1pdp

Fitting of gp9 structure into the bacteriophage T4 baseplate cryoEM reconstruction

Method: ELECTRON MICROSCOPY D_max: 714.9 Å Quality: REASONABLE

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	1pdp
沉积日期 deposition_date	2003-05-19
结构标题 title	Fitting of gp9 structure into the bacteriophage T4 baseplate cryoEM reconstruction
关键词 keywords	Structural protein; STRUCTURAL PROTEIN
实验方法 method	ELECTRON MICROSCOPY

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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	— Å
回转半径 Rg (电子) rg_electron	177.10 Å
零角强度 I(0) i0	4399140000.00
分子量 molecular_weight	557950.0 kDa
排除体积 excluded_volume	679350 Å³
包络体积 envelope_volume	1771900 Å³
水化壳体积 shell_volume	86643 Å³
包络直径 envelope_diameter	420.6 Å
壳层 Rg shell_rg	187.90 Å
包络 Rg envelope_rg	146.10 Å
形状 Rg shape_rg	177.10 Å
总 Rg total_rg	177.10 Å
总原子数 total_atoms	—
残基数 n_residues	—
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	714.9 Å
Rg (实空间) rg_real	170.70 Å
Rg 误差 (实空间) rg_real_error	12.46 Å
I(0) (实空间) i0_real	4.3650e+09
I(0) 误差 (实空间) i0_real_error	1.3160e+08
Rg (倒空间) rg_reciprocal	127.50 Å
I(0) (倒空间) i0_reciprocal	3294000000.0000
解质量估计 total_estimate	0.6451
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	238.3 Å
偏度 Skewness skewness	-1.974
峰度 Kurtosis kurtosis	-8.525
角度范围 angular_range	— – 0.0450 Å⁻¹
当前正则化参数 α current_alpha	0.2264
最高正则化参数 α highest_alpha	249500000.0000
实空间数据点数 n_real_points	10
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 16.360; Oscil: 0.001; Stabil: 0.847; Sysdev: 1.000; Positv: 1.000; Valcen: 0.854; 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 (1)

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6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (18 domains)

结构域编号 domain_id	d1pdpa_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.19 — Bacteriophage T4 3D cryo-EM reconstruction
超家族 Superfamily superfamily	i.19.1 — Bacteriophage T4 3D cryo-EM reconstruction
家族 Family family	i.19.1.1 — Bacteriophage T4 3D cryo-EM reconstruction

结构域编号 domain_id	d1pdpb_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.19 — Bacteriophage T4 3D cryo-EM reconstruction
超家族 Superfamily superfamily	i.19.1 — Bacteriophage T4 3D cryo-EM reconstruction
家族 Family family	i.19.1.1 — Bacteriophage T4 3D cryo-EM reconstruction

结构域编号 domain_id	d1pdpc_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.19 — Bacteriophage T4 3D cryo-EM reconstruction
超家族 Superfamily superfamily	i.19.1 — Bacteriophage T4 3D cryo-EM reconstruction
家族 Family family	i.19.1.1 — Bacteriophage T4 3D cryo-EM reconstruction

结构域编号 domain_id	d1pdpd_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.19 — Bacteriophage T4 3D cryo-EM reconstruction
超家族 Superfamily superfamily	i.19.1 — Bacteriophage T4 3D cryo-EM reconstruction
家族 Family family	i.19.1.1 — Bacteriophage T4 3D cryo-EM reconstruction

结构域编号 domain_id	d1pdpe_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.19 — Bacteriophage T4 3D cryo-EM reconstruction
超家族 Superfamily superfamily	i.19.1 — Bacteriophage T4 3D cryo-EM reconstruction
家族 Family family	i.19.1.1 — Bacteriophage T4 3D cryo-EM reconstruction

结构域编号 domain_id	d1pdpf_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.19 — Bacteriophage T4 3D cryo-EM reconstruction
超家族 Superfamily superfamily	i.19.1 — Bacteriophage T4 3D cryo-EM reconstruction
家族 Family family	i.19.1.1 — Bacteriophage T4 3D cryo-EM reconstruction

结构域编号 domain_id	d1pdpg_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.19 — Bacteriophage T4 3D cryo-EM reconstruction
超家族 Superfamily superfamily	i.19.1 — Bacteriophage T4 3D cryo-EM reconstruction
家族 Family family	i.19.1.1 — Bacteriophage T4 3D cryo-EM reconstruction

