1h0m

Three-dimensional structure of the quorum sensing protein TraR bound to its autoinducer and to its target DNA

Method: X-RAY DIFFRACTION D_max: 125.5 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	1h0m
沉积日期 deposition_date	2002-06-25
结构标题 title	Three-dimensional structure of the quorum sensing protein TraR bound to its autoinducer and to its target DNA
关键词 keywords	;TRANSCRIPTION/DNA, LUXR-TYPE PROTEIN, QUORUM SENSING, TRANSCRIPTIONAL REGULATOR, DNA-BINDING PROTEIN, HOMOSERINE LACTONE, TRAR, 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	38.50 Å
回转半径 Rg (电子) rg_electron	38.16 Å
零角强度 I(0) i0	313041000.00
分子量 molecular_weight	128900.0 kDa
排除体积 excluded_volume	154620 Å³
包络体积 envelope_volume	206100 Å³
水化壳体积 shell_volume	46443 Å³
包络直径 envelope_diameter	137.5 Å
壳层 Rg shell_rg	42.39 Å
包络 Rg envelope_rg	37.87 Å
形状 Rg shape_rg	38.17 Å
总 Rg total_rg	38.35 Å
总原子数 total_atoms	8929
残基数 n_residues	966
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	125.5 Å
Rg (实空间) rg_real	38.65 Å
Rg 误差 (实空间) rg_real_error	1.40 Å
I(0) (实空间) i0_real	3.1300e+08
I(0) 误差 (实空间) i0_real_error	6.1780e+06
Rg (倒空间) rg_reciprocal	38.56 Å
I(0) (倒空间) i0_reciprocal	313000000.0000
解质量估计 total_estimate	0.8691
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	45.9 Å
偏度 Skewness skewness	0.416
峰度 Kurtosis kurtosis	-0.268
角度范围 angular_range	— – 0.2050 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	18230000.0000
实空间数据点数 n_real_points	42
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.904; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.598

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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	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
原子数 atom_count	9013

MQHWLDKLTDLAAIEGDECILKTGLADIADHFGFTGYAYLHIQHRHITAVTNYHRQWQSTYFDKKFEALDPVVKRARSRKHIFTWSGEHERPTLSKDERAFYDHASDFGIRSGITIPIKTANGFMSMFTMASDKPVIDLDREIDAVAAAATIGQIHARISFLRTTPTAEDAAWLDPKEATYLRWIAVGKTMEEIADVEGVKYNSVRVKLREAMKRFDVRSKAHLTALAIRRKLI

来源 Source

来源生物 organism	Rhizobium radiobacter
通用名 common_name	Agrobacterium tumefaciens
NCBI 分类编号 ncbi_taxonomy_id	358
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 polymer

描述 description	;5'-D(APTPGPTPGPCPAPGPAPTP CPTPGPCPAPCPAPT)-3' ;
分子量 formula_weight	5515.6 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

ATGTGCAGATCTGCACAT

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	84

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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	d1h0ma1
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	d1h0ma2
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	d1h0mb1
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	d1h0mb2
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	d1h0mc1
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	d1h0mc2
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	d1h0md1
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	d1h0md2
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	1h0mA01
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	1h0mA02
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	1h0mB01
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	1h0mB02
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	1h0mC01
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	1h0mC02
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	1h0mD01
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	1h0mD02
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 (2)

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晶胞边长 a length_a	66.993 Å
晶胞边长 b length_b	94.678 Å
晶胞边长 c length_c	209.669 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	16

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	3.000 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	—
R_work r_work	0.2330
R_free r_free	0.2850

fit	/app/data/saxs_computation/h0/1h0m/1h0m.fit
pddf	/app/data/pr_computation/h0/1h0m/1h0m.pr.out
profile	/app/data/saxs_computation/h0/1h0m/1h0m.dat

Three-dimensional structure of the quorum sensing protein TraR bound to its autoinducer and to its target 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

来源 Source

Entity 2 polymer

聚合体 Polymer

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 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)