SAXSdb — 1e5j

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

ENDOGLUCANASE 5A

BACILLUS AGARADHAERENS

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	其他组合单体蛋白 × 1 其他聚合物 1 PDB 声明：monomeric（1）与蛋白拷贝数一致	链 A； UniProt 27–331	片段：CATALYTIC CORE DOMAIN, RESIDUES 27-331	alpha-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-methyl beta-D-glucopyranoside × 1 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray结晶条件：pH 7；PROTEIN (20MGML-1) WAS CRYSTALLISED FROM 28% PEG400 AS PRECIPITANT, 100MM HEPES AT PH 7.0 AS BUFFER AND 200 MM CACL2. THE PROTEIN WAS INCUBATED WITH THE 1MM OF SUBSTRATE FOR AN HOUR PRIOR TO COCRYSTALLISATIOM	分辨率 1.85 Å R-free 0.222

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 1E5J	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
1A3H ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHERANS AT 1.6A RESOLUTION 提交 1998-01-21	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 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 30–329（300 aa）片段：CATALYTIC CORE DOMAIN	未记录	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 pH 4.5；pH 4.5	分辨率 1.57 Å R-free 0.170
1H11 2-DEOXY-2-FLURO-B-D-CELLOTRIOSYL/ENZYME INTERMEDIATE COMPLEX OF THE ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHEARANS AT 1.08 ANGSTROM RESOLUTION 提交 2002-07-01	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合单体；蛋白 × 1 PDB 声明：monomeric	链 A 27–329（303 aa）片段：CATALYTIC CORE DOMAIN ONLY, RESIDUES 27-329	未记录	SO4 SULFATE ION × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray结晶条件 pH 5.5；PROTEIN CONCENTRATION 20MG/ML, 2M AMMONIUM SULPHATE, 25% GLYCEROL AS CRYOPROTECTANT, pH 5.50	分辨率 1.08 Å R-free 0.125
1H2J ENDOGLUCANASE CEL5A IN COMPLEX WITH UNHYDROLYSED AND COVALENTLY LINKED 2,4-DINITROPHENYL-2-DEOXY-2-FLUORO-CELLOBIOSIDE AT 1.15 A RESOLUTION 提交 2002-08-09	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 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 27–329（303 aa）片段：CATALYTIC CORE DOMAIN ONLY, RESIDUES 27-329	未记录	DCB 2,4-DINITROPHENYL-2-DEOXY-2-FLUORO-BETA-D-CELLOBIOSIDE × 1 GOL GLYCEROL × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray结晶条件 pH 4.6；PROTEIN CONCENTRATION 20MG/ML, 2M AMMONIUM SULPHATE, 25% GLYCEROL AS CRYOPROTECTANT, pH 4.60	分辨率 1.15 Å R-free 0.136
1H5V Thiopentasaccharide complex of the endoglucanase Cel5A from Bacillus agaradharens at 1.1 A resolution in the tetragonal crystal form 提交 2001-05-28	构建体不同配体/离子不同结构质量不同	Assembly 1 其他组合单体；蛋白 × 1 PDB 声明：monomeric	链 A 27–330（304 aa）片段：CATALYTIC CORE DOMAIN RESIDUES 27-331	未记录	CA CALCIUM ION × 10 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray结晶条件 pH 7；PROTEIN (20MGML-1) WAS CRYSTALLISED FROM 28% PEG400 AS PRECIPITANT, 100MM HEPES AT PH 7.0 AS BUFFER AND 200 MM CACL2. THE PROTEIN WAS INCUBATED WITH THE 1MM OF SUBSTRATE FOR AN HOUR PRIOR TO COCRYSTALLISATIOM	分辨率 1.10 Å R-free 0.138
1HF6 ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHAERENS IN THE ORTHORHOMBIC CRYSTAL FORM IN COMPLEX WITH CELLOTRIOSE 提交 2000-11-29	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合单体；蛋白 × 1 PDB 声明：monomeric	链 A 27–329（303 aa）片段：CATALYTIC CORE DOMAIN ONLY	未记录	SO4 SULFATE ION × 1 ACY ACETIC ACID × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray结晶条件 pH 4.6；PROTEIN CONCENTRATION 20MG/ML, 2M AMMONIUM SULPHATE, 100MM SODIUM CITRATE PH 5.5, 25% GLYCEROL AS CRYOPROTECTANT	分辨率 1.15 Å R-free 0.137
1OCQ COMPLEX OF THE ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHEARANS AT 1.08 ANGSTROM RESOLUTION with cellobio-derived isofagomine 提交 2003-02-09	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 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 27–329（303 aa）片段：CATALYTIC CORE DOMAIN ONLY, RESIDUES 27-329	未记录	IFM 5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE × 1 BGC beta-D-glucopyranose × 1 GOL GLYCEROL × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；pH 5.2；PROTEIN WAS USED AT A CONCENTRATION OF 10MG/ML. IT WAS INCUBATED WITH 5MM CELLOBIO-DERIVED ISOFAGOMINE FOR AN HOUR PRIOR CRYSTALLISATION. THE VAPOR DIFFUSION METHOD WAS USED. 1.3 M AMMONIUM SULPHATE WERE USED AS PRECIPITANT. 20 % GLYCEROL WAS ADDED FOR CRYOPROTECTION, pH 5.20	分辨率 1.08 Å R-free 0.127
