1w8x

Structural analysis of PRD1

Method: X-RAY DIFFRACTION D_max: 215.9 Å Quality: GOOD

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

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1w8x
沉积日期 deposition_date	2004-10-01
结构标题 title	Structural analysis of PRD1
关键词 keywords	VIRUS, P3 MAJOR CAPSID PROTEIN, P30 TAPE MEASURE, P31 PENTON PROTEIN, P16 MEMBRANE PROTEIN, VIRUS/VIRAL PROTEIN, ICOSAHEDRAL 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	61.52 Å
回转半径 Rg (电子) rg_electron	61.57 Å
零角强度 I(0) i0	4082980000.00
分子量 molecular_weight	539360.0 kDa
排除体积 excluded_volume	674340 Å³
包络体积 envelope_volume	977830 Å³
水化壳体积 shell_volume	130290 Å³
包络直径 envelope_diameter	232.0 Å
壳层 Rg shell_rg	63.39 Å
包络 Rg envelope_rg	61.90 Å
形状 Rg shape_rg	61.56 Å
总 Rg total_rg	61.62 Å
总原子数 total_atoms	38116
残基数 n_residues	4904
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	215.9 Å
Rg (实空间) rg_real	61.77 Å
Rg 误差 (实空间) rg_real_error	2.41 Å
I(0) (实空间) i0_real	4.0830e+09
I(0) 误差 (实空间) i0_real_error	8.3920e+07
Rg (倒空间) rg_reciprocal	61.29 Å
I(0) (倒空间) i0_reciprocal	4080000000.0000
解质量估计 total_estimate	0.7940
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	66.4 Å
偏度 Skewness skewness	0.471
峰度 Kurtosis kurtosis	-0.128
角度范围 angular_range	— – 0.1300 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	1152000000.0000
实空间数据点数 n_real_points	27
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.774; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.000

▶

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

▶

5. 实体与聚合体信息 (4)

Entity 1 polymer

描述 description	MAJOR CAPSID PROTEIN (PROTEIN P3)
分子量 formula_weight	43477.4 kDa
来源方法 src_method	nat
拷贝数 entity_count	12

聚合体 Polymer

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
原子数 atom_count	38116

MAQVQQLTPAQQAALRNQQAMAANLQARQIVLQQSYPVIQQVETQTFDPANRSVFDVTPANVGIVKGFLVKVTAAITNNHATEAVALTDFGPANLVQRVIYYDPDNQRHTETSGWHLHFVNTAKQGAPFLSSMVTDSPIKYGDVMNVIDAPATIAAGATGELTMYYWVPLAYSETDLTGAVLANVPQSKQRLKLEFANNNTAFAAVGANPLEAIYQGAGAADCEFEEISYTVYQSYLDQLPVGQNGYILPLIDLSTLYNLENSAQAGLTPNVDFVVQYANLYRYLSTIAVFDNGGSFNAGTDINYLSQRTANFSDTRKLDPKTWAAQTRRRIATDFPKGVYYCDNRDKPIYTLQYGNVGFVVNPKTVNQNARLLMGYEYFTSRTELVNAGTISTT

Entity 2 polymer

描述 description	PROTEIN P30
分子量 formula_weight	9061.3 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	M

ALINPQFPYAGPVPIPGPAPTETMPLLNYRVEGRIAGIQQARQFMPFLQGPHRAVAEQTYHAIGTGIQMGQTFNQPLINTQEG

Entity 3 polymer

描述 description	PROTEIN P31
分子量 formula_weight	13757.4 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	N

MNVNNPNQMTVTPVYNGCDSGEGPQSVRGYFDAVAGENVKYDLTYLADTQGFTGVQCIYIDNAENDGAFEIDVEETGQRIKCPAGKQGYFPLLVPGRAKFVARHLGSGKKSVPLFFLNFTIAQGVW

