SAXSdb — 1mqt

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1mqt
沉积日期 deposition_date	2002-09-17
结构标题 title	Swine Vesicular Disease Virus coat protein
关键词 keywords	swine vesicular disease virus, SVDV coat protein, enterovirus, Icosahedral virus, Virus; VIRUS
实验方法 method	X-RAY DIFFRACTION

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	29.67 Å
回转半径 Rg (电子) rg_electron	28.62 Å
零角强度 I(0) i0	133099000.00
分子量 molecular_weight	90552.0 kDa
排除体积 excluded_volume	112860 Å³
包络体积 envelope_volume	139920 Å³
水化壳体积 shell_volume	39832 Å³
包络直径 envelope_diameter	104.9 Å
壳层 Rg shell_rg	36.60 Å
包络 Rg envelope_rg	29.38 Å
形状 Rg shape_rg	28.62 Å
总 Rg total_rg	29.33 Å
总原子数 total_atoms	6363
残基数 n_residues	818
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

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	99.4 Å
Rg (实空间) rg_real	29.64 Å
Rg 误差 (实空间) rg_real_error	0.67 Å
I(0) (实空间) i0_real	1.3310e+08
I(0) 误差 (实空间) i0_real_error	1.7930e+06
Rg (倒空间) rg_reciprocal	29.65 Å
I(0) (倒空间) i0_reciprocal	133100000.0000
解质量估计 total_estimate	0.8804
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	35.6 Å
偏度 Skewness skewness	0.358
峰度 Kurtosis kurtosis	-0.237
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	23450000.0000
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: 0.824; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.969

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (6)

Entity 1 polymer

描述 description	Polyprotein
分子量 formula_weight	31370.2 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	6393

GPPGGVTEGIIARVADTVGSGPVNSESIPALTAAETGHTSQVVPSDTMQTRHVKNYHSRSESTVENFLCRSACVFYTTYKNHDSDGDNFAYWVINARQVAQLRRKLEMFTYARFDLELTFVITSTQEQSTTQGQDTPVLTHQIMYVPPGGPVPTKVNSYSWQTSTNPSVFWTEGNAPPRMSIPFIGIGNAYSMFYDGWARFDKQGTYGISTLNSMGTLYMRHVNGGGPGPIVSTVRIYFKPKHVKTWVPRPPRLCQYKKAGNVNFIPTSVTEGRTDITTMKTT

Entity 2 polymer

描述 description	Polyprotein Capsid Protein
分子量 formula_weight	28505.2 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B

SPSAEECGYSDRVRSITLGNSTITTQECANVVVGYGVWPAYLKDEEATAEDQPTQPDVATCRFYTLESVMWQQGSPGWWWKFPDALSNMGLFGQNMQYHYLGRAGYTIHVQCNASKFHQGCLLVVCVPEAEMGCATLANKPDPKSLSKGEIASTFESQNSTGETAVQANVINAGMGVGVGNLTIFPHQWINLRTNNSATIVMPYINSVPMDNMFRHNNFTLMVIPFAPLSYSAGATTYVPITVTVAPMCAEYNGLRLAGKQ

Entity 3 polymer

描述 description	Polyprotein Capsid Protein
分子量 formula_weight	26071.5 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C

GLPTLATPGSNQFLTSDDFQSPSAMPQFDVTPEMDIPGQVNNLMEIAEVDSVVPVNNTEGKEMSIEAYQIPVQSNPTNGSQVFGFPLTPGASSVLNRTLLGEILNYYAHWSGSIKLTFMFCGSAMATGKFLLAYSPPGAGAPTTRKEAMLGTHVIWDVGLQSSCVLCIPWISQTHYRYVVMDEYTAGGYITCWYQTNIVVPADAQSDCKILCFVSACNDFSVRMLKDTPFIKQDNFFQ

Entity 4 polymer

描述 description	Polyprotein Capsid Protein
分子量 formula_weight	7353.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	D

GAQVSTQKTGAHETSLNAAGNSVIHYTNINYYKDAASNSANRQDFTQDPGKFTEPVKDIMVKSMPALN

Entity 5 non-polymer

描述 description	OCTANOIC ACID (2-HYDROXY-1-HYDROXYMETHYL-HEPTADEC-3-ENYL)-AMIDE
分子量 formula_weight	425.7 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 6 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	30

▼

6. 折叠分类 (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

结构域编号 domain_id	d1mqt.1
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.121.4.1 — Picornaviridae-like VP (VP1, VP2, VP3 and VP4)

结构域编号 domain_id	d1mqta_
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.121.4.1 — Picornaviridae-like VP (VP1, VP2, VP3 and VP4)

结构域编号 domain_id	d1mqtc_
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.121.4.1 — Picornaviridae-like VP (VP1, VP2, VP3 and VP4)

CATH v4.4 (4 domains)

结构域编号 domain_id	1mqtA00
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	1mqtB00
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	1mqtC00
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	1mqtD00
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	80 — Rhinovirus 14, subunit 4
同源超家族 H-superfamily homologous superfamily	10 — Picornavirus coat protein VP4

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	318.350 Å
晶胞边长 b length_b	349.960 Å
晶胞边长 c length_c	371.720 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	90.00 °
晶胞分子数 Z z_pdb	120

空间群 space_group	I 2 2 2
空间群编号 int_tables_number	23
晶系 crystal_system	—

分辨率 resolution	3.300 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	—
R_work r_work	0.2570
R_free r_free	0.2790

fit	/app/data/saxs_computation/mq/1mqt/1mqt.fit
pddf	/app/data/pr_computation/mq/1mqt/1mqt.pr.out
profile	/app/data/saxs_computation/mq/1mqt/1mqt.dat

Swine Vesicular Disease Virus coat 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 (6)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

Entity 4 polymer

聚合体 Polymer

Entity 5 non-polymer

Entity 6 water

6. 折叠分类 (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

CATH v4.4 (4 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)