1l3l

Crystal structure of a bacterial quorum-sensing transcription factor complexed with pheromone and DNA

Method: X-RAY DIFFRACTION

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

Transcriptional activator protein traR

Agrobacterium tumefaciens

当前结构中的状态

Assembly	物理组成	蛋白状态	分子拷贝数	共同组分	数据核对
1	蛋白–DNA	同源多聚体	蛋白 2 DNA 2	5'-D(GPAPTPGPTPGPCPAPGPAPTPCPTPGPCPAPCPAPTPC)-3' × 2 3-OXO-OCTANOIC ACID (2-OXO-TETRAHYDRO-FURAN-3-YL)-AMIDE × 2 water × 4	与全部聚合物一致
2	蛋白–DNA	同源多聚体	蛋白 2 DNA 2	5'-D(GPAPTPGPTPGPCPAPGPAPTPCPTPGPCPAPCPAPTPC)-3' × 2 3-OXO-OCTANOIC ACID (2-OXO-TETRAHYDRO-FURAN-3-YL)-AMIDE × 2 water × 4	与全部聚合物一致

数据库中的同蛋白其他状态

查看构建体与数据证据

UniProt名称	TRAR_9RHIZ
Isoform	—
PDB实体	2
链与序列区间	作者链 A； PDB构建体 1–234； UniProt 1–234 作者链 B； PDB构建体 1–234； UniProt 1–234 作者链 C； PDB构建体 1–234； UniProt 1–234 作者链 D； PDB构建体 1–234； UniProt 1–234

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	1l3l
沉积日期 deposition_date	2002-02-27
结构标题 title	Crystal structure of a bacterial quorum-sensing transcription factor complexed with pheromone and DNA
关键词 keywords	helix-turn-helix DNA binding motif, alpha/beta/alpha sandwich, asymmetry of the protein-DNA complex, TRANSCRIPTION-DNA COMPLEX; TRANSCRIPTION/DNA
实验方法 method	X-RAY DIFFRACTION

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3. Official assembly/model 理论 SAXS Official SAXS Profiles

页面只读取最新 assembly 计算结果。每一条曲线都对应明确的 PDB、official biological assembly 和 coordinate model。

1l3l__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

下载该曲线 .dat

1l3l__assembly_1__model_1 | I(q)

100 个绘图点；横轴和纵轴均采用对数尺度。

1l3l__assembly_1__model_1 | P(r) · Pending

P(r) 将按相同 assembly/model 分别计算和展示。

Rg（Guinier）	28.15 Å
Rg（电子密度）	26.68 Å
总 Rg	27.38 Å
原子数	4512
残基数	487
排除体积	77788 Å³
最大 q	0.500 Å⁻¹

Assembly	Model	结构单元	聚集说明	状态	CRYSOL	操作
1	1	`1l3l__assembly_1__model_1`	tetrameric （4）	成功	4.1.3-1-20251215 (887e7ef)	查看下载
2	1	`1l3l__assembly_2__model_1`	tetrameric （4）	成功	4.1.3-1-20251215 (887e7ef)	查看下载

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4. 晶体学与实验 4. Crystallography & Experiment

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5. 实体与聚合物信息 Entities & Polymers (4)

实体 1 Entity 1 polymer

描述 description	5'-D(GPAPTPGPTPGPCPAPGPAPTPCPTPGPCPAPCPAPTPC)-3'
分子量 formula_weight	6134.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

聚合物 Polymer

聚合物类型 type	polydeoxyribonucleotide
链编号 strand_id	E,F,G,H
原子数 atom_count	9942

GATGTGCAGATCTGCACATC

实体 2 Entity 2 polymer

描述 description	Transcriptional activator protein traR
分子量 formula_weight	27060.0 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D

MQHWLDKLTDLAAIEGDECILKTGLADIADHFGFTGYAYLHIQHRHITAVTNYHRQWQSTYFDKKFEALDPVVKRARSRKHIFTWSGEHERPTLSKDERAFYDHASDFGIRSGITIPIKTANGFMSMFTMASDKPVIDLDREIDAVAAAATIGQIHARISFLRTTPTAEDAAWLDPKEATYLRWIAVGKTMEEIADVEGVKYNSVRVKLREAMKRFDVRSKAHLTALAIRRKLI

来源 Source

来源生物 organism	Agrobacterium tumefaciens
NCBI 分类编号 ncbi_taxonomy_id	358
宿主生物 host_organism	Escherichia coli

实体 3 Entity 3 non-polymer

描述 description	3-OXO-OCTANOIC ACID (2-OXO-TETRAHYDRO-FURAN-3-YL)-AMIDE
分子量 formula_weight	241.3 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	914

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6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1l3la1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
超家族 Superfamily superfamily	a.4.6 — C-terminal effector domain of the bipartite response regulators
家族 Family family	a.4.6.2 — GerE-like (LuxR/UhpA family of transcriptional regulators)

结构域编号 domain_id	d1l3la2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.110 — Profilin-like
超家族 Superfamily superfamily	d.110.5 — Pheromone-binding domain of LuxR-like quorum-sensing transcription factors
家族 Family family	d.110.5.1 — Pheromone-binding domain of LuxR-like quorum-sensing transcription factors