结构域编号 domain_id	d1pdph_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.19 — Bacteriophage T4 3D cryo-EM reconstruction
超家族 Superfamily superfamily	i.19.1 — Bacteriophage T4 3D cryo-EM reconstruction
家族 Family family	i.19.1.1 — Bacteriophage T4 3D cryo-EM reconstruction

结构域编号 domain_id	d1pdpi_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.19 — Bacteriophage T4 3D cryo-EM reconstruction
超家族 Superfamily superfamily	i.19.1 — Bacteriophage T4 3D cryo-EM reconstruction
家族 Family family	i.19.1.1 — Bacteriophage T4 3D cryo-EM reconstruction

结构域编号 domain_id	d1pdpj_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.19 — Bacteriophage T4 3D cryo-EM reconstruction
超家族 Superfamily superfamily	i.19.1 — Bacteriophage T4 3D cryo-EM reconstruction
家族 Family family	i.19.1.1 — Bacteriophage T4 3D cryo-EM reconstruction

结构域编号 domain_id	d1pdpk_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.19 — Bacteriophage T4 3D cryo-EM reconstruction
超家族 Superfamily superfamily	i.19.1 — Bacteriophage T4 3D cryo-EM reconstruction
家族 Family family	i.19.1.1 — Bacteriophage T4 3D cryo-EM reconstruction

结构域编号 domain_id	d1pdpl_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.19 — Bacteriophage T4 3D cryo-EM reconstruction
超家族 Superfamily superfamily	i.19.1 — Bacteriophage T4 3D cryo-EM reconstruction
家族 Family family	i.19.1.1 — Bacteriophage T4 3D cryo-EM reconstruction

结构域编号 domain_id	d1pdpm_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.19 — Bacteriophage T4 3D cryo-EM reconstruction
超家族 Superfamily superfamily	i.19.1 — Bacteriophage T4 3D cryo-EM reconstruction
家族 Family family	i.19.1.1 — Bacteriophage T4 3D cryo-EM reconstruction

结构域编号 domain_id	d1pdpn_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.19 — Bacteriophage T4 3D cryo-EM reconstruction
超家族 Superfamily superfamily	i.19.1 — Bacteriophage T4 3D cryo-EM reconstruction
家族 Family family	i.19.1.1 — Bacteriophage T4 3D cryo-EM reconstruction

结构域编号 domain_id	d1pdpo_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.19 — Bacteriophage T4 3D cryo-EM reconstruction
超家族 Superfamily superfamily	i.19.1 — Bacteriophage T4 3D cryo-EM reconstruction
家族 Family family	i.19.1.1 — Bacteriophage T4 3D cryo-EM reconstruction

结构域编号 domain_id	d1pdpp_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.19 — Bacteriophage T4 3D cryo-EM reconstruction
超家族 Superfamily superfamily	i.19.1 — Bacteriophage T4 3D cryo-EM reconstruction
家族 Family family	i.19.1.1 — Bacteriophage T4 3D cryo-EM reconstruction

结构域编号 domain_id	d1pdpq_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.19 — Bacteriophage T4 3D cryo-EM reconstruction
超家族 Superfamily superfamily	i.19.1 — Bacteriophage T4 3D cryo-EM reconstruction
家族 Family family	i.19.1.1 — Bacteriophage T4 3D cryo-EM reconstruction

结构域编号 domain_id	d1pdpr_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.19 — Bacteriophage T4 3D cryo-EM reconstruction
超家族 Superfamily superfamily	i.19.1 — Bacteriophage T4 3D cryo-EM reconstruction
家族 Family family	i.19.1.1 — Bacteriophage T4 3D cryo-EM reconstruction

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7. 引用文献 (2)

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分辨率 resolution	12.00 Å
分辨率测定方法 resolution_method	model based projection matching
颗粒数 num_particles	945

描述 description	Baseplate structural protein Gp9
分子量 formula_weight	31024.7 kDa
来源方法 src_method	nat
拷贝数 entity_count	18

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R
原子数 atom_count	5184

fit	/app/data/saxs_computation/pd/1pdp/1pdp.fit
pddf	/app/data/pr_computation/pd/1pdp/1pdp.pr.out
profile	/app/data/saxs_computation/pd/1pdp/1pdp.dat

Fitting of gp9 structure into the bacteriophage T4 baseplate cryoEM reconstruction

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

冷冻电镜 EM 3D

5. 实体与聚合体信息 (1)

Entity 1 polymer

聚合体 Polymer

6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (18 domains)

7. 引用文献 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)