1jt0

Crystal structure of a cooperative QacR-DNA complex

Method: X-RAY DIFFRACTION D_max: 122.9 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	1jt0
沉积日期 deposition_date	2001-08-20
结构标题 title	Crystal structure of a cooperative QacR-DNA complex
关键词 keywords	multidrug binding protein, cooperative DNA binding, dimer of dimers, 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	36.25 Å
回转半径 Rg (电子) rg_electron	36.48 Å
零角强度 I(0) i0	198481000.00
分子量 molecular_weight	105820.0 kDa
排除体积 excluded_volume	128710 Å³
包络体积 envelope_volume	168130 Å³
水化壳体积 shell_volume	39275 Å³
包络直径 envelope_diameter	126.2 Å
壳层 Rg shell_rg	41.60 Å
包络 Rg envelope_rg	36.18 Å
形状 Rg shape_rg	36.50 Å
总 Rg total_rg	36.72 Å
总原子数 total_atoms	7406
残基数 n_residues	805
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	122.9 Å
Rg (实空间) rg_real	36.36 Å
Rg 误差 (实空间) rg_real_error	1.42 Å
I(0) (实空间) i0_real	1.9850e+08
I(0) 误差 (实空间) i0_real_error	3.6330e+06
Rg (倒空间) rg_reciprocal	36.30 Å
I(0) (倒空间) i0_reciprocal	198500000.0000
解质量估计 total_estimate	0.8773
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	36.3 Å
偏度 Skewness skewness	0.355
峰度 Kurtosis kurtosis	-0.450
角度范围 angular_range	— – 0.2200 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	22050000.0000
实空间数据点数 n_real_points	45
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.875; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.894; Smooth: 0.884

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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	QACA operator
分子量 formula_weight	8604.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	E,F
原子数 atom_count	7451

CTTATAGACCGATCGATCGGTCTATAAG

Entity 2 polymer

描述 description	;HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN QACA 5'REGION ;
分子量 formula_weight	22983.0 kDa
突变 mutation	C72A, C141S
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

MNLKDKILGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFKTKENLFLEILNIEESKWQEQWKKEQIKAKTNREKFYLYNELSLTTEYYYPLQNAIIEFYTEYYKTNSINEKMNKLENKYIDAYHVIFKEGNLNGEWSINDVNAVSKIAANAVNGIVTFTHEQNINERIKLMNKFSQIFLNGLSKHHHHHH

来源 Source

来源生物 organism	Staphylococcus aureus
NCBI 分类编号 ncbi_taxonomy_id	1280
宿主生物 host_organism	Escherichia coli

Entity 3 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	5

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	45

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6. 折叠分类 (SCOP + CATH) 19 domains

SCOP 2.08 (11 domains)

结构域编号 domain_id	d1jt0a1
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.4.1 — Homeodomain-like
家族 Family family	a.4.1.9 — Tetracyclin repressor-like, N-terminal domain

结构域编号 domain_id	d1jt0a2
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.121 — Tetracyclin repressor-like, C-terminal domain
超家族 Superfamily superfamily	a.121.1 — Tetracyclin repressor-like, C-terminal domain
家族 Family family	a.121.1.1 — Tetracyclin repressor-like, C-terminal domain

结构域编号 domain_id	d1jt0a3
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d1jt0b1
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.4.1 — Homeodomain-like
家族 Family family	a.4.1.9 — Tetracyclin repressor-like, N-terminal domain

结构域编号 domain_id	d1jt0b2
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.121 — Tetracyclin repressor-like, C-terminal domain
超家族 Superfamily superfamily	a.121.1 — Tetracyclin repressor-like, C-terminal domain
家族 Family family	a.121.1.1 — Tetracyclin repressor-like, C-terminal domain

结构域编号 domain_id	d1jt0b3
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d1jt0c1
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.4.1 — Homeodomain-like
家族 Family family	a.4.1.9 — Tetracyclin repressor-like, N-terminal domain

结构域编号 domain_id	d1jt0c2
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.121 — Tetracyclin repressor-like, C-terminal domain
超家族 Superfamily superfamily	a.121.1 — Tetracyclin repressor-like, C-terminal domain
家族 Family family	a.121.1.1 — Tetracyclin repressor-like, C-terminal domain

结构域编号 domain_id	d1jt0c3
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d1jt0d1
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.4.1 — Homeodomain-like
家族 Family family	a.4.1.9 — Tetracyclin repressor-like, N-terminal domain

结构域编号 domain_id	d1jt0d2
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.121 — Tetracyclin repressor-like, C-terminal domain
超家族 Superfamily superfamily	a.121.1 — Tetracyclin repressor-like, C-terminal domain
家族 Family family	a.121.1.1 — Tetracyclin repressor-like, C-terminal domain

CATH v4.4 (8 domains)

结构域编号 domain_id	1jt0A01
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	60 — Homeodomain-like

结构域编号 domain_id	1jt0A02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	357 — Tetracycline Repressor; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Tetracycline Repressor, domain 2

结构域编号 domain_id	1jt0B01
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	60 — Homeodomain-like

结构域编号 domain_id	1jt0B02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	357 — Tetracycline Repressor; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Tetracycline Repressor, domain 2

结构域编号 domain_id	1jt0C01
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	60 — Homeodomain-like

结构域编号 domain_id	1jt0C02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	357 — Tetracycline Repressor; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Tetracycline Repressor, domain 2

结构域编号 domain_id	1jt0D01
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	60 — Homeodomain-like

结构域编号 domain_id	1jt0D02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	357 — Tetracycline Repressor; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Tetracycline Repressor, domain 2

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7. 引用文献 (1)

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晶胞边长 a length_a	174.700 Å
晶胞边长 b length_b	174.700 Å
晶胞边长 c length_c	151.950 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	120.00 °
晶胞分子数 Z z_pdb	24

空间群 space_group	P 65
空间群编号 int_tables_number	170
晶系 crystal_system	—

分辨率 resolution	2.900 Å
最低分辨率 resolution_low	75.730 Å
R 因子 r_factor	0.2220
R_work r_work	0.2220
R_free r_free	0.2580

fit	/app/data/saxs_computation/jt/1jt0/1jt0.fit
pddf	/app/data/pr_computation/jt/1jt0/1jt0.pr.out
profile	/app/data/saxs_computation/jt/1jt0/1jt0.dat

Crystal structure of a cooperative QacR-DNA complex

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) 19 domains

SCOP 2.08 (11 domains)

CATH v4.4 (8 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)