1sxg

Structural studies on the apo transcription factor form B. megaterium

Method: X-RAY DIFFRACTION D_max: 510.0 Å Quality: SUSPICIOUS

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	1sxg
沉积日期 deposition_date	2004-03-30
结构标题 title	Structural studies on the apo transcription factor form B. megaterium
关键词 keywords	allosterism; phosphoprotein; transcription regulation, transcription; TRANSCRIPTION
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	— Å
回转半径 Rg (电子) rg_electron	107.80 Å
零角强度 I(0) i0	470374000.00
分子量 molecular_weight	182130.0 kDa
排除体积 excluded_volume	228450 Å³
包络体积 envelope_volume	442660 Å³
水化壳体积 shell_volume	47921 Å³
包络直径 envelope_diameter	326.6 Å
壳层 Rg shell_rg	51.60 Å
包络 Rg envelope_rg	101.30 Å
形状 Rg shape_rg	107.80 Å
总 Rg total_rg	106.50 Å
总原子数 total_atoms	12800
残基数 n_residues	1642
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	510.0 Å
Rg (实空间) rg_real	106.10 Å
Rg 误差 (实空间) rg_real_error	15.59 Å
I(0) (实空间) i0_real	4.7040e+08
I(0) 误差 (实空间) i0_real_error	1.5350e+07
Rg (倒空间) rg_reciprocal	87.84 Å
I(0) (倒空间) i0_reciprocal	447700000.0000
解质量估计 total_estimate	0.3291
解质量评级 solution_quality	SUSPICIOUS a SUSPICIOUS solution
P(r) 峰数 n_peaks	5
主峰位置 r_peak_primary	34.0 Å
偏度 Skewness skewness	0.317
峰度 Kurtosis kurtosis	-1.651
角度范围 angular_range	— – 0.0750 Å⁻¹
当前正则化参数 α current_alpha	0.0359
最高正则化参数 α highest_alpha	11910000.0000
实空间数据点数 n_real_points	16
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.000; Stabil: 0.791; Sysdev: 0.000; Positv: 0.999; Valcen: 0.003; Smooth: 0.000

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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	Glucose-resistance amylase regulator
分子量 formula_weight	30992.1 kDa
突变 mutation	residues 53-332
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,D,B,I,P,F
原子数 atom_count	12939

RGLASKKTTTVGVIIPDISNIFYAELARGIEDIATMYKYNIILSNSDQNQDKELHLLNNMLGKQVDGIIFMSGNVTEEHVEELKKSPVPVVLAASIESTNQIPSVTIDYEQAAFDAVQSLIDSGHKNIAFVSGTLEEPINHAKKVKGYKRALTESGLPVRDSYIVEGDYTYDSGIEAVEKLLEEDEKPTAIFVGTDEMALGVIHGAQDRGLNVPNDLEIIGFDNTRLSTMVRPQLTSVVQPMYDIGAVAMRLLTKYMNKETVDSSIVQLPHRIEFRQSTK

来源 Source

来源生物 organism	Bacillus megaterium
NCBI 分类编号 ncbi_taxonomy_id	1404
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	2-PHENYLAMINO-ETHANESULFONIC ACID
分子量 formula_weight	201.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	139

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6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d1sxga_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.93 — Periplasmic binding protein-like I
超家族 Superfamily superfamily	c.93.1 — Periplasmic binding protein-like I
家族 Family family	c.93.1.1 — L-arabinose binding protein-like

结构域编号 domain_id	d1sxgb_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.93 — Periplasmic binding protein-like I
超家族 Superfamily superfamily	c.93.1 — Periplasmic binding protein-like I
家族 Family family	c.93.1.1 — L-arabinose binding protein-like

结构域编号 domain_id	d1sxgd_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.93 — Periplasmic binding protein-like I
超家族 Superfamily superfamily	c.93.1 — Periplasmic binding protein-like I
家族 Family family	c.93.1.1 — L-arabinose binding protein-like

结构域编号 domain_id	d1sxgf_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.93 — Periplasmic binding protein-like I
超家族 Superfamily superfamily	c.93.1 — Periplasmic binding protein-like I
家族 Family family	c.93.1.1 — L-arabinose binding protein-like

结构域编号 domain_id	d1sxgi_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.93 — Periplasmic binding protein-like I
超家族 Superfamily superfamily	c.93.1 — Periplasmic binding protein-like I
家族 Family family	c.93.1.1 — L-arabinose binding protein-like

结构域编号 domain_id	d1sxgp_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.93 — Periplasmic binding protein-like I
超家族 Superfamily superfamily	c.93.1 — Periplasmic binding protein-like I
家族 Family family	c.93.1.1 — L-arabinose binding protein-like

CATH v4.4 (12 domains)

结构域编号 domain_id	1sxgA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	2300 — Response regulator

结构域编号 domain_id	1sxgA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	2300 — Response regulator

结构域编号 domain_id	1sxgB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	2300 — Response regulator

结构域编号 domain_id	1sxgB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	2300 — Response regulator

结构域编号 domain_id	1sxgD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	2300 — Response regulator

结构域编号 domain_id	1sxgD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	2300 — Response regulator

结构域编号 domain_id	1sxgF01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	2300 — Response regulator

结构域编号 domain_id	1sxgF02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	2300 — Response regulator

结构域编号 domain_id	1sxgI01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	2300 — Response regulator

结构域编号 domain_id	1sxgI02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	2300 — Response regulator

结构域编号 domain_id	1sxgP01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	2300 — Response regulator

结构域编号 domain_id	1sxgP02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	2300 — Response regulator

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7. 引用文献 (1)

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晶胞边长 a length_a	375.390 Å
晶胞边长 b length_b	60.140 Å
晶胞边长 c length_c	75.650 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	95.59 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	24

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	2.750 Å
最低分辨率 resolution_low	75.290 Å
R 因子 r_factor	0.2141
R_work r_work	0.2140
R_free r_free	0.2630

fit	/app/data/saxs_computation/sx/1sxg/1sxg.fit
pddf	/app/data/pr_computation/sx/1sxg/1sxg.pr.out
profile	/app/data/saxs_computation/sx/1sxg/1sxg.dat