1pdi

Fitting of the C-terminal part of the short tail fibers into the cryo-EM reconstruction of T4 baseplate

Method: ELECTRON MICROSCOPY D_max: 628.7 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	1pdi
沉积日期 deposition_date	2003-05-19
结构标题 title	Fitting of the C-terminal part of the short tail fibers into the cryo-EM reconstruction of T4 baseplate
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	169.30 Å
零角强度 I(0) i0	4563130000.00
分子量 molecular_weight	536800.0 kDa
排除体积 excluded_volume	646550 Å³
包络体积 envelope_volume	1952500 Å³
水化壳体积 shell_volume	101420 Å³
包络直径 envelope_diameter	379.8 Å
壳层 Rg shell_rg	178.00 Å
包络 Rg envelope_rg	137.10 Å
形状 Rg shape_rg	169.40 Å
总 Rg total_rg	169.30 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	628.7 Å
Rg (实空间) rg_real	166.80 Å
Rg 误差 (实空间) rg_real_error	8.33 Å
I(0) (实空间) i0_real	4.5510e+09
I(0) 误差 (实空间) i0_real_error	1.4670e+08
Rg (倒空间) rg_reciprocal	129.20 Å
I(0) (倒空间) i0_reciprocal	3579000000.0000
解质量估计 total_estimate	0.6538
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	4
主峰位置 r_peak_primary	349.3 Å
偏度 Skewness skewness	-1.002
峰度 Kurtosis kurtosis	-3.780
角度范围 angular_range	— – 0.0450 Å⁻¹
当前正则化参数 α current_alpha	0.1022
最高正则化参数 α highest_alpha	305700000.0000
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: 7.910; Oscil: 0.000; Stabil: 0.861; Sysdev: 1.000; Positv: 0.971; Valcen: 0.974; 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	d1pdia_
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	d1pdib_
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	d1pdic_
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	d1pdid_
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	d1pdie_
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	d1pdif_
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	d1pdig_
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	d1pdih_
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	d1pdii_
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	d1pdij_
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	d1pdik_
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	d1pdil_
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	d1pdim_
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	d1pdin_
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	d1pdio_
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	d1pdip_
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	d1pdiq_
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	d1pdir_
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 (3)

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晶胞边长 a length_a	1.000 Å
晶胞边长 b length_b	1.000 Å
晶胞边长 c length_c	1.000 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	1

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

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	Short tail fiber protein
分子量 formula_weight	29856.0 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	5004

Fitting of the C-terminal part of the short tail fibers into the cryo-EM reconstruction of T4 baseplate

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

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 (3)

8. 文件与曲线 (10)

Files (7)

Curves (3)

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