SAXSdb — 7abp

▼

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

L-ARABINOSE-BINDING PROTEIN

Escherichia coli

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 24–329	未记录	FCA alpha-D-fucopyranose × 1 FCB beta-D-fucopyranose × 1	X-RAY DIFFRACTION mmCIF 未提供已读取环境条件	分辨率 1.67 Å

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 7ABP	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
1ABE NOVEL STEREOSPECIFICITY OF THE L-ARABINOSE-BINDING PROTEIN 提交 1992-04-23	配体/离子不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 24–329（306 aa）	未记录	ARA alpha-L-arabinopyranose × 1 ARB beta-L-arabinopyranose × 1	X-RAY DIFFRACTION mmCIF 未提供已读取条件	分辨率 1.70 Å
1ABF SUBSTRATE SPECIFICITY AND AFFINITY OF A PROTEIN MODULATED BY BOUND WATER MOLECULES 提交 1992-04-23	结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 24–329（306 aa）	未记录	FCA alpha-D-fucopyranose × 1 FCB beta-D-fucopyranose × 1	X-RAY DIFFRACTION mmCIF 未提供已读取条件	分辨率 1.90 Å
1APB A PRO TO GLY MUTATION IN THE HINGE OF THE ARABINOSE-BINDING PROTEIN ENHANCES BINDING AND ALTERS SPECIFICITY: SUGAR-BINDING AND CRYSTALLOGRAPHIC STUDIES 提交 1991-11-15	结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 24–329（306 aa）	未记录	FCA alpha-D-fucopyranose × 1 FCB beta-D-fucopyranose × 1	X-RAY DIFFRACTION mmCIF 未提供已读取条件	分辨率 1.76 Å
1BAP A PRO TO GLY MUTATION IN THE HINGE OF THE ARABINOSE-BINDING PROTEIN ENHANCES BINDING AND ALTERS SPECIFICITY: SUGAR-BINDING AND CRYSTALLOGRAPHIC STUDIES 提交 1991-11-15	配体/离子不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 24–329（306 aa）	未记录	ARA alpha-L-arabinopyranose × 1 ARB beta-L-arabinopyranose × 1	X-RAY DIFFRACTION mmCIF 未提供已读取条件	分辨率 1.75 Å
2WRZ Crystal structure of an arabinose binding protein with designed serotonin binding site in open, ligand-free state 提交 2009-09-03	突变/修饰不同配体/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 24–329（306 aa）	突变：YES	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 pH 8；20% PEG 3350, 0.2M (NH4)CITRATE, 2UMOL/ML SEROTONIN, pH 8.0	分辨率 2.20 Å R-free 0.272
2WRZ Crystal structure of an arabinose binding protein with designed serotonin binding site in open, ligand-free state 提交 2009-09-03	突变/修饰不同配体/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 24–329（306 aa）	突变：YES	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 pH 8；20% PEG 3350, 0.2M (NH4)CITRATE, 2UMOL/ML SEROTONIN, pH 8.0	分辨率 2.20 Å R-free 0.272
5ABP SUBSTRATE SPECIFICITY AND AFFINITY OF A PROTEIN MODULATED BY BOUND WATER MOLECULES 提交 1990-12-26	配体/离子不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 24–329（306 aa）	未记录	GLA alpha-D-galactopyranose × 1 GAL beta-D-galactopyranose × 1	X-RAY DIFFRACTION mmCIF 未提供已读取条件	分辨率 1.80 Å
6ABP SUGAR-BINDING AND CRYSTALLOGRAPHIC STUDIES OF AN ARABINOSE-BINDING PROTEIN MUTANT (MET108LEU) WHICH EXHIBITS ENHANCED AFFINITY AND ALTERED SPECIFICITY 提交 1991-04-25	配体/离子不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 24–329（306 aa）	未记录	ARA alpha-L-arabinopyranose × 1 ARB beta-L-arabinopyranose × 1	X-RAY DIFFRACTION mmCIF 未提供已读取条件	分辨率 1.67 Å
8ABP SUGAR-BINDING AND CRYSTALLOGRAPHIC STUDIES OF AN ARABINOSE-BINDING PROTEIN MUTANT (MET108LEU) WHICH EXHIBITS ENHANCED AFFINITY AND ALTERED SPECIFICITY 提交 1991-04-25	配体/离子不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 24–329（306 aa）	未记录	GLA alpha-D-galactopyranose × 1 GAL beta-D-galactopyranose × 1	X-RAY DIFFRACTION mmCIF 未提供已读取条件	分辨率 1.49 Å
9ABP A PRO TO GLY MUTATION IN THE HINGE OF THE ARABINOSE-BINDING PROTEIN ENHANCES BINDING AND ALTERS SPECIFICITY: SUGAR-BINDING AND CRYSTALLOGRAPHIC STUDIES 提交 1991-11-15	配体/离子不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 24–329（306 aa）	未记录	GLA alpha-D-galactopyranose × 1 GAL beta-D-galactopyranose × 1	X-RAY DIFFRACTION mmCIF 未提供已读取条件	分辨率 1.97 Å

共 9 个其他 PDB 条目、10 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	ARAF_ECOLI
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 1–306； UniProt 24–329

