SAXSdb — 1fmd

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1fmd
沉积日期 deposition_date	1994-02-10
结构标题 title	THE STRUCTURE AND ANTIGENICITY OF A TYPE C FOOT-AND-MOUTH DISEASE VIRUS
关键词 keywords	VIRUS, Icosahedral virus; 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	31.42 Å
回转半径 Rg (电子) rg_electron	30.84 Å
零角强度 I(0) i0	88744600.00
分子量 molecular_weight	73278.0 kDa
排除体积 excluded_volume	91288 Å³
包络体积 envelope_volume	129720 Å³
水化壳体积 shell_volume	35583 Å³
包络直径 envelope_diameter	115.6 Å
壳层 Rg shell_rg	36.88 Å
包络 Rg envelope_rg	31.81 Å
形状 Rg shape_rg	30.82 Å
总 Rg total_rg	31.47 Å
总原子数 total_atoms	5168
残基数 n_residues	670
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	107.9 Å
Rg (实空间) rg_real	31.46 Å
Rg 误差 (实空间) rg_real_error	0.99 Å
I(0) (实空间) i0_real	8.8740e+07
I(0) 误差 (实空间) i0_real_error	1.3020e+06
Rg (倒空间) rg_reciprocal	31.45 Å
I(0) (倒空间) i0_reciprocal	88740000.0000
解质量估计 total_estimate	0.8828
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	34.5 Å
偏度 Skewness skewness	0.366
峰度 Kurtosis kurtosis	-0.345
角度范围 angular_range	— – 0.2500 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	16100000.0000
实空间数据点数 n_real_points	51
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.841; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.978; Smooth: 0.970

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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	FOOT-AND-MOUTH DISEASE VIRUS (SUBUNIT VP1)
分子量 formula_weight	22694.6 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	1
原子数 atom_count	5168

TTTTGESADPVTTTVENYGGETQVQRRHHTDVAFVLDRFVKVTVSDNQHTLDVMQAHKDNIVGALLRAATYYFSDLEIAVTHTGKLTWVPNGAPVSALNNTTNPTAYHKGPVTRLALPYTAPHRVLATAYTGTTTYTASARGDLAHLTTTHAAHLPTSFNFGAVKAETITELLVRMKRAELYCPRPILPIQPTGDRHKQPLVAPAKQL

来源 Source

来源生物 organism	Foot-and-mouth disease virus
NCBI 分类编号 ncbi_taxonomy_id	12110
宿主生物 host_organism	Mesocricetus auratus

Entity 2 polymer

描述 description	FOOT-AND-MOUTH DISEASE VIRUS (SUBUNIT VP2)
分子量 formula_weight	24297.4 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	2

DKKTEETTLLEDRILTTRNGHTTSTTQSSVGVTFGYATAEDSTSGPNTSALETRVHQAERFFKMALFDWVPSQNFGHMHKVVLPHEPKGVYGGLVKSYAYMRNGWDVEVTAVGNQFNGGCLLVALVPEMGDISDREKYQLTLYPHQFINPRTNMTAHITVPYVGVNRYDQYKQHRPWTLVVMVVAPLTTNTAGAQQIKVYANIAPTNVHVAGELPSKE

来源 Source

来源生物 organism	Foot-and-mouth disease virus
NCBI 分类编号 ncbi_taxonomy_id	12110
宿主生物 host_organism	Mesocricetus auratus

Entity 3 polymer

描述 description	FOOT-AND-MOUTH DISEASE VIRUS (SUBUNIT VP3)
分子量 formula_weight	24020.9 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	3

GIFPVACSDGYGNMVTTDPKTADPAYGKVYNPPRTALPGRFTNYLDVAEACPTFLMFENVPYVSTRTDGQRLLAKFDVSLAAKHMSNTYLAGLAQYYTQYTGTINLHFMFTGPTDAKARYMVAYVPPGMDAPDNPEEAAHCIHAEWDTGLNSKFTFSIPYISAADYTYTASHEAETTCVQGWVCVYQITHGKADADALVVSASAGKDFELRLPVDARQQ

来源 Source

来源生物 organism	Foot-and-mouth disease virus
NCBI 分类编号 ncbi_taxonomy_id	12110
宿主生物 host_organism	Mesocricetus auratus

Entity 4 polymer

描述 description	FOOT-AND-MOUTH DISEASE VIRUS (SUBUNIT VP4)
分子量 formula_weight	8778.1 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	4

GAGQSSPATGSQNQSGNTGSIINNYYMQQYQNSMDTQLGDNAISGGSNEGSTDTTSTHTTNTQNNDWFSKLASSAFSGLFGALLA

来源 Source

来源生物 organism	Foot-and-mouth disease virus
NCBI 分类编号 ncbi_taxonomy_id	12110
宿主生物 host_organism	Mesocricetus auratus

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6. 折叠分类 (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

结构域编号 domain_id	d1fmd.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	d1fmd1_
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	d1fmd3_
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	1fmd100
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	1fmd200
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	1fmd300
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	1fmd400
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	90 — Foot-And-Mouth Disease Virus, subunit 4
同源超家族 H-superfamily homologous superfamily	10 — Capsid protein VP4 superfamily, Picornavirus

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7. 引用文献 (3)

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晶胞边长 a length_a	347.600 Å
晶胞边长 b length_b	347.600 Å
晶胞边长 c length_c	347.600 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 3
空间群编号 int_tables_number	197
晶系 crystal_system	—

分辨率 resolution	3.500 Å
最低分辨率 resolution_low	27.000 Å
R 因子 r_factor	0.2040
R_work r_work	0.2040
R_free r_free	—

fit	/app/data/saxs_computation/fm/1fmd/1fmd.fit
pddf	/app/data/pr_computation/fm/1fmd/1fmd.pr.out
profile	/app/data/saxs_computation/fm/1fmd/1fmd.dat

THE STRUCTURE AND ANTIGENICITY OF A TYPE C FOOT-AND-MOUTH DISEASE VIRUS

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 (4)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 polymer

聚合体 Polymer

来源 Source

Entity 4 polymer

聚合体 Polymer

来源 Source

6. 折叠分类 (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

CATH v4.4 (4 domains)

7. 引用文献 (3)

8. 文件与曲线 (10)

Files (7)

Curves (3)