1wrn

Metal Ion dependency of the antiterminator protein, HutP, for binding to the terminator region of hut mRNA- A structural basis

Method: X-RAY DIFFRACTION D_max: 80.3 Å Quality: EXCELLENT

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	1wrn
沉积日期 deposition_date	2004-10-25
结构标题 title	Metal Ion dependency of the antiterminator protein, HutP, for binding to the terminator region of hut mRNA- A structural basis
关键词 keywords	HutP, RNA binding protein, Antitermination, L-histidine, metal ions, conformational change; RNA BINDING PROTEIN
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	26.55 Å
回转半径 Rg (电子) rg_electron	25.51 Å
零角强度 I(0) i0	37006700.00
分子量 molecular_weight	46806.0 kDa
排除体积 excluded_volume	58556 Å³
包络体积 envelope_volume	73235 Å³
水化壳体积 shell_volume	24360 Å³
包络直径 envelope_diameter	84.0 Å
壳层 Rg shell_rg	32.28 Å
包络 Rg envelope_rg	25.84 Å
形状 Rg shape_rg	25.56 Å
总 Rg total_rg	26.12 Å
总原子数 total_atoms	3286
残基数 n_residues	435
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	80.3 Å
Rg (实空间) rg_real	26.53 Å
Rg 误差 (实空间) rg_real_error	0.46 Å
I(0) (实空间) i0_real	3.7010e+07
I(0) 误差 (实空间) i0_real_error	5.2350e+05
Rg (倒空间) rg_reciprocal	26.54 Å
I(0) (倒空间) i0_reciprocal	37010000.0000
解质量估计 total_estimate	0.9077
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	25.4 Å
偏度 Skewness skewness	0.192
峰度 Kurtosis kurtosis	-0.752
角度范围 angular_range	— – 0.3000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	8440000.0000
实空间数据点数 n_real_points	61
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.974; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.903

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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 (5)

Entity 1 polymer

描述 description	Hut operon positive regulatory protein
分子量 formula_weight	16101.4 kDa
突变 mutation	V51I
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C
原子数 atom_count	3653

TLHKERRIGRLSVLLLLNEAEESTQVEELERDGWKVCLGKVGSMDAHKVIAAIETASKKSGVIQSEGYRESHALYHATMEALHGVTRGEMLLGSLLRTVGLRFAVLRGNPYESEAEGDWIAVSLYGTIGAPIKGLEHETFGVGINHI

来源 Source

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

Entity 2 non-polymer

描述 description	MANGANESE (II) ION
分子量 formula_weight	54.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 3 non-polymer

描述 description	HISTIDINE
分子量 formula_weight	156.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 4 non-polymer

描述 description	DI(HYDROXYETHYL)ETHER
分子量 formula_weight	106.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

Entity 5 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	367

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6. 折叠分类 (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

结构域编号 domain_id	d1wrna_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.275 — Hut operon positive regulatory protein HutP
超家族 Superfamily superfamily	d.275.1 — Hut operon positive regulatory protein HutP
家族 Family family	d.275.1.1 — Hut operon positive regulatory protein HutP

结构域编号 domain_id	d1wrnb_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.275 — Hut operon positive regulatory protein HutP
超家族 Superfamily superfamily	d.275.1 — Hut operon positive regulatory protein HutP
家族 Family family	d.275.1.1 — Hut operon positive regulatory protein HutP

结构域编号 domain_id	d1wrnc_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.275 — Hut operon positive regulatory protein HutP
超家族 Superfamily superfamily	d.275.1 — Hut operon positive regulatory protein HutP
家族 Family family	d.275.1.1 — Hut operon positive regulatory protein HutP

CATH v4.4 (3 domains)

结构域编号 domain_id	1wrnA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1510 — Hut operon positive regulatory protein HutP
同源超家族 H-superfamily homologous superfamily	10 — Hut operon regulatory protein HutP

结构域编号 domain_id	1wrnB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1510 — Hut operon positive regulatory protein HutP
同源超家族 H-superfamily homologous superfamily	10 — Hut operon regulatory protein HutP

结构域编号 domain_id	1wrnC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1510 — Hut operon positive regulatory protein HutP
同源超家族 H-superfamily homologous superfamily	10 — Hut operon regulatory protein HutP

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7. 引用文献 (4)

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晶胞边长 a length_a	77.760 Å
晶胞边长 b length_b	81.400 Å
晶胞边长 c length_c	76.040 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	12

空间群 space_group	P 21 21 2
空间群编号 int_tables_number	18
晶系 crystal_system	—

分辨率 resolution	2.300 Å
最低分辨率 resolution_low	19.660 Å
R 因子 r_factor	0.2540
R_work r_work	0.2540
R_free r_free	0.3050

fit	/app/data/saxs_computation/wr/1wrn/1wrn.fit
pddf	/app/data/pr_computation/wr/1wrn/1wrn.pr.out
profile	/app/data/saxs_computation/wr/1wrn/1wrn.dat