1W3K ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHAERENS IN COMPLEX WITH CELLOBIO DERIVED-TETRAHYDROOXAZINE 提交 2004-07-16	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 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 27–329（303 aa）片段：CATALYTIC CORE DOMAIN, RESIDUES 30-329	未记录	BGC beta-D-glucopyranose × 1 OXZ TETRAHYDROOXAZINE × 1 GOL GLYCEROL × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray结晶条件 pH 5；PROTEIN CONCENTRATION 20MG/ML, 1.3 M AMMONIUM SULPHATE PH 5.0, 25% GLYCEROL AS CRYOPROTECTANT	分辨率 1.20 Å R-free 0.132
1W3L ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHAERENS IN COMPLEX WITH CELLOTRI DERIVED-TETRAHYDROOXAZINE 提交 2004-07-16	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合单体；蛋白 × 1 PDB 声明：monomeric	链 A 27–329（303 aa）片段：CATALYTIC MODULE, RESIDUES 27-329	未记录	GOL GLYCEROL × 2 SO4 SULFATE ION × 1 OXZ TETRAHYDROOXAZINE × 1	X-RAY DIFFRACTION X-ray结晶条件 pH 5；PROTEIN CONCENTRATION 20MG/ML, 1.3 M AMMONIUM SULPHATE PH 5.0, 25% GLYCEROL AS CRYOPROTECTANT	分辨率 1.04 Å R-free 0.121
2A3H CELLOBIOSE COMPLEX OF THE ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHERANS AT 2.0 A RESOLUTION 提交 1998-01-22	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合单体；蛋白 × 1 PDB 声明：monomeric	链 A 30–329（300 aa）片段：CATALYTIC CORE	未记录	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 pH 4.5；pH 4.5	分辨率 2.00 Å R-free 0.190
2V38 Family 5 endoglucanase Cel5A from Bacillus agaradhaerens in complex with cellobio-derived noeuromycin 提交 2007-06-13	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 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 27–331（305 aa）片段：RESIDUES 27-331	未记录	GOL GLYCEROL × 3 SO4 SULFATE ION × 1 IFL (3S,4R,5R)-3,4-DIHYDROXY-5-(HYDROXYMETHYL)PIPERIDIN-2-ONE × 1 IDR alpha-L-idopyranuronic acid × 1	X-RAY DIFFRACTION X-ray结晶条件 10 MG/ML PROTEIN. 1.5-1.8 M AMMONIUM SULPHATE. 25% GLYCEROL AS CRYO.	分辨率 1.50 Å R-free 0.143
3A3H CELLOTRIOSE COMPLEX OF THE ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHERANS AT 1.6 A RESOLUTION 提交 1998-02-01	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合单体；蛋白 × 1 PDB 声明：monomeric	链 A 30–329（300 aa）片段：CATALYTIC CORE	未记录	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 pH 4.5；pH 4.5	分辨率 1.64 Å R-free 0.176
5A3H 2-DEOXY-2-FLURO-B-D-CELLOBIOSYL/ENZYME INTERMEDIATE COMPLEX OF THE ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHEARANS AT 1.8 ANGSTROMS RESOLUTION 提交 1998-07-23	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合单体；蛋白 × 1 PDB 声明：monomeric	链 A 27–329（303 aa）片段：CATALYTIC CORE DOMAIN ONLY	未记录	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 pH 5.5；pH 5.5	分辨率 1.82 Å R-free 0.186
6A3H 2-DEOXY-2-FLURO-B-D-CELLOTRIOSYL/ENZYME INTERMEDIATE COMPLEX OF THE ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHEARANS AT 1.6 ANGSTROM RESOLUTION 提交 1998-07-22	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合单体；蛋白 × 1 PDB 声明：monomeric	链 A 27–329（303 aa）片段：CATALYTIC CORE DOMAIN ONLY	未记录	GOL GLYCEROL × 8	X-RAY DIFFRACTION X-ray结晶条件 pH 5.5；pH 5.5	分辨率 1.68 Å R-free 0.185
7A3H NATIVE ENDOGLUCANASE CEL5A CATALYTIC CORE DOMAIN AT 0.95 ANGSTROMS RESOLUTION 提交 1998-08-05	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 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 27–329（303 aa）片段：CATALYTIC CORE DOMAIN	未记录	GOL GLYCEROL × 1 EOH ETHANOL × 1	X-RAY DIFFRACTION X-ray结晶条件 pH 5.5；pH 5.5	分辨率 0.95 Å R-free 0.130

