SAXSdb — 1bug

▼

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

PROTEIN (CATECHOL OXIDASE)

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 1–345	未记录	CU COPPER (II) ION × 2 URS N-PHENYLTHIOUREA × 1	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, HANGING DROP；pH 7；CRYSTALS WERE GROWN AT 277K FROM SOLUTIONS CONTAINING 14 MG/ML PROTEIN, 120 MG/ML PEG6000, 500 MM NACL, 50 MM HEPES, PH 7.0 EQUILIBRATED AGAINST A SOLUTION CONTAINING 200 MG/ML PEG6000., VAPOR DIFFUSION, HANGING DROP	分辨率 2.70 Å R-free 0.273
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 1–345	未记录	CU COPPER (II) ION × 2 URS N-PHENYLTHIOUREA × 1	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, HANGING DROP；pH 7；CRYSTALS WERE GROWN AT 277K FROM SOLUTIONS CONTAINING 14 MG/ML PROTEIN, 120 MG/ML PEG6000, 500 MM NACL, 50 MM HEPES, PH 7.0 EQUILIBRATED AGAINST A SOLUTION CONTAINING 200 MG/ML PEG6000., VAPOR DIFFUSION, HANGING DROP	分辨率 2.70 Å R-free 0.273

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 1BUG	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
1BT1 CATECHOL OXIDASE FROM IPOMOEA BATATAS (SWEET POTATOES) IN THE NATIVE CU(II)-CU(II) STATE 提交 1998-09-02	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 1–345（345 aa）	未记录	C2O CU-O-CU LINKAGE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7；CRYSTALS WERE GROWN AT 277 K FROM SOLUTIONS CONTAINING 14 MG/ML PROTEIN, 120 MG/ML PEG6000, 500 MM NACL, 50 MM HEPES, PH 7.0, EQUILIBRATED AGAINST A SOLUTION CONTAINING 200 MG/ML PEG6000., VAPOR DIFFUSION, HANGING DROP	分辨率 2.70 Å R-free 0.256
1BT1 CATECHOL OXIDASE FROM IPOMOEA BATATAS (SWEET POTATOES) IN THE NATIVE CU(II)-CU(II) STATE 提交 1998-09-02	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 1–345（345 aa）	未记录	C2O CU-O-CU LINKAGE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7；CRYSTALS WERE GROWN AT 277 K FROM SOLUTIONS CONTAINING 14 MG/ML PROTEIN, 120 MG/ML PEG6000, 500 MM NACL, 50 MM HEPES, PH 7.0, EQUILIBRATED AGAINST A SOLUTION CONTAINING 200 MG/ML PEG6000., VAPOR DIFFUSION, HANGING DROP	分辨率 2.70 Å R-free 0.256
1BT2 CATECHOL OXIDASE FROM IPOMOEA BATATAS (SWEET POTATOES) IN THE REDUCED CU(I)-CU(I) STATE 提交 1998-09-02	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 1–345（345 aa）	未记录	C2O CU-O-CU LINKAGE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7；CRYSTALS WERE GROWN AT 277 K FROM SOLUTIONS CONTAINING 14 MG/ML PROTEIN, 120 MG/ML PEG6000, 500 MM NACL, 50 MM HEPES, PH 7.0, EQUILIBRATED AGAINST A SOLUTION CONTAINING 200 MG/ML PEG6000. 2 MM DTT WAS USED TO REDUCE THE ACTIVE SITE., VAPOR DIFFUSION, HANGING DROP	分辨率 2.70 Å R-free 0.278
1BT2 CATECHOL OXIDASE FROM IPOMOEA BATATAS (SWEET POTATOES) IN THE REDUCED CU(I)-CU(I) STATE 提交 1998-09-02	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 1–345（345 aa）	未记录	C2O CU-O-CU LINKAGE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7；CRYSTALS WERE GROWN AT 277 K FROM SOLUTIONS CONTAINING 14 MG/ML PROTEIN, 120 MG/ML PEG6000, 500 MM NACL, 50 MM HEPES, PH 7.0, EQUILIBRATED AGAINST A SOLUTION CONTAINING 200 MG/ML PEG6000. 2 MM DTT WAS USED TO REDUCE THE ACTIVE SITE., VAPOR DIFFUSION, HANGING DROP	分辨率 2.70 Å R-free 0.278
1BT3 CATECHOL OXIDASE FROM IPOMOEA BATATAS (SWEET POTATOES) IN THE NATIVE CU(II)-CU(II) STATE 提交 1998-09-02	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 1–345（345 aa）	未记录	C2O CU-O-CU LINKAGE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7；CRYSTALS WERE GROWN AT 277 K FROM SOLUTIONS CONTAINING 14 MG/ML PROTEIN, 120 MG/ML PEG6000, 500 MM NACL, 50 MM HEPES, PH 7.0, EQUILIBRATED AGAINST A SOLUTION CONTAINING 200 MG/ML PEG6000., VAPOR DIFFUSION, HANGING DROP	分辨率 2.50 Å R-free 0.250

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	PPO1_IPOBA
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 1–345； UniProt 1–345 作者链 B； PDB构建体 1–345； UniProt 1–345