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	7abp
沉积日期 deposition_date	1991-04-25
结构标题 title	SUGAR-BINDING AND CRYSTALLOGRAPHIC STUDIES OF AN ARABINOSE-BINDING PROTEIN MUTANT (MET108LEU) WHICH EXHIBITS ENHANCED AFFINITY AND ALTERED SPECIFICITY
关键词 keywords	BINDING PROTEINS; BINDING PROTEINS
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	20.85 Å
回转半径 Rg (电子) rg_electron	20.11 Å
零角强度 I(0) i0	18291200.00
分子量 molecular_weight	33076.0 kDa
排除体积 excluded_volume	41687 Å³
包络体积 envelope_volume	46917 Å³
水化壳体积 shell_volume	19911 Å³
包络直径 envelope_diameter	71.0 Å
壳层 Rg shell_rg	26.19 Å
包络 Rg envelope_rg	20.36 Å
形状 Rg shape_rg	20.11 Å
总 Rg total_rg	20.92 Å
总原子数 total_atoms	2327
残基数 n_residues	305
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	68.6 Å
Rg (实空间) rg_real	20.88 Å
Rg 误差 (实空间) rg_real_error	0.43 Å
I(0) (实空间) i0_real	1.8290e+07
I(0) 误差 (实空间) i0_real_error	2.3530e+05
Rg (倒空间) rg_reciprocal	20.88 Å
I(0) (倒空间) i0_reciprocal	18290000.0000
解质量估计 total_estimate	0.7975
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	23.9 Å
偏度 Skewness skewness	0.429
峰度 Kurtosis kurtosis	-0.257
角度范围 angular_range	— – 0.3800 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	7236000.0000
实空间数据点数 n_real_points	70
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.793; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.000

▶

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	L-ARABINOSE-BINDING PROTEIN
分子量 formula_weight	33233.0 kDa
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	2531

ENLKLGFLVKQPEEPWFQTEWKFADKAGKDLGFEVIKIAVPDGEKTLNAIDSLAASGAKGFVICTPDPKLGSAIVAKARGYDMKVIAVDDQFVNAKGKPMDTVPLVMLAATKIGERQGQELYKEMQKRGWDVKESAVMAITANELDTARRRTTGSMDALKAAGFPEKQIYQVPTKSNDIPGAFDAANSMLVQHPEVKHWLIVGMNDSTVLGGVRATEGQGFKAADIIGIGINGVDAVSELSKAQATGFYGSLLPSPDVHGYKSSEMLYNWVAKDVEPPKFTEVTDVVLITRDNFKEELEKKGLGGK

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562

实体 2 Entity 2 non-polymer

描述 description	alpha-D-fucopyranose
分子量 formula_weight	164.2 kDa
来源方法 src_method	man
拷贝数 entity_count	1

实体 3 Entity 3 non-polymer

描述 description	beta-D-fucopyranose
分子量 formula_weight	164.2 kDa
来源方法 src_method	man
拷贝数 entity_count	1

实体 4 Entity 4 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	man
拷贝数 entity_count	193

▼

7. 折叠分类 (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

结构域编号 domain_id	d7abpa_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.93 — Periplasmic binding protein-like I
超家族 Superfamily superfamily	c.93.1 — Periplasmic binding protein-like I
家族 Family family	c.93.1.1 — L-arabinose binding protein-like

CATH v4.4 (2 domains)

结构域编号 domain_id	7abpA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	2300 — Response regulator

结构域编号 domain_id	7abpA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	2300 — Response regulator

▶

8. 引用文献 (11)

;Sugar-binding and crystallographic studies of an arabinose-binding protein mutant (Met108Leu) that exhibits enhanced affinity and altered specificity. ;

Biochemistry (1991)

PMID: 2069949 · DOI: 10.1021/bi00242a009 PRIMARY

Substrate Specificity and Affinity of a Protein Modulated by Bound Water Molecules

Nature (1989)

Novel Stereospecificity of the L-Arabinose-Binding Protein

Nature (1984)

;Hinge-Bending in L-Arabinose-Binding Protein. The "Venus'S-Flytrap" Model ;

J.Biol.Chem. (1982)

Structure of the L-Arabinose-Binding Protein from Escherichia Coli at 2.4 Angstroms Resolution

J.Mol.Biol. (1981)

L-Arabinose-Binding Protein-Sugar Complex at 2.4 Angstroms Resolution. Stereochemistry and Evidence for a Structural Change

J.Biol.Chem. (1981)

The Radius of Gyration of L-Arabinose-Binding Protein Decreases Upon Binding of Ligand

J.Biol.Chem. (1981)

The Thiol Group of the L-Arabinose-Binding Protein. Chromophoric Labeling and Chemical Identification of the Sugar-Binding Site

J.Biol.Chem. (1979)

;Location of the Sugar-Binding Site of L-Arabinose-Binding Protein. Sugar Derivative Syntheses, Sugar Binding Specificity, and Difference Fourier Analyses ;

J.Biol.Chem. (1979)

The 2.8-Angstroms Resolution Structure of the L-Arabinose-Binding Protein from Escherichia Coli

J.Biol.Chem. (1977)

Structure of L-Arabinose-Binding Protein from Escherichia Coli at 5 Angstroms Resolution and Preliminary Results at 3.5 Angstroms

Proc.Natl.Acad.Sci.USA (1976)

▶

晶胞边长 a length_a	55.750 Å
晶胞边长 b length_b	71.830 Å
晶胞边长 c length_c	78.140 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	1.670 Å
最低分辨率 resolution_low	8.000 Å
R 因子 r_factor	0.1620
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/ab/7abp/7abp.fit
pddf	/app/data/pr_computation/ab/7abp/7abp.pr.out
profile	/app/data/saxs_computation/ab/7abp/7abp.dat

SUGAR-BINDING AND CRYSTALLOGRAPHIC STUDIES OF AN ARABINOSE-BINDING PROTEIN MUTANT (MET108LEU) WHICH EXHIBITS ENHANCED AFFINITY AND ALTERED SPECIFICITY