共 14 个其他 PDB 条目、14 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	GUN5_BACAG
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 1–305； UniProt 27–331

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	1e5j
沉积日期 deposition_date	2000-07-26
结构标题 title	ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHAERENS IN THE TETRAGONAL CRYSTAL FORM IN COMPLEX WITH METHYL-4II-S-ALPHA-CELLOBIOSYL-4II-THIO-BETA-CELLOBIOSIDE
关键词 keywords	HYDROLASE, CELLULOSE DEGRADATION, GLYCOSHYDROLASE FAMILY 5; 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	18.94 Å
回转半径 Rg (电子) rg_electron	17.56 Å
零角强度 I(0) i0	21711200.00
分子量 molecular_weight	34630.0 kDa
排除体积 excluded_volume	42711 Å³
包络体积 envelope_volume	45966 Å³
水化壳体积 shell_volume	20960 Å³
包络直径 envelope_diameter	56.3 Å
壳层 Rg shell_rg	24.74 Å
包络 Rg envelope_rg	17.77 Å
形状 Rg shape_rg	17.55 Å
总 Rg total_rg	18.53 Å
总原子数 total_atoms	2438
残基数 n_residues	302
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	55.5 Å
Rg (实空间) rg_real	18.75 Å
Rg 误差 (实空间) rg_real_error	0.23 Å
I(0) (实空间) i0_real	2.1710e+07
I(0) 误差 (实空间) i0_real_error	2.4160e+05
Rg (倒空间) rg_reciprocal	18.78 Å
I(0) (倒空间) i0_reciprocal	21710000.0000
解质量估计 total_estimate	0.9026
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	25.4 Å
偏度 Skewness skewness	-0.006
峰度 Kurtosis kurtosis	-0.543
角度范围 angular_range	— – 0.4200 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	7410000.0000
实空间数据点数 n_real_points	73
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.929; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.964; Smooth: 0.980

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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	ENDOGLUCANASE 5A
分子量 formula_weight	34156.2 kDa
EC 编号 ec_number	3.2.1.4
来源方法 src_method	man
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	2771

DNDSVVEEHGQLSISNGELVNERGEQVQLKGMSSHGLQWYGQFVNYESMKWLRDDWGINVFRAAMYTSSGGYIDDPSVKEKVKEAVEAAIDLDIYVIIDWHILSDNDPNIYKEEAKDFFDEMSELYGDYPNVIYEIANEPNGSDVTWGNQIKPYAEEVIPIIRNNDPNNIIIVGTGTWSQDVHHAADNQLADPNVMYAFHFYAGTHGQNLRDQVDYALDQGAAIFVSEWGTSAATGDGGVFLDEAQVWIDFMDERNLSWANWSLTHKDESSAALMPGANPTGGWTEAELSPSGTFVREKIRESAS

来源 Source

来源生物 organism	BACILLUS AGARADHAERENS
NCBI 分类编号 ncbi_taxonomy_id	76935
宿主生物 host_organism	BACILLUS SUBTILIS

实体 2 Entity 2 branched

描述 description	alpha-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-methyl beta-D-glucopyranoside
分子量 formula_weight	712.7 kDa
来源方法 src_method	man
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	4

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	328

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7. 折叠分类 (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

结构域编号 domain_id	d1e5ja_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.8 — (Trans)glycosidases
家族 Family family	c.1.8.3 — beta-glycanases

CATH v4.4 (1 domains)

结构域编号 domain_id	1e5jA00
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

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8. 引用文献 (1)

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晶胞边长 a length_a	74.520 Å
晶胞边长 b length_b	74.520 Å
晶胞边长 c length_c	136.193 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 43 21 2
空间群编号 int_tables_number	96
晶系 crystal_system	—

分辨率 resolution	1.850 Å
最低分辨率 resolution_low	15.000 Å
R 因子 r_factor	0.1790
R_work r_work	0.1770
R_free r_free	0.2220

fit	/app/data/saxs_computation/e5/1e5j/1e5j.fit
pddf	/app/data/pr_computation/e5/1e5j/1e5j.pr.out
profile	/app/data/saxs_computation/e5/1e5j/1e5j.dat

ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHAERENS IN THE TETRAGONAL CRYSTAL FORM IN COMPLEX WITH METHYL-4II-S-ALPHA-CELLOBIOSYL-4II-THIO-BETA-CELLOBIOSIDE

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

ENDOGLUCANASE 5A

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