1l0q

Tandem YVTN beta-propeller and PKD domains from an archaeal surface layer protein

Method: X-RAY DIFFRACTION D_max: 176.1 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	1l0q
沉积日期 deposition_date	2002-02-12
结构标题 title	Tandem YVTN beta-propeller and PKD domains from an archaeal surface layer protein
关键词 keywords	surface layer protein, SLP, S-layer, 7-bladed beta-propeller, PKD superfamily, PROTEIN BINDING; PROTEIN BINDING
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	46.31 Å
回转半径 Rg (电子) rg_electron	47.01 Å
零角强度 I(0) i0	401893000.00
分子量 molecular_weight	163080.0 kDa
排除体积 excluded_volume	203260 Å³
包络体积 envelope_volume	285780 Å³
水化壳体积 shell_volume	53355 Å³
包络直径 envelope_diameter	189.8 Å
壳层 Rg shell_rg	46.92 Å
包络 Rg envelope_rg	48.00 Å
形状 Rg shape_rg	47.10 Å
总 Rg total_rg	46.68 Å
总原子数 total_atoms	11400
残基数 n_residues	1540
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	176.1 Å
Rg (实空间) rg_real	46.80 Å
Rg 误差 (实空间) rg_real_error	2.41 Å
I(0) (实空间) i0_real	4.0190e+08
I(0) 误差 (实空间) i0_real_error	7.9160e+06
Rg (倒空间) rg_reciprocal	46.31 Å
I(0) (倒空间) i0_reciprocal	401700000.0000
解质量估计 total_estimate	0.8172
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	57.0 Å
偏度 Skewness skewness	0.622
峰度 Kurtosis kurtosis	0.255
角度范围 angular_range	— – 0.1700 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	16920000.0000
实空间数据点数 n_real_points	35
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.590; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.909; Smooth: 0.942

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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) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1l0qa1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.3 — PKD domain
家族 Family family	b.1.3.1 — PKD domain

结构域编号 domain_id	d1l0qa2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.69 — 7-bladed beta-propeller
超家族 Superfamily superfamily	b.69.2 — YVTN repeat-like/Quinoprotein amine dehydrogenase
家族 Family family	b.69.2.3 — YVTN repeat

结构域编号 domain_id	d1l0qb1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.3 — PKD domain
家族 Family family	b.1.3.1 — PKD domain

结构域编号 domain_id	d1l0qb2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.69 — 7-bladed beta-propeller
超家族 Superfamily superfamily	b.69.2 — YVTN repeat-like/Quinoprotein amine dehydrogenase
家族 Family family	b.69.2.3 — YVTN repeat

结构域编号 domain_id	d1l0qc1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.3 — PKD domain
家族 Family family	b.1.3.1 — PKD domain

结构域编号 domain_id	d1l0qc2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.69 — 7-bladed beta-propeller
超家族 Superfamily superfamily	b.69.2 — YVTN repeat-like/Quinoprotein amine dehydrogenase
家族 Family family	b.69.2.3 — YVTN repeat

结构域编号 domain_id	d1l0qd1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.3 — PKD domain
家族 Family family	b.1.3.1 — PKD domain

结构域编号 domain_id	d1l0qd2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.69 — 7-bladed beta-propeller
超家族 Superfamily superfamily	b.69.2 — YVTN repeat-like/Quinoprotein amine dehydrogenase
家族 Family family	b.69.2.3 — YVTN repeat

CATH v4.4 (8 domains)

结构域编号 domain_id	1l0qA01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	130 — 7 Propeller
拓扑 Topology topology	10 — Methylamine Dehydrogenase; Chain H
同源超家族 H-superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

结构域编号 domain_id	1l0qA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	1l0qB01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	130 — 7 Propeller
拓扑 Topology topology	10 — Methylamine Dehydrogenase; Chain H
同源超家族 H-superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

结构域编号 domain_id	1l0qB02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	1l0qC01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	130 — 7 Propeller
拓扑 Topology topology	10 — Methylamine Dehydrogenase; Chain H
同源超家族 H-superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

结构域编号 domain_id	1l0qC02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	1l0qD01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	130 — 7 Propeller
拓扑 Topology topology	10 — Methylamine Dehydrogenase; Chain H
同源超家族 H-superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

结构域编号 domain_id	1l0qD02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

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7. 引用文献 (6)

;Archaeal Surface Layer Proteins Contain beta Propeller, PKD, and beta Helix Domains and Are Related to Metazoan Cell Surface Proteins. ;

Structure (2002)

PMID: 12377130 · DOI: 10.1016/S0969-2126(02)00840-7 PRIMARY

Implications for familial hypercholesterolemia from structure of the LDL receptor YWTD-EGF doman pair

Nat.Struct.Biol. (2001)

DOI: 10.1038/88556

The structure of a PKD domain from polycystin-1: implications for polycystic kidney disease

Embo J. (1999)

DOI: 10.1093/emboj/18.2.297

Structure, organization, and expression of genes coding for envelope components in the archaeon Methanosarcina mazei S-6

Arch.Microbiol. (1998)

DOI: 10.1007/s002030050580

;An extracellular beta-propeller module predicted in lipoprotein and scavenger receptors, tyrosine kinases, epidermal growth factor precursor, and extracellular matrix components ;

J.Mol.Biol. (1998)

DOI: 10.1006/jmbi.1998.2115

The genome of Methanosarcina acetivorans reveals extensive metabolic and physiological diversity

To be Published

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晶胞边长 a length_a	188.181 Å
晶胞边长 b length_b	65.885 Å
晶胞边长 c length_c	140.030 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	124.25 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	16

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	2.400 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.2170
R_work r_work	0.2140
R_free r_free	0.2630

描述 description	Surface layer protein
分子量 formula_weight	40796.6 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	12764

Tandem YVTN beta-propeller and PKD domains from an archaeal surface layer protein

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) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. 引用文献 (6)

8. 文件与曲线 (10)

Files (7)

Curves (3)

来源生物 organism	Methanosarcina mazei
NCBI 分类编号 ncbi_taxonomy_id	213585
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	1364

fit	/app/data/saxs_computation/l0/1l0q/1l0q.fit
pddf	/app/data/pr_computation/l0/1l0q/1l0q.pr.out
profile	/app/data/saxs_computation/l0/1l0q/1l0q.dat