å
形状 Rg shape_rg	34.23 Å
总 Rg total_rg	34.65 Å
总原子数 total_atoms	7788
残基数 n_residues	966
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	119.4 Å
Rg (实空间) rg_real	34.92 Å
Rg 误差 (实空间) rg_real_error	1.34 Å
I(0) (实空间) i0_real	1.9280e+08
I(0) 误差 (实空间) i0_real_error	3.5240e+06
Rg (倒空间) rg_reciprocal	34.87 Å
I(0) (倒空间) i0_reciprocal	192800000.0000
解质量估计 total_estimate	0.8728
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	34.5 Å
偏度 Skewness skewness	0.393
峰度 Kurtosis kurtosis	-0.305
角度范围 angular_range	— – 0.2250 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	25050000.0000
实空间数据点数 n_real_points	46
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.846; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.952; Smooth: 0.853

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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	Alpha-amylase
分子量 formula_weight	54902.2 kDa
EC 编号 ec_number	3.2.1.1
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	8435

VNGTLMQYFEWYTPNDGQHWKRLQNDAEHLSDIGITAVWIPPAYKGLSQSDNGYGPYDLYDLGEFQQKGTVRTKYGTKSELQDAIGSLHSRNVQVYGDVVLNHKAGADATEDVTAVEVNPANRNQETSEEYQIKAWTDFRFPGRGNTYSDFKWHWYHFDGADWDESRKISRIFKFRGEGKAWDWEVSSENGNYDYLMYADVDYDHPDVVAETKKWGIWYANELSLDGFRIDAAKHIKFSFLRDWVQAVRQATGKEMFTVAEYWQNNAGKLENYLNKTSFNQSVFDVPLHFNLQAASSQGGGYDMRRLLDGTVVSRHPEKAVTFVENHDTQPGQSLESTVQTWFKPLAYAFILTRESGYPQVFYGDMYGTKGTSPKEIPSLKDNIEPILKARKEYAYGPQHDYIDHPDVIGWTREGDSSAAKSGLAALITDGPGGSKRMYAGLKNAGETWYDITGNRSDTVKIGSDGWGEFHVNDGSVSIYVQK

来源 Source

来源生物 organism	Bacillus amyloliquefaciens
NCBI 分类编号 ncbi_taxonomy_id	1390

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	8

实体 3 Entity 3 non-polymer

描述 description	SODIUM ION
分子量 formula_weight	23.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	647

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7. 折叠分类 (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

结构域编号 domain_id	3bh4A01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	80 — Glycosidases

结构域编号 domain_id	3bh4A02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
同源超家族 H-superfamily homologous superfamily	140 —

结构域编号 domain_id	3bh4A03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	1180 — Golgi alpha-mannosidase II

结构域编号 domain_id	3bh4B01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	80 — Glycosidases

结构域编号 domain_id	3bh4B02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
同源超家族 H-superfamily homologous superfamily	140 —

结构域编号 domain_id	3bh4B03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	1180 — Golgi alpha-mannosidase II

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8. 引用文献 (1)

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晶胞边长 a length_a	89.760 Å
晶胞边长 b length_b	148.676 Å
晶胞边长 c length_c	76.197 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	8

空间群 space_group	P 21 21 2
空间群编号 int_tables_number	18
晶系 crystal_system	—

分辨率 resolution	1.400 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	0.2060
R_work r_work	0.2060
R_free r_free	0.2190

fit	/app/data/saxs_computation/bh/3bh4/3bh4.fit
pddf	/app/data/pr_computation/bh/3bh4/3bh4.pr.out
profile	/app/data/saxs_computation/bh/3bh4/3bh4.dat

High resolution crystal structure of Bacillus amyloliquefaciens alpha-amylase

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

Alpha-amylase

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