2bgc

PrfA-G145S, a constitutive active mutant of the Transcriptional Regulator In L.monocytogenes

Method: X-RAY DIFFRACTION D_max: 133.8 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	2bgc
沉积日期 deposition_date	2004-12-20
结构标题 title	PrfA-G145S, a constitutive active mutant of the Transcriptional Regulator In L.monocytogenes
关键词 keywords	BACTERIAL INFECTION, HUMAN PATHOGEN, TRANSCRIPTIONAL REGULATOR, 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	41.18 Å
回转半径 Rg (电子) rg_electron	40.70 Å
零角强度 I(0) i0	605972000.00
分子量 molecular_weight	216140.0 kDa
排除体积 excluded_volume	276080 Å³
包络体积 envelope_volume	361440 Å³
水化壳体积 shell_volume	72421 Å³
包络直径 envelope_diameter	134.7 Å
壳层 Rg shell_rg	47.58 Å
包络 Rg envelope_rg	39.75 Å
形状 Rg shape_rg	40.72 Å
总 Rg total_rg	41.01 Å
总原子数 total_atoms	15255
残基数 n_residues	1859
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	133.8 Å
Rg (实空间) rg_real	41.04 Å
Rg 误差 (实空间) rg_real_error	1.22 Å
I(0) (实空间) i0_real	6.0600e+08
I(0) 误差 (实空间) i0_real_error	1.1260e+07
Rg (倒空间) rg_reciprocal	41.18 Å
I(0) (倒空间) i0_reciprocal	606100000.0000
解质量估计 total_estimate	0.8844
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	52.8 Å
偏度 Skewness skewness	0.212
峰度 Kurtosis kurtosis	-0.420
角度范围 angular_range	— – 0.1900 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	217800000.0000
实空间数据点数 n_real_points	39
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.885; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.855

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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	PRFA
分子量 formula_weight	27430.5 kDa
突变 mutation	YES
来源方法 src_method	man
拷贝数 entity_count	8

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,D,E,F,G,H,I
原子数 atom_count	15644

GSNAQAEEFKKYLETNGIKPKQFHKKELIFNQWDPQEYCIFLYDGITKLTSISENGTIMNLQYYKGAFVIMSGFIDTETSVGYYNLEVISEQATAYVIKINELKELLSKNLTHFFYVFQTLQKQVSYSLAKFNDFSINGKLGSICSQLLILTYVYGKETPDGIKITLDNLTMQELGYSSGIAHSSAVSRIISKLKQEKVIVYKNSCFYVQNLDYLKRYAPKLDEWFYLACPATWGKLN

来源 Source

来源生物 organism	LISTERIA MONOCYTOGENES
NCBI 分类编号 ncbi_taxonomy_id	169963
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 non-polymer

描述 description	(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
分子量 formula_weight	154.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	2,3-DIHYDROXY-1,4-DITHIOBUTANE
分子量 formula_weight	154.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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	389

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6. 折叠分类 (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

结构域编号 domain_id	d2bgca1
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.4.5.4 — CAP C-terminal domain-like

结构域编号 domain_id	d2bgca2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.82 — Double-stranded beta-helix
超家族 Superfamily superfamily	b.82.3 — cAMP-binding domain-like
家族 Family family	b.82.3.3 — Listeriolysin regulatory protein PrfA, N-terminal domain

结构域编号 domain_id	d2bgcb1
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.4.5.4 — CAP C-terminal domain-like

结构域编号 domain_id	d2bgcb2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.82 — Double-stranded beta-helix
超家族 Superfamily superfamily	b.82.3 — cAMP-binding domain-like
家族 Family family	b.82.3.3 — Listeriolysin regulatory protein PrfA, N-terminal domain

结构域编号 domain_id	d2bgcd1
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.4.5.4 — CAP C-terminal domain-like

结构域编号 domain_id	d2bgcd2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.82 — Double-stranded beta-helix
超家族 Superfamily superfamily	b.82.3 — cAMP-binding domain-like
家族 Family family	b.82.3.3 — Listeriolysin regulatory protein PrfA, N-terminal domain

结构域编号 domain_id	d2bgce1
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.4.5.4 — CAP C-terminal domain-like

结构域编号 domain_id	d2bgce2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.82 — Double-stranded beta-helix
超家族 Superfamily superfamily	b.82.3 — cAMP-binding domain-like
家族 Family family	b.82.3.3 — Listeriolysin regulatory protein PrfA, N-terminal domain

结构域编号 domain_id	d2bgcf1
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.4.5.4 — CAP C-terminal domain-like

结构域编号 domain_id	d2bgcf2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.82 — Double-stranded beta-helix
超家族 Superfamily superfamily	b.82.3 — cAMP-binding domain-like
家族 Family family	b.82.3.3 — Listeriolysin regulatory protein PrfA, N-terminal domain

结构域编号 domain_id	d2bgcg1
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.4.5.4 — CAP C-terminal domain-like

结构域编号 domain_id	d2bgcg2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.82 — Double-stranded beta-helix
超家族 Superfamily superfamily	b.82.3 — cAMP-binding domain-like
家族 Family family	b.82.3.3 — Listeriolysin regulatory protein PrfA, N-terminal domain

结构域编号 domain_id	d2bgch1
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.4.5.4 — CAP C-terminal domain-like

结构域编号 domain_id	d2bgch2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.82 — Double-stranded beta-helix
超家族 Superfamily superfamily	b.82.3 — cAMP-binding domain-like
家族 Family family	b.82.3.3 — Listeriolysin regulatory protein PrfA, N-terminal domain

结构域编号 domain_id	d2bgci1
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.4.5.4 — CAP C-terminal domain-like

结构域编号 domain_id	d2bgci2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.82 — Double-stranded beta-helix
超家族 Superfamily superfamily	b.82.3 — cAMP-binding domain-like
家族 Family family	b.82.3.3 — Listeriolysin regulatory protein PrfA, N-terminal domain

CATH v4.4 (16 domains)

结构域编号 domain_id	2bgcA01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	10 — Jelly Rolls

结构域编号 domain_id	2bgcA02
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	2bgcB01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	10 — Jelly Rolls

结构域编号 domain_id	2bgcB02
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	2bgcD01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	10 — Jelly Rolls

结构域编号 domain_id	2bgcD02
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	2bgcE01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	10 — Jelly Rolls

结构域编号 domain_id	2bgcE02
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	2bgcF01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	10 — Jelly Rolls

结构域编号 domain_id	2bgcF02
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	2bgcG01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	10 — Jelly Rolls

结构域编号 domain_id	2bgcG02
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	2bgcH01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	10 — Jelly Rolls

结构域编号 domain_id	2bgcH02
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	2bgcI01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	10 — Jelly Rolls

结构域编号 domain_id	2bgcI02
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 (1)

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晶胞边长 a length_a	117.247 Å
晶胞边长 b length_b	100.243 Å
晶胞边长 c length_c	189.563 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.33 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	32

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	2.300 Å
最低分辨率 resolution_low	182.570 Å
R 因子 r_factor	0.1990
R_work r_work	0.1950
R_free r_free	0.2680

fit	/app/data/saxs_computation/bg/2bgc/2bgc.fit
pddf	/app/data/pr_computation/bg/2bgc/2bgc.pr.out
profile	/app/data/saxs_computation/bg/2bgc/2bgc.dat