SAXSdb — 1hk9

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1hk9
沉积日期 deposition_date	2003-03-06
结构标题 title	Crystal structure of the Hfq protein from Escherichia coli
关键词 keywords	RNA-BINDING PROTEIN, SM-LIKE, PLEIOTROPIC REGULATOR, RNA BINDING PROTEIN, RNA CHAPERONE; 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	23.95 Å
回转半径 Rg (电子) rg_electron	22.48 Å
零角强度 I(0) i0	29377100.00
分子量 molecular_weight	43976.0 kDa
排除体积 excluded_volume	56150 Å³
包络体积 envelope_volume	66988 Å³
水化壳体积 shell_volume	24544 Å³
包络直径 envelope_diameter	70.4 Å
壳层 Rg shell_rg	29.42 Å
包络 Rg envelope_rg	22.46 Å
形状 Rg shape_rg	22.45 Å
总 Rg total_rg	23.43 Å
总原子数 total_atoms	3104
残基数 n_residues	394
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	70.7 Å
Rg (实空间) rg_real	23.84 Å
Rg 误差 (实空间) rg_real_error	0.35 Å
I(0) (实空间) i0_real	2.9380e+07
I(0) 误差 (实空间) i0_real_error	3.6080e+05
Rg (倒空间) rg_reciprocal	23.86 Å
I(0) (倒空间) i0_reciprocal	29380000.0000
解质量估计 total_estimate	0.9165
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	30.9 Å
偏度 Skewness skewness	0.153
峰度 Kurtosis kurtosis	-0.638
角度范围 angular_range	— – 0.3300 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	14380000.0000
实空间数据点数 n_real_points	65
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.982; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.965

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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 (2)

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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	d1hk9a_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.38 — Sm-like fold
超家族 Superfamily superfamily	b.38.1 — Sm-like ribonucleoproteins
家族 Family family	b.38.1.2 — Pleiotropic translational regulator Hfq

结构域编号 domain_id	d1hk9b_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.38 — Sm-like fold
超家族 Superfamily superfamily	b.38.1 — Sm-like ribonucleoproteins
家族 Family family	b.38.1.2 — Pleiotropic translational regulator Hfq

结构域编号 domain_id	d1hk9c_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.38 — Sm-like fold
超家族 Superfamily superfamily	b.38.1 — Sm-like ribonucleoproteins
家族 Family family	b.38.1.2 — Pleiotropic translational regulator Hfq

结构域编号 domain_id	d1hk9d_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.38 — Sm-like fold
超家族 Superfamily superfamily	b.38.1 — Sm-like ribonucleoproteins
家族 Family family	b.38.1.2 — Pleiotropic translational regulator Hfq

结构域编号 domain_id	d1hk9e_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.38 — Sm-like fold
超家族 Superfamily superfamily	b.38.1 — Sm-like ribonucleoproteins
家族 Family family	b.38.1.2 — Pleiotropic translational regulator Hfq

结构域编号 domain_id	d1hk9f_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.38 — Sm-like fold
超家族 Superfamily superfamily	b.38.1 — Sm-like ribonucleoproteins
家族 Family family	b.38.1.2 — Pleiotropic translational regulator Hfq

CATH v4.4 (6 domains)

结构域编号 domain_id	1hk9A00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	100 —

结构域编号 domain_id	1hk9B00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	100 —

结构域编号 domain_id	1hk9C00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	100 —

结构域编号 domain_id	1hk9D00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	100 —

结构域编号 domain_id	1hk9E00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	100 —

结构域编号 domain_id	1hk9F00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	100 —

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7. 引用文献 (6)

Sm-Like Proteins in Eubacteria: The Crystal Structure of the Hfq Protein from Escherichia Coli

Nucleic Acids Res. (2003)

PMID: 12853626 · DOI: 10.1093/NAR/GKG480 PRIMARY

The Sm-Like Hfq Protein Increases Oxys RNA Interaction with Target Mrnas

Mol.Cell (2002)

PMID: 11804582 · DOI: 10.1016/S1097-2765(01)00437-3

Hfq: A Bacterial Sm-Like Protein that Mediates RNA-RNA Interaction

Mol.Cell (2002)

PMID: 11804583 · DOI: 10.1016/S1097-2765(01)00436-1

Structures of the Pleiotropic Translational Regulator Hfq and an Hfq-RNA Complex: A Bacterial Sm-Like Protein

Embo J. (2002)

PMID: 12093755 · DOI: 10.1093/EMBOJ/CDF322

Characterization of Broadly Pleiotropic Phenotypes Caused by an Hfq Insertion Mutation in Escherichia Coli K-12

Mol.Microbiol. (1994)

PMID: 7984093 · DOI: 10.1111/J.1365-2958.1994.TB00400.X

;Bacterial Proteins Required for Replication of Phage Q Ribonucleic Acid. Purification and Properties of Host Factor I, a Ribonucleic Acid-Binding Protein ;

J.Biol.Chem. (1972)

PMID: 4550762

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晶胞边长 a length_a	61.350 Å
晶胞边长 b length_b	61.350 Å
晶胞边长 c length_c	166.100 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	120.00 °
晶胞分子数 Z z_pdb	36

空间群 space_group	P 61
空间群编号 int_tables_number	169
晶系 crystal_system	—

分辨率 resolution	2.150 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.2080
R_work r_work	0.2080
R_free r_free	0.2620

描述 description	PROTEIN HFQ
分子量 formula_weight	8257.6 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	3240

Crystal structure of the Hfq protein from Escherichia coli

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) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. 引用文献 (6)

8. 文件与曲线 (10)

Files (7)

Curves (3)

来源生物 organism	ESCHERICHIA COLI
NCBI 分类编号 ncbi_taxonomy_id	562
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	136

fit	/app/data/saxs_computation/hk/1hk9/1hk9.fit
pddf	/app/data/pr_computation/hk/1hk9/1hk9.pr.out
profile	/app/data/saxs_computation/hk/1hk9/1hk9.dat