1l3l

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

Method: X-RAY DIFFRACTION D_max: 155.4 Å Quality: GOOD

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

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1. 结构基本信息 1. 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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2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	44.09 Å
回转半径 Rg (电子) rg_electron	44.12 Å
零角强度 I(0) i0	321045000.00
分子量 molecular_weight	130370.0 kDa
排除体积 excluded_volume	155750 Å³
包络体积 envelope_volume	218680 Å³
水化壳体积 shell_volume	43938 Å³
包络直径 envelope_diameter	154.6 Å
壳层 Rg shell_rg	45.12 Å
包络 Rg envelope_rg	43.44 Å
形状 Rg shape_rg	44.11 Å
总 Rg total_rg	44.19 Å
总原子数 total_atoms	9028
残基数 n_residues	974
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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3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	155.4 Å
Rg (实空间) rg_real	44.59 Å
Rg 误差 (实空间) rg_real_error	2.27 Å
I(0) (实空间) i0_real	3.2100e+08
I(0) 误差 (实空间) i0_real_error	5.9090e+06
Rg (倒空间) rg_reciprocal	44.10 Å
I(0) (倒空间) i0_reciprocal	320900000.0000
解质量估计 total_estimate	0.8060
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	43.2 Å
偏度 Skewness skewness	0.540
峰度 Kurtosis kurtosis	-0.409
角度范围 angular_range	— – 0.1800 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	11980000.0000
实空间数据点数 n_real_points	37
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.701; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.662; Smooth: 0.710

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

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5. 实体与聚合体信息 (4)

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

聚合体 Polymer

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

GATGTGCAGATCTGCACATC

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

聚合体 Polymer

聚合体类型 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

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

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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7. 引用文献 (1)

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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

fit	/app/data/saxs_computation/l3/1l3l/1l3l.fit
pddf	/app/data/pr_computation/l3/1l3l/1l3l.pr.out
profile	/app/data/saxs_computation/l3/1l3l/1l3l.dat

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

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

1. 结构基本信息 1. Structure Basics

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

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. 实体与聚合体信息 (4)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

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)

8. 文件与曲线 (10)

Files (7)

Curves (3)