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。

▼

2. 结构基本信息 2. Structure Basics

条目编号 entry_id	1bug
沉积日期 deposition_date	1998-09-03
结构标题 title	CATECHOL OXIDASE FROM IPOMOEA BATATAS (SWEET POTATOES)-INHIBITOR COMPLEX WITH PHENYLTHIOUREA (PTU)
关键词 keywords	CATECHOL OXIDASE, DICOPPER ENZYME, IPOMOEA BATATAS, OXIDOREDUCTASE; OXIDOREDUCTASE
实验方法 method	X-RAY DIFFRACTION

▼

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

回转半径 Rg (Guinier) rg_guinier	30.64 Å
回转半径 Rg (电子) rg_electron	30.01 Å
零角强度 I(0) i0	93754200.00
分子量 molecular_weight	76064.0 kDa
排除体积 excluded_volume	94531 Å³
包络体积 envelope_volume	111410 Å³
水化壳体积 shell_volume	31400 Å³
包络直径 envelope_diameter	98.5 Å
壳层 Rg shell_rg	36.58 Å
包络 Rg envelope_rg	29.86 Å
形状 Rg shape_rg	30.02 Å
总 Rg total_rg	30.54 Å
总原子数 total_atoms	5356
残基数 n_residues	672
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

▼

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

最大尺寸 Dmax dmax	96.5 Å
Rg (实空间) rg_real	30.74 Å
Rg 误差 (实空间) rg_real_error	0.63 Å
I(0) (实空间) i0_real	9.3750e+07
I(0) 误差 (实空间) i0_real_error	1.5010e+06
Rg (倒空间) rg_reciprocal	30.70 Å
I(0) (倒空间) i0_reciprocal	93750000.0000
解质量估计 total_estimate	0.8689
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	27.8 Å
偏度 Skewness skewness	0.328
峰度 Kurtosis kurtosis	-0.767
角度范围 angular_range	— – 0.2600 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	34210000.0000
实空间数据点数 n_real_points	53
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.836; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.889; Smooth: 0.895

▶

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

▶

6. 实体与聚合物信息 Entities & Polymers (4)

实体 1 Entity 1 polymer

描述 description	PROTEIN (CATECHOL OXIDASE)
分子量 formula_weight	38814.6 kDa
EC 编号 ec_number	1.10.3.1
来源方法 src_method	nat
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	5537

APIQAPEISKCVVPPADLPPGAVVDNCCPPVASNIVDYKLPAVTTMKVRPAAHTMDKDAIAKFAKAVELMKALPADDPRNFYQQALVHCAYCNGGYDQVNFPDQEIQVHNSWLFFPFHRWYLYFYERILGKLIGDPSFGLPFWNWDNPGGMVLPDFLNDSTSSLYDSNRNQSHLPPVVVDLGYNGADTDVTDQQRITDNLALMYKQMVTNAGTAELFLGKAYRAGDAPSPGAGSIETSPHIPIHRWVGDPRNTNNEDMGNFYSAGRDIAFYCHHSNVDRMWTIWQQLAGKPRKRDYTDSDWLNATFLFYDENGQAVKVRIGDSLDNQKMGYKYAKTPLPWLDSKP

实体 2 Entity 2 non-polymer

描述 description	COPPER (II) ION
分子量 formula_weight	63.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

实体 3 Entity 3 non-polymer

描述 description	N-PHENYLTHIOUREA
分子量 formula_weight	152.2 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	181

▼

7. 折叠分类 (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1buga_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.86 — Di-copper centre-containing domain
超家族 Superfamily superfamily	a.86.1 — Di-copper centre-containing domain
家族 Family family	a.86.1.2 — Catechol oxidase

结构域编号 domain_id	d1bugb_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.86 — Di-copper centre-containing domain
超家族 Superfamily superfamily	a.86.1 — Di-copper centre-containing domain
家族 Family family	a.86.1.2 — Catechol oxidase

CATH v4.4 (2 domains)

结构域编号 domain_id	1bugA00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1280 — di-copper center containing domain from catechol oxidase
同源超家族 H-superfamily homologous superfamily	10 — Di-copper center containing domain from catechol oxidase

结构域编号 domain_id	1bugB00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1280 — di-copper center containing domain from catechol oxidase
同源超家族 H-superfamily homologous superfamily	10 — Di-copper center containing domain from catechol oxidase

▶

8. 引用文献 (1)

▶

晶胞边长 a length_a	45.820 Å
晶胞边长 b length_b	164.750 Å
晶胞边长 c length_c	52.160 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	97.50 °
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	2.700 Å
最低分辨率 resolution_low	8.000 Å
R 因子 r_factor	0.1810
R_work r_work	0.1810
R_free r_free	0.2730

fit	/app/data/saxs_computation/bu/1bug/1bug.fit
pddf	/app/data/pr_computation/bu/1bug/1bug.pr.out
profile	/app/data/saxs_computation/bu/1bug/1bug.dat

CATECHOL OXIDASE FROM IPOMOEA BATATAS (SWEET POTATOES)-INHIBITOR COMPLEX WITH PHENYLTHIOUREA (PTU)

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

PROTEIN (CATECHOL OXIDASE)

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