SAXSdb — 1qo0

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1qo0
沉积日期 deposition_date	1999-10-26
结构标题 title	Amide receptor of the amidase operon of Pseudomonas aeruginosa (AmiC) complexed with the negative regulator AmiR.
关键词 keywords	BINDING PROTEIN, GENE REGULATOR, RECEPTOR; 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	36.32 Å
回转半径 Rg (电子) rg_electron	35.45 Å
零角强度 I(0) i0	246803000.00
分子量 molecular_weight	124850.0 kDa
排除体积 excluded_volume	155450 Å³
包络体积 envelope_volume	200530 Å³
水化壳体积 shell_volume	48087 Å³
包络直径 envelope_diameter	118.5 Å
壳层 Rg shell_rg	40.86 Å
包络 Rg envelope_rg	35.98 Å
形状 Rg shape_rg	35.48 Å
总 Rg total_rg	35.73 Å
总原子数 total_atoms	8810
残基数 n_residues	1130
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	118.0 Å
Rg (实空间) rg_real	36.36 Å
Rg 误差 (实空间) rg_real_error	0.77 Å
I(0) (实空间) i0_real	2.4680e+08
I(0) 误差 (实空间) i0_real_error	3.9760e+06
Rg (倒空间) rg_reciprocal	36.34 Å
I(0) (倒空间) i0_reciprocal	246800000.0000
解质量估计 total_estimate	0.8911
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	37.6 Å
偏度 Skewness skewness	0.328
峰度 Kurtosis kurtosis	-0.558
角度范围 angular_range	— – 0.2200 Å⁻¹
当前正则化参数 α current_alpha	0.0003
最高正则化参数 α highest_alpha	100400000.0000
实空间数据点数 n_real_points	45
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.910; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.972; Smooth: 0.878

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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	AMIC
分子量 formula_weight	42960.0 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	A,B
原子数 atom_count	9661

MGSHQERPLIGLLFSETGVTADIERSQRYGALLAVEQLNREGGVGGRPIETLSQDPGGDPDRYRLCAEDFIRNRGVRFLVGCYMSHTRKAVMPVVERADALLCYPTPYEGFEYSPNIVYGGPAPNQNSAPLAAYLIRHYGERVVFIGSDYIYPRESNHVMRHLYRQHGGTVLEEIYIPLYPSDDDLQRAVERIYQARADVVFSTVVGTGTAELYRAIARRYGDGRRPPIASLTTSEAEVAKMESDVAEGQVVVAPYFSSIDTPASRAFVQACHGFFPENATITAWAEAAYWQTLLLGRAAQAAGNWRVEDVQRHLYDIDIDAPQGPVRVERQNNHSRLSSRIAEIDARGVFQVRWQSPEPIRPDPYVVVHNLDDWSASMGGGPLP

来源 Source

来源生物 organism	PSEUDOMONAS AERUGINOSA
NCBI 分类编号 ncbi_taxonomy_id	287
宿主生物 host_organism	PSEUDOMONAS AERUGINOSA

Entity 2 polymer

描述 description	AMIR
分子量 formula_weight	21903.3 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	D,E

MSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPEAFDVPVDVVFTSIFQNRHHDEIAALLAAGTPRTTLVALVEYESPAVLSQIIELECHGVITQPLDAHRVLPVLVSARRISEEMAKLKQKTEQLQDRIAGQARINQAKVLLMQRHGWDEREAHQHLSREAMKRREPILKIAQELLGNEPSA

来源 Source

来源生物 organism	PSEUDOMONAS AERUGINOSA
NCBI 分类编号 ncbi_taxonomy_id	287
宿主生物 host_organism	PSEUDOMONAS AERUGINOSA

Entity 3 non-polymer

描述 description	BUTYRAMIDE
分子量 formula_weight	87.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	851

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6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1qo0a_
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	d1qo0b_
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	d1qo0d_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.23 — Flavodoxin-like
超家族 Superfamily superfamily	c.23.1 — CheY-like
家族 Family family	c.23.1.3 — Positive regulator of the amidase operon AmiR

结构域编号 domain_id	d1qo0e_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.23 — Flavodoxin-like
超家族 Superfamily superfamily	c.23.1 — CheY-like
家族 Family family	c.23.1.3 — Positive regulator of the amidase operon AmiR

CATH v4.4 (8 domains)

结构域编号 domain_id	1qo0A01
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	1qo0A02
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	1qo0B01
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	1qo0B02
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	1qo0D01
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	1qo0D02
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	1qo0E01
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	1qo0E02
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 (4)

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晶胞边长 a length_a	308.440 Å
晶胞边长 b length_b	67.150 Å
晶胞边长 c length_c	76.410 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	103.33 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

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	2.250 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	—
R_work r_work	0.1860
R_free r_free	0.2560

fit	/app/data/saxs_computation/qo/1qo0/1qo0.fit
pddf	/app/data/pr_computation/qo/1qo0/1qo0.pr.out
profile	/app/data/saxs_computation/qo/1qo0/1qo0.dat

Amide receptor of the amidase operon of Pseudomonas aeruginosa (AmiC) complexed with the negative regulator AmiR.

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 (4)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

Entity 4 water

6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. 引用文献 (4)

8. 文件与曲线 (10)

Files (7)

Curves (3)