1f9n

CRYSTAL STRUCTURE OF AHRC, THE ARGININE REPRESSOR/ACTIVATOR PROTEIN FROM BACILLUS SUBTILIS

Method: X-RAY DIFFRACTION D_max: 94.6 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

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1f9n
沉积日期 deposition_date	2000-07-11
结构标题 title	CRYSTAL STRUCTURE OF AHRC, THE ARGININE REPRESSOR/ACTIVATOR PROTEIN FROM BACILLUS SUBTILIS
关键词 keywords	WINGED-HELIX-TURN-HELIX, ARGININE REPRESSOR, DNA BINDING PROTEIN; DNA BINDING PROTEIN
实验方法 method	X-RAY DIFFRACTION

▼

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

回转半径 Rg (Guinier) rg_guinier	30.51 Å
回转半径 Rg (电子) rg_electron	29.51 Å
零角强度 I(0) i0	156072000.00
分子量 molecular_weight	98348.0 kDa
排除体积 excluded_volume	123040 Å³
包络体积 envelope_volume	163520 Å³
水化壳体积 shell_volume	45092 Å³
包络直径 envelope_diameter	99.3 Å
壳层 Rg shell_rg	37.79 Å
包络 Rg envelope_rg	29.26 Å
形状 Rg shape_rg	29.55 Å
总 Rg total_rg	30.13 Å
总原子数 total_atoms	6868
残基数 n_residues	887
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

▼

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

最大尺寸 Dmax dmax	94.6 Å
Rg (实空间) rg_real	30.30 Å
Rg 误差 (实空间) rg_real_error	0.50 Å
I(0) (实空间) i0_real	1.5610e+08
I(0) 误差 (实空间) i0_real_error	2.2530e+06
Rg (倒空间) rg_reciprocal	30.39 Å
I(0) (倒空间) i0_reciprocal	156100000.0000
解质量估计 total_estimate	0.8928
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	40.0 Å
偏度 Skewness skewness	0.135
峰度 Kurtosis kurtosis	-0.378
角度范围 angular_range	— – 0.2600 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	26190000.0000
实空间数据点数 n_real_points	53
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.891; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.953

▶

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

▶

5. 实体与聚合体信息 (2)

▼

6. 折叠分类 (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

结构域编号 domain_id	d1f9na1
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.4.5 — 'Winged helix' DNA-binding domain
家族 Family family	a.4.5.3 — Arginine repressor (ArgR), N-terminal DNA-binding domain

结构域编号 domain_id	d1f9na2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.74 — DCoH-like
超家族 Superfamily superfamily	d.74.2 — C-terminal domain of arginine repressor
家族 Family family	d.74.2.1 — C-terminal domain of arginine repressor

结构域编号 domain_id	d1f9nb1
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.4.5 — 'Winged helix' DNA-binding domain
家族 Family family	a.4.5.3 — Arginine repressor (ArgR), N-terminal DNA-binding domain

结构域编号 domain_id	d1f9nb2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.74 — DCoH-like
超家族 Superfamily superfamily	d.74.2 — C-terminal domain of arginine repressor
家族 Family family	d.74.2.1 — C-terminal domain of arginine repressor

结构域编号 domain_id	d1f9nc1
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.4.5 — 'Winged helix' DNA-binding domain
家族 Family family	a.4.5.3 — Arginine repressor (ArgR), N-terminal DNA-binding domain

结构域编号 domain_id	d1f9nc2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.74 — DCoH-like
超家族 Superfamily superfamily	d.74.2 — C-terminal domain of arginine repressor
家族 Family family	d.74.2.1 — C-terminal domain of arginine repressor

结构域编号 domain_id	d1f9nd1
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.4.5 — 'Winged helix' DNA-binding domain
家族 Family family	a.4.5.3 — Arginine repressor (ArgR), N-terminal DNA-binding domain

结构域编号 domain_id	d1f9nd2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.74 — DCoH-like
超家族 Superfamily superfamily	d.74.2 — C-terminal domain of arginine repressor
家族 Family family	d.74.2.1 — C-terminal domain of arginine repressor

结构域编号 domain_id	d1f9ne1
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.4.5 — 'Winged helix' DNA-binding domain
家族 Family family	a.4.5.3 — Arginine repressor (ArgR), N-terminal DNA-binding domain

结构域编号 domain_id	d1f9ne2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.74 — DCoH-like
超家族 Superfamily superfamily	d.74.2 — C-terminal domain of arginine repressor
家族 Family family	d.74.2.1 — C-terminal domain of arginine repressor

结构域编号 domain_id	d1f9nf1
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.4.5 — 'Winged helix' DNA-binding domain
家族 Family family	a.4.5.3 — Arginine repressor (ArgR), N-terminal DNA-binding domain

结构域编号 domain_id	d1f9nf2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.74 — DCoH-like
超家族 Superfamily superfamily	d.74.2 — C-terminal domain of arginine repressor
家族 Family family	d.74.2.1 — C-terminal domain of arginine repressor

CATH v4.4 (12 domains)

结构域编号 domain_id	1f9nA01
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	1f9nA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1360 — Gyrase A; domain 2
同源超家族 H-superfamily homologous superfamily	40 —

结构域编号 domain_id	1f9nB01
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	1f9nB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1360 — Gyrase A; domain 2
同源超家族 H-superfamily homologous superfamily	40 —

结构域编号 domain_id	1f9nC01
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	1f9nC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1360 — Gyrase A; domain 2
同源超家族 H-superfamily homologous superfamily	40 —

结构域编号 domain_id	1f9nD01
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	1f9nD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1360 — Gyrase A; domain 2
同源超家族 H-superfamily homologous superfamily	40 —

结构域编号 domain_id	1f9nE01
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	1f9nE02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1360 — Gyrase A; domain 2
同源超家族 H-superfamily homologous superfamily	40 —

结构域编号 domain_id	1f9nF01
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	1f9nF02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1360 — Gyrase A; domain 2
同源超家族 H-superfamily homologous superfamily	40 —

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	230.310 Å
晶胞边长 b length_b	73.860 Å
晶胞边长 c length_c	138.900 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	48

空间群 space_group	C 2 2 21
空间群编号 int_tables_number	20
晶系 crystal_system	—

分辨率 resolution	2.700 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	0.2200
R_work r_work	0.2200
R_free r_free	0.2700

描述 description	ARGININE REPRESSOR/ACTIVATOR PROTEIN
分子量 formula_weight	16854.5 kDa
来源方法 src_method	man
拷贝数 entity_count	6

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F
原子数 atom_count	7108

CRYSTAL STRUCTURE OF AHRC, THE ARGININE REPRESSOR/ACTIVATOR PROTEIN FROM BACILLUS SUBTILIS

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 (2)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 water

6. 折叠分类 (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)

来源生物 organism	Bacillus subtilis
NCBI 分类编号 ncbi_taxonomy_id	1423
宿主生物 host_organism	Escherichia coli

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	240

fit	/app/data/saxs_computation/f9/1f9n/1f9n.fit
pddf	/app/data/pr_computation/f9/1f9n/1f9n.pr.out
profile	/app/data/saxs_computation/f9/1f9n/1f9n.dat