结构域编号 domain_id	d1l3lb1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
超家族 Superfamily superfamily	a.4.6 — C-terminal effector domain of the bipartite response regulators
家族 Family family	a.4.6.2 — GerE-like (LuxR/UhpA family of transcriptional regulators)

结构域编号 domain_id	d1l3lb2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.110 — Profilin-like
超家族 Superfamily superfamily	d.110.5 — Pheromone-binding domain of LuxR-like quorum-sensing transcription factors
家族 Family family	d.110.5.1 — Pheromone-binding domain of LuxR-like quorum-sensing transcription factors

结构域编号 domain_id	d1l3lc1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
超家族 Superfamily superfamily	a.4.6 — C-terminal effector domain of the bipartite response regulators
家族 Family family	a.4.6.2 — GerE-like (LuxR/UhpA family of transcriptional regulators)

结构域编号 domain_id	d1l3lc2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.110 — Profilin-like
超家族 Superfamily superfamily	d.110.5 — Pheromone-binding domain of LuxR-like quorum-sensing transcription factors
家族 Family family	d.110.5.1 — Pheromone-binding domain of LuxR-like quorum-sensing transcription factors

结构域编号 domain_id	d1l3ld1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
超家族 Superfamily superfamily	a.4.6 — C-terminal effector domain of the bipartite response regulators
家族 Family family	a.4.6.2 — GerE-like (LuxR/UhpA family of transcriptional regulators)

结构域编号 domain_id	d1l3ld2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.110 — Profilin-like
超家族 Superfamily superfamily	d.110.5 — Pheromone-binding domain of LuxR-like quorum-sensing transcription factors
家族 Family family	d.110.5.1 — Pheromone-binding domain of LuxR-like quorum-sensing transcription factors

CATH v4.4 (8 domains)

结构域编号 domain_id	1l3lA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	450 — Beta-Lactamase
同源超家族 H-superfamily homologous superfamily	80 — Transcription factor LuxR-like, autoinducer-binding domain

结构域编号 domain_id	1l3lA02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	10 — Arc Repressor Mutant, subunit A
同源超家族 H-superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

结构域编号 domain_id	1l3lB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	450 — Beta-Lactamase
同源超家族 H-superfamily homologous superfamily	80 — Transcription factor LuxR-like, autoinducer-binding domain

结构域编号 domain_id	1l3lB02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	10 — Arc Repressor Mutant, subunit A
同源超家族 H-superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

结构域编号 domain_id	1l3lC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	450 — Beta-Lactamase
同源超家族 H-superfamily homologous superfamily	80 — Transcription factor LuxR-like, autoinducer-binding domain

结构域编号 domain_id	1l3lC02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	10 — Arc Repressor Mutant, subunit A
同源超家族 H-superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

结构域编号 domain_id	1l3lD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	450 — Beta-Lactamase
同源超家族 H-superfamily homologous superfamily	80 — Transcription factor LuxR-like, autoinducer-binding domain

结构域编号 domain_id	1l3lD02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	10 — Arc Repressor Mutant, subunit A
同源超家族 H-superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

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晶胞边长 a length_a	92.298 Å
晶胞边长 b length_b	58.370 Å
晶胞边长 c length_c	127.453 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	102.81 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

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	1.660 Å
最低分辨率 resolution_low	39.600 Å
R 因子 r_factor	—
R_work r_work	0.2460
R_free r_free	0.2660

Crystal structure of a bacterial quorum-sensing transcription factor complexed with pheromone and DNA

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

Transcriptional activator protein traR

当前结构中的状态

数据库中的同蛋白其他状态

2. 结构基本信息 2. Structure Basics

3. Official assembly/model 理论 SAXS Official SAXS Profiles

1l3l__assembly_1__model_1

1l3l__assembly_1__model_1 | I(q)

1l3l__assembly_1__model_1 | P(r) · Pending

4. 晶体学与实验 4. Crystallography & Experiment

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

衍射实验 Diffraction

5. 实体与聚合物信息 Entities & Polymers (4)

实体 1 Entity 1 polymer

聚合物 Polymer

实体 2 Entity 2 polymer

聚合物 Polymer

来源 Source

实体 3 Entity 3 non-polymer

实体 4 Entity 4 water

6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. 引用文献 (1)

Crystal structure of a bacterial quorum-sensing transcription factor complexed with pheromone and DNA

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

Transcriptional activator protein traR

当前结构中的状态

数据库中的同蛋白其他状态

单体

同源二聚体

同源四聚体

其他同源多聚体

异源或核酸复合物

2. 结构基本信息 2. Structure Basics

3. Official assembly/model 理论 SAXS Official SAXS Profiles

1l3l__assembly_1__model_1

1l3l__assembly_1__model_1 | I(q)

1l3l__assembly_1__model_1 | P(r) · Pending

4. 晶体学与实验 4. Crystallography & Experiment

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

衍射实验 Diffraction

5. 实体与聚合物信息 Entities & Polymers (4)

实体 1 Entity 1 polymer

聚合物 Polymer

实体 2 Entity 2 polymer

聚合物 Polymer

来源 Source

实体 3 Entity 3 non-polymer

实体 4 Entity 4 water

6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. 引用文献 (1)