Entity 4 polymer

描述 description	PROTEIN P16
分子量 formula_weight	12559.2 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	P

MDKKKLLYWVGGGLVLILIWLWFRNRPAAQVASNWEGPPYMTYNQPQAGSVTLPVAGYTSPSPTLPNRNRSCGCNPAVSAAMAQGADLASKLTDSITSQLNDYASSLNDYLASQAGV

▼

6. 折叠分类 (SCOP + CATH) 15 domains

SCOP 2.08 (15 domains)

结构域编号 domain_id	d1w8xa_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.6 — Viruses and virus-receptor complexes
超家族 Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
家族 Family family	i.6.1.1 — Viruses and virus-receptor complexes

结构域编号 domain_id	d1w8xb_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.6 — Viruses and virus-receptor complexes
超家族 Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
家族 Family family	i.6.1.1 — Viruses and virus-receptor complexes

结构域编号 domain_id	d1w8xc_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.6 — Viruses and virus-receptor complexes
超家族 Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
家族 Family family	i.6.1.1 — Viruses and virus-receptor complexes

结构域编号 domain_id	d1w8xd_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.6 — Viruses and virus-receptor complexes
超家族 Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
家族 Family family	i.6.1.1 — Viruses and virus-receptor complexes

结构域编号 domain_id	d1w8xe_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.6 — Viruses and virus-receptor complexes
超家族 Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
家族 Family family	i.6.1.1 — Viruses and virus-receptor complexes

结构域编号 domain_id	d1w8xf_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.6 — Viruses and virus-receptor complexes
超家族 Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
家族 Family family	i.6.1.1 — Viruses and virus-receptor complexes

结构域编号 domain_id	d1w8xg_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.6 — Viruses and virus-receptor complexes
超家族 Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
家族 Family family	i.6.1.1 — Viruses and virus-receptor complexes

结构域编号 domain_id	d1w8xh_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.6 — Viruses and virus-receptor complexes
超家族 Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
家族 Family family	i.6.1.1 — Viruses and virus-receptor complexes

结构域编号 domain_id	d1w8xi_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.6 — Viruses and virus-receptor complexes
超家族 Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
家族 Family family	i.6.1.1 — Viruses and virus-receptor complexes

结构域编号 domain_id	d1w8xj_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.6 — Viruses and virus-receptor complexes
超家族 Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
家族 Family family	i.6.1.1 — Viruses and virus-receptor complexes

结构域编号 domain_id	d1w8xk_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.6 — Viruses and virus-receptor complexes
超家族 Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
家族 Family family	i.6.1.1 — Viruses and virus-receptor complexes

结构域编号 domain_id	d1w8xl_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.6 — Viruses and virus-receptor complexes
超家族 Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
家族 Family family	i.6.1.1 — Viruses and virus-receptor complexes

结构域编号 domain_id	d1w8xm_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.6 — Viruses and virus-receptor complexes
超家族 Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
家族 Family family	i.6.1.1 — Viruses and virus-receptor complexes

结构域编号 domain_id	d1w8xn_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.6 — Viruses and virus-receptor complexes
超家族 Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
家族 Family family	i.6.1.1 — Viruses and virus-receptor complexes

结构域编号 domain_id	d1w8xp_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.6 — Viruses and virus-receptor complexes
超家族 Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
家族 Family family	i.6.1.1 — Viruses and virus-receptor complexes

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	903.000 Å
晶胞边长 b length_b	920.600 Å
晶胞边长 c length_c	926.200 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	2880

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	4.200 Å
最低分辨率 resolution_low	100.000 Å
R 因子 r_factor	—
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/w8/1w8x/1w8x.fit
pddf	/app/data/pr_computation/w8/1w8x/1w8x.pr.out
profile	/app/data/saxs_computation/w8/1w8x/1w8x.dat

Structural analysis of PRD1

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 (4)

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

6. 折叠分类 (SCOP + CATH) 15 domains

SCOP 2.08 (15 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)