1hqy

Nucleotide-Dependent Conformational Changes in a Protease-Associated ATPase HslU

Method: X-RAY DIFFRACTION D_max: 179.5 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	1hqy
沉积日期 deposition_date	2000-12-20
结构标题 title	Nucleotide-Dependent Conformational Changes in a Protease-Associated ATPase HslU
关键词 keywords	HSLVU, PEPTIDASE-ATPASE COMPLEX, CHAPERONE; CHAPERONE
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	52.96 Å
回转半径 Rg (电子) rg_electron	53.40 Å
零角强度 I(0) i0	424642000.00
分子量 molecular_weight	168160.0 kDa
排除体积 excluded_volume	210230 Å³
包络体积 envelope_volume	335220 Å³
水化壳体积 shell_volume	56932 Å³
包络直径 envelope_diameter	178.7 Å
壳层 Rg shell_rg	49.66 Å
包络 Rg envelope_rg	52.01 Å
形状 Rg shape_rg	53.43 Å
总 Rg total_rg	53.17 Å
总原子数 total_atoms	11818
残基数 n_residues	1512
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	179.5 Å
Rg (实空间) rg_real	53.23 Å
Rg 误差 (实空间) rg_real_error	1.93 Å
I(0) (实空间) i0_real	4.2460e+08
I(0) 误差 (实空间) i0_real_error	8.1270e+06
Rg (倒空间) rg_reciprocal	52.71 Å
I(0) (倒空间) i0_reciprocal	424300000.0000
解质量估计 total_estimate	0.8100
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	47.9 Å
偏度 Skewness skewness	0.358
峰度 Kurtosis kurtosis	-0.632
角度范围 angular_range	— – 0.1500 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	19710000.0000
实空间数据点数 n_real_points	31
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.869; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.919; 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	HEAT SHOCK LOCUS HSLV
分子量 formula_weight	18986.6 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	11818

TTIVSVRRNGHVVIAGDGQATLGNTVMKGNVKKVRRLYNDKVIAGFAGGTADAFTLFELFERKLEMHQGHLVKAAVELAKDWRTDRMLRKLEALLAVADETASLIITGNGDVVQPENDLIAIGSGGPYAQAAARALLENTELSAREIAEKALDIAGDICIYTNHFHTIEELSYKA

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	469008
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

描述 description	HEAT SHOCK LOCUS HSLU
分子量 formula_weight	50495.5 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	E,F

HHHHHHHSEMTPREIVSELDKHIIGQDNAKRSVAIALRNRWRRMQLNEELRHEVTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGKEVDSIIRDLTDAAVKMVRVQAIEKNRYRAEELAEERILDVLIPPAKNNWGQTEQQQEPSAARQAFRKKLREGQLDDKEIEIDLAAAPMGVEIMAPPGMEEMTSQLQSMFQNLGGQKQKARKLKIKDAMKLLIEEEAAKLVNPEELKQDAIDAVEQHGIVFIDEIDKICKRGESSGPDVSREGVQRDLLPLVEGCTVSTKHGMVKTDHILFIASGAFQIAKPSDLIPELQGRLPIRVELQALTTSDFERILTEPNASITVQYKALMATEGVNIEFTDSGIKRIAEAAWQVNESTENIGARRLHTVLERLMEEISYDASDLSGQNITIDADYVSKHLDALVADEDLSRFIL

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	469008
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 non-polymer

描述 description	ADENOSINE-5'-DIPHOSPHATE
分子量 formula_weight	427.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1hqya_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.153 — Ntn hydrolase-like
超家族 Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family family	d.153.1.4 — Proteasome subunits

结构域编号 domain_id	d1hqyb_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.153 — Ntn hydrolase-like
超家族 Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family family	d.153.1.4 — Proteasome subunits

结构域编号 domain_id	d1hqyc_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.153 — Ntn hydrolase-like
超家族 Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family family	d.153.1.4 — Proteasome subunits

结构域编号 domain_id	d1hqyd_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.153 — Ntn hydrolase-like
超家族 Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family family	d.153.1.4 — Proteasome subunits

结构域编号 domain_id	d1hqye1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.20 — Extended AAA-ATPase domain

结构域编号 domain_id	d1hqye2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d1hqyf1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.20 — Extended AAA-ATPase domain

结构域编号 domain_id	d1hqyf2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

CATH v4.4 (10 domains)

结构域编号 domain_id	1hqyA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

结构域编号 domain_id	1hqyB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

结构域编号 domain_id	1hqyC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

结构域编号 domain_id	1hqyD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

结构域编号 domain_id	1hqyE01
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	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	1hqyE02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily	10 — Ubiquitin-associated (UBA) domain

结构域编号 domain_id	1hqyE03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily	60 —

结构域编号 domain_id	1hqyF01
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	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	1hqyF02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily	10 — Ubiquitin-associated (UBA) domain

结构域编号 domain_id	1hqyF03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily	60 —

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7. 引用文献 (7)

Nucleotide-dependent conformational changes in a protease-associated ATPase HsIU.

Structure (2001)

PMID: 11709174 · DOI: 10.1016/S0969-2126(01)00670-0 PRIMARY

Crystal Structures of the Hslvu Peptidase-ATPase Complex Reveal an ATP-Dependent Proteolysis Mechanism

Structure (2001)

DOI: 10.1016/S0969-2126(01)00570-6

A corrected quaternary arrangement of the peptidase hslv and atpase hslu in a cocrystal structure

J.STRUCT.BIOL. (2001)

DOI: 10.1006/jsbi.2001.4347

Mutational Studies of Hslu and its Docking Mode With Hslv.

Proc.Natl.Acad.Sci.USA (2000)

DOI: 10.1073/pnas.250491797

The Structures of Hslu and the ATP-Dependent Protease HslU-HslV.

Nature (2000)

DOI: 10.1038/35001629

Crystal and Solution Structures of an HslUV Protease-chaperone Complex.

Cell(Cambridge,Mass.) (2000)

DOI: 10.1016/S0092-8674(00)00166-5

ATP-dependent proteases: Docking of Components in a Bacterial Complex

Nature (2000)

DOI: 10.1038/35047165

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晶胞边长 a length_a	172.022 Å
晶胞边长 b length_b	172.022 Å
晶胞边长 c length_c	276.569 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	48

空间群 space_group	P 63 2 2
空间群编号 int_tables_number	182
晶系 crystal_system	—

分辨率 resolution	2.800 Å
最低分辨率 resolution_low	29.620 Å
R 因子 r_factor	0.2870
R_work r_work	0.2870
R_free r_free	0.3330

fit	/app/data/saxs_computation/hq/1hqy/1hqy.fit
pddf	/app/data/pr_computation/hq/1hqy/1hqy.pr.out
profile	/app/data/saxs_computation/hq/1hqy/1hqy.dat

Nucleotide-Dependent Conformational Changes in a Protease-Associated ATPase HslU

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 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (8 domains)

CATH v4.4 (10 domains)

7. 引用文献 (7)

8. 文件与曲线 (10)

Files (7)

Curves (3)