SAXSdb — 1xxb

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1xxb
沉积日期 deposition_date	1995-11-03
结构标题 title	C-TERMINAL DOMAIN OF ESCHERICHIA COLI ARGININE REPRESSOR/ L-ARGININE COMPLEX
关键词 keywords	COMPLEX (DNA BINDING PROTEIN-PEPTIDE), COMPLEX (DNA BINDING PROTEIN-PEPTIDE) complex; COMPLEX (DNA BINDING PROTEIN/PEPTIDE)
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	22.32 Å
回转半径 Rg (电子) rg_electron	21.48 Å
零角强度 I(0) i0	32112100.00
分子量 molecular_weight	46381.0 kDa
排除体积 excluded_volume	59301 Å³
包络体积 envelope_volume	66997 Å³
水化壳体积 shell_volume	25483 Å³
包络直径 envelope_diameter	69.3 Å
壳层 Rg shell_rg	28.54 Å
包络 Rg envelope_rg	21.69 Å
形状 Rg shape_rg	21.50 Å
总 Rg total_rg	22.29 Å
总原子数 total_atoms	3278
残基数 n_residues	428
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	68.9 Å
Rg (实空间) rg_real	22.26 Å
Rg 误差 (实空间) rg_real_error	0.31 Å
I(0) (实空间) i0_real	3.2110e+07
I(0) 误差 (实空间) i0_real_error	4.0170e+05
Rg (倒空间) rg_reciprocal	22.27 Å
I(0) (倒空间) i0_reciprocal	32110000.0000
解质量估计 total_estimate	0.7142
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	67.9 Å
偏度 Skewness skewness	0.287
峰度 Kurtosis kurtosis	-0.424
角度范围 angular_range	— – 0.3550 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	24150000.0000
实空间数据点数 n_real_points	67
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.909; Stabil: 1.000; Sysdev: 0.189; Positv: 1.000; Valcen: 0.997; Smooth: 0.989

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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 (3)

Entity 1 polymer

描述 description	ARGININE REPRESSOR
分子量 formula_weight	8351.5 kDa
来源方法 src_method	man
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F
原子数 atom_count	3388

MSPLKNLVLDIDYNDAVVVIHTSPGAAQLIARLLDSLGKAEGILGTIAGDDTIFTTPANGFTVKDLYEAILELFDQEL

来源 Source

来源生物 organism	Escherichia coli K12
NCBI 分类编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	ARGININE
分子量 formula_weight	175.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

Entity 3 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	110

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6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d1xxba_
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	d1xxbb_
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	d1xxbc_
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	d1xxbd_
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	d1xxbe_
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	d1xxbf_
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 (6 domains)

结构域编号 domain_id	1xxbA00
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	1xxbB00
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	1xxbC00
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	1xxbD00
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	1xxbE00
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	1xxbF00
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 —

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7. 引用文献 (3)

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晶胞边长 a length_a	53.500 Å
晶胞边长 b length_b	85.400 Å
晶胞边长 c length_c	217.000 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	2.600 Å
最低分辨率 resolution_low	8.000 Å
R 因子 r_factor	0.2000
R_work r_work	0.2000
R_free r_free	0.3500

fit	/app/data/saxs_computation/xx/1xxb/1xxb.fit
pddf	/app/data/pr_computation/xx/1xxb/1xxb.pr.out
profile	/app/data/saxs_computation/xx/1xxb/1xxb.dat

C-TERMINAL DOMAIN OF ESCHERICHIA COLI ARGININE REPRESSOR/ L-ARGININE 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

5. 实体与聚合体信息 (3)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 non-polymer

Entity 3 water

6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. 引用文献 (3)

8. 文件与曲线 (10)

Files (7)

Curves (3)