SAXSdb — 1qjz

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1qjz
沉积日期 deposition_date	1999-07-07
结构标题 title	Three Dimensional Structure of Physalis Mottle Virus : Implications for the Viral Assembly
关键词 keywords	VIRUS, COAT PROTEIN (VIRAL), ICOSAHEDRAL VIRUS, CAPSID PROTEIN, VIRION; VIRUS
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	29.85 Å
回转半径 Rg (电子) rg_electron	29.45 Å
零角强度 I(0) i0	50308800.00
分子量 molecular_weight	57355.0 kDa
排除体积 excluded_volume	72557 Å³
包络体积 envelope_volume	94946 Å³
水化壳体积 shell_volume	27750 Å³
包络直径 envelope_diameter	102.8 Å
壳层 Rg shell_rg	35.33 Å
包络 Rg envelope_rg	29.98 Å
形状 Rg shape_rg	29.42 Å
总 Rg total_rg	30.14 Å
总原子数 total_atoms	4038
残基数 n_residues	555
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	97.3 Å
Rg (实空间) rg_real	29.88 Å
Rg 误差 (实空间) rg_real_error	0.79 Å
I(0) (实空间) i0_real	5.0310e+07
I(0) 误差 (实空间) i0_real_error	7.9760e+05
Rg (倒空间) rg_reciprocal	29.87 Å
I(0) (倒空间) i0_reciprocal	50310000.0000
解质量估计 total_estimate	0.8973
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	29.4 Å
偏度 Skewness skewness	0.257
峰度 Kurtosis kurtosis	-0.623
角度范围 angular_range	— – 0.2650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	8137000.0000
实空间数据点数 n_real_points	54
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.931; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.931; Smooth: 0.939

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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 (1)

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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	d1qjza_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
超家族 Superfamily superfamily	b.121.4 — Positive stranded ssRNA viruses
家族 Family family	b.121.4.6 — Tymoviridae-like VP

结构域编号 domain_id	d1qjzb_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
超家族 Superfamily superfamily	b.121.4 — Positive stranded ssRNA viruses
家族 Family family	b.121.4.6 — Tymoviridae-like VP

结构域编号 domain_id	d1qjzc_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
超家族 Superfamily superfamily	b.121.4 — Positive stranded ssRNA viruses
家族 Family family	b.121.4.6 — Tymoviridae-like VP

CATH v4.4 (3 domains)

结构域编号 domain_id	1qjzA00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1qjzB00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1qjzC00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	20 —

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7. 引用文献 (8)

Three Dimensional Structure of Physalis Movirus: Implications for the Viral Assembly

J.Mol.Biol. (1999)

PMID: 10369772 · DOI: 10.1006/JMBI.1999.2787 PRIMARY

Identification of a Discrete Intermediate in the Assembly/Disassembly of Physalis Mottle Tymovirus Through Mutational Analysis

J.Mol.Biol. (1999)

PMID: 10369771 · DOI: 10.1006/JMBI.1999.2786

;Assembly of Physalis Mottle Virus Capsid Protein in Escherichia Coli and the Role of Amino and Carboxy Termini in the Formation of the Icosahedral Particles ;

J.Mol.Biol. (1997)

PMID: 9325111 · DOI: 10.1006/JMBI.1997.1258

Architecture of Physalis Mottle Tymovirus as Probed by Monoclonal Antibodies and Cross-Linking Studies

Virology (1993)

PMID: 8460497 · DOI: 10.1006/VIRO.1993.1205

Structure of Belladonna Mottle Virus: Cross Rotation Function Studies with Southern Bean Mosaic Virus

Acta Crystallogr.,Sect.B (1990)

DOI: 10.1107/S0108768190003056

Primary Structure of Belladonna Mottle Virus Coat Protein

J.Biol.Chem. (1989)

PMID: 2467911

Stability of Belladonna Mottle Virus Particles: The Role of Polyamines and Calcium

J.Gen.Virol. (1987)

DOI: 10.1099/0022-1317-68-6-1533

Symmetry of Belladonna Mottle Virus: Rotation Function Studies

Acta Crystallogr.,Sect.B (1987)

DOI: 10.1107/S0108768187097702

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晶胞边长 a length_a	294.650 Å
晶胞边长 b length_b	294.650 Å
晶胞边长 c length_c	294.650 Å
晶胞夹角 α angle_alpha	59.91 °
晶胞夹角 β angle_beta	59.91 °
晶胞夹角 γ angle_gamma	59.91 °
晶胞分子数 Z z_pdb	9

空间群 space_group	R 3
空间群编号 int_tables_number	146
晶系 crystal_system	—

分辨率 resolution	3.800 Å
最低分辨率 resolution_low	10.000 Å
R 因子 r_factor	0.3260
R_work r_work	0.3260
R_free r_free	—

描述 description	COAT PROTEIN
分子量 formula_weight	19989.9 kDa
来源方法 src_method	nat
拷贝数 entity_count	3

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C
原子数 atom_count	4038

Three Dimensional Structure of Physalis Mottle Virus : Implications for the Viral Assembly

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 (1)

Entity 1 polymer

聚合体 Polymer

6. 折叠分类 (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. 引用文献 (8)

8. 文件与曲线 (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/qj/1qjz/1qjz.fit
pddf	/app/data/pr_computation/qj/1qjz/1qjz.pr.out
profile	/app/data/saxs_computation/qj/1qjz/1qjz.dat