SAXSdb — 1qex

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1qex
沉积日期 deposition_date	1999-03-30
结构标题 title	BACTERIOPHAGE T4 GENE PRODUCT 9 (GP9), THE TRIGGER OF TAIL CONTRACTION AND THE LONG TAIL FIBERS CONNECTOR
关键词 keywords	BACTERIOPHAGE T4, BASEPLATE, GENE PRODUCT 9, OLIGOMERIZATION, Viral protein; VIRAL 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	58.70 Å
回转半径 Rg (电子) rg_electron	60.00 Å
零角强度 I(0) i0	60228700.00
分子量 molecular_weight	62452.0 kDa
排除体积 excluded_volume	77699 Å³
包络体积 envelope_volume	161380 Å³
水化壳体积 shell_volume	25519 Å³
包络直径 envelope_diameter	192.0 Å
壳层 Rg shell_rg	50.98 Å
包络 Rg envelope_rg	56.03 Å
形状 Rg shape_rg	59.90 Å
总 Rg total_rg	59.94 Å
总原子数 total_atoms	4380
残基数 n_residues	576
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	179.2 Å
Rg (实空间) rg_real	59.73 Å
Rg 误差 (实空间) rg_real_error	2.48 Å
I(0) (实空间) i0_real	6.0230e+07
I(0) 误差 (实空间) i0_real_error	1.3790e+06
Rg (倒空间) rg_reciprocal	57.73 Å
I(0) (倒空间) i0_reciprocal	60040000.0000
解质量估计 total_estimate	0.6140
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	39.8 Å
偏度 Skewness skewness	0.371
峰度 Kurtosis kurtosis	-1.048
角度范围 angular_range	— – 0.1350 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	2281000.0000
实空间数据点数 n_real_points	28
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.272; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.162; Smooth: 0.000

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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 (3)

Entity 1 polymer

描述 description	PROTEIN (BACTERIOPHAGE T4 GENE PRODUCT 9 (GP9))
分子量 formula_weight	31024.7 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	4672

MFIQEPKKLIDTGEIGNASTGDILFDGGNKINSDFNAIYNAFGDQRKMAVANGTGADGQIIHATGYYQKHSITEYATPVKVGTRHDIDTSTVGVKVIIERGELGDCVEFINSNGSISVTNPLTIQAIDSIKGVSGNLVVTSPYSKVTLRCISSDNSTSVWNYSIESMFGQKESPAEGTWNISTSGSVDIPLFHRTEYNMAKLLVTCQSVDGRKIKTAEINILVDTVNSEVISSEYAVMRVGNETEEDEIANIAFSIKENYVTATISSSTVGMRAAVKVIATQKIGVAQ

来源 Source

来源生物 organism	Enterobacteria phage T4
NCBI 分类编号 ncbi_taxonomy_id	10665
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
分子量 formula_weight	238.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 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	292

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1qexa_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.32 — gp9
超家族 Superfamily superfamily	b.32.1 — gp9
家族 Family family	b.32.1.1 — gp9

结构域编号 domain_id	d1qexb_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.32 — gp9
超家族 Superfamily superfamily	b.32.1 — gp9
家族 Family family	b.32.1.1 — gp9

CATH v4.4 (6 domains)

结构域编号 domain_id	1qexA01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	960 — Bacteriophage t4 gene product 9 (gp9)

结构域编号 domain_id	1qexA02
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	640 — gp9

结构域编号 domain_id	1qexA03
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	1680 — 4-oxalocrotonate tautomerase-like

结构域编号 domain_id	1qexB01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	960 — Bacteriophage t4 gene product 9 (gp9)

结构域编号 domain_id	1qexB02
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	640 — gp9

结构域编号 domain_id	1qexB03
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	1680 — 4-oxalocrotonate tautomerase-like

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7. 引用文献 (2)

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晶胞边长 a length_a	94.330 Å
晶胞边长 b length_b	94.330 Å
晶胞边长 c length_c	440.940 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	120.00 °
晶胞分子数 Z z_pdb	36

空间群 space_group	H 3 2
空间群编号 int_tables_number	155
晶系 crystal_system	—

分辨率 resolution	2.300 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	—
R_work r_work	0.2390
R_free r_free	0.2770

fit	/app/data/saxs_computation/qe/1qex/1qex.fit
pddf	/app/data/pr_computation/qe/1qex/1qex.pr.out
profile	/app/data/saxs_computation/qe/1qex/1qex.dat

BACTERIOPHAGE T4 GENE PRODUCT 9 (GP9), THE TRIGGER OF TAIL CONTRACTION AND THE LONG TAIL FIBERS CONNECTOR

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