9hgi

;HSV-1 Origin Binding Protein in complex with double-stranded DNA recognition sequence OriS with 6 basepairs removed from the AT-rich region ;

Method: ELECTRON MICROSCOPY D_max: 120.6 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	9hgi
沉积日期 deposition_date	2024-11-19
结构标题 title	;HSV-1 Origin Binding Protein in complex with double-stranded DNA recognition sequence OriS with 6 basepairs removed from the AT-rich region ;
关键词 keywords	DNA, Helicase, Complex, DNA BINDING PROTEIN; DNA BINDING PROTEIN
实验方法 method	ELECTRON MICROSCOPY

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	40.20 Å
回转半径 Rg (电子) rg_electron	38.91 Å
零角强度 I(0) i0	630436000.00
分子量 molecular_weight	195280.0 kDa
排除体积 excluded_volume	240230 Å³
包络体积 envelope_volume	335370 Å³
水化壳体积 shell_volume	68999 Å³
包络直径 envelope_diameter	122.2 Å
壳层 Rg shell_rg	47.03 Å
包络 Rg envelope_rg	38.46 Å
形状 Rg shape_rg	38.90 Å
总 Rg total_rg	39.37 Å
总原子数 total_atoms	13657
残基数 n_residues	1671
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	120.6 Å
Rg (实空间) rg_real	39.99 Å
Rg 误差 (实空间) rg_real_error	0.60 Å
I(0) (实空间) i0_real	6.3040e+08
I(0) 误差 (实空间) i0_real_error	9.4310e+06
Rg (倒空间) rg_reciprocal	40.20 Å
I(0) (倒空间) i0_reciprocal	630600000.0000
解质量估计 total_estimate	0.8851
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	55.7 Å
偏度 Skewness skewness	0.059
峰度 Kurtosis kurtosis	-0.559
角度范围 angular_range	— – 0.1950 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	85470000.0000
实空间数据点数 n_real_points	40
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.956; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.978; Smooth: 0.656

▶

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

▶

5. 实体与聚合体信息 (3)

Entity 1 polymer

描述 description	Replication origin-binding protein
分子量 formula_weight	95677.1 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	13657

MWSHPQFEKSAMPFVGGAESGDPLGAGRPIGDDECEQYTSSVSLARMLYGGDLAEWVPRVHPKTTIERQQHGPVTFPNASAPTARCVTVVRAPMGSGKTTALIRWLREAIHSPDTSVLVVSCRRSFTQTLATRFAESGLVDFVTYFSSTNYIMNDRPFHRLIVQVESLHRVGPNLLNNYDVLVLDEVMSTLGQLYSPTMQQLGRVDALMLRLLRTCPRIIAMDATANAQLVDFLCGLRGEKNVHVVVGEYAMPGFSARRCLFLPRLGTELLQAALRPPGPPSGPSPDASPDARGATFFGELEARLGGGDNICIFSSTVSFAEIVARFCRQFTDRVLLLHSLTPLGDVTTWGQYRVVIYTTVVTVGLSFDPLHFDGMFAYVKPMNYGPDMVSVYQSLGRVRTLRKGELLIYMDGSGARSEPVFTPMLLNHVVSSCGQWPAQFSQVTNLLCRRFKGRCDASACDTSLGRGSRIYNKFRYKHYFERCTLACLSDSLNILHMLLTLNCIRVRFWGHDDTLTPKDFCLFLRGVHFDALRAQRDLRELRCRDPEASLPAQAAETEEVGLFVEKYLRSDVAPAEIVALMRNLNSLMGRTRFIYLALLEACLRVPMATRSSAIFRRIYDHYATGVIPTINVTGELELVALPPTLNVTPVWELLCLCSTMAARLHWDSAAGGSGRTFGPDDVLDLLTPHYDRYMQLVFELGHCNVTDGLLLSEEAVKRVADALSGCPPRGSVSETDHAVALFKIIWGELFGVQMAKSTQTFPGAGRVKNLTKQTIVGLLDAHHIDHSACRTHRQLYALLMAHKREFAGARFKLRVPAWGRCLRTHSSSANPNADIILEAALSELPTEAWPMMQGAVNFSTL

来源 Source

来源生物 organism	Human alphaherpesvirus 1 strain KOS
NCBI 分类编号 ncbi_taxonomy_id	10306
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 polymer

描述 description	;DNA (5'-D(PTPAPTPTPGPGPGPAPCPGPAPAPGPTPGPCPGPAPAPCPGPCPTPT)-3') ;
分子量 formula_weight	22701.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	C

GGCGCCAGTGCTCGCACTTCGCCCTAATAATATATTGGGACGAAGTGCGAACGCTTCGCGTTCTCACTTCTTTT

Entity 3 polymer

描述 description	;DNA (5'-D(PAPAPGPCPGPTPTPCPGPCPAPCPTPTPCPGPTPCPCPCPAPAPTPA)-3') ;
分子量 formula_weight	22933.7 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	D

AAAAGAAGTGAGAACGCGAAGCGTTCGCACTTCGTCCCAATATATTATTAGGGCGAAGTGCGAGCACTGGCGCC

▶

7. 引用文献 (1)

▶

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	—

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

分辨率 resolution	2.770 Å
最低分辨率 resolution_low	2.770 Å
R 因子 r_factor	0.3190
R_work r_work	0.3190
R_free r_free	—

分辨率 resolution	2.77 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	293067

fit	/app/data/saxs_computation/hg/9hgi/9hgi.fit
pddf	/app/data/pr_computation/hg/9hgi/9hgi.pr.out
profile	/app/data/saxs_computation/hg/9hgi/9hgi.dat

;HSV-1 Origin Binding Protein in complex with double-stranded DNA recognition sequence OriS with 6 basepairs removed from the AT-rich region ;

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

冷冻电镜 EM 3D

5. 实体与聚合体信息 (3)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)