9pi6

Single stranded DNA-binding protein (ICP8) from Herpes simplex virus-1, apo form.Mutations: K166A, E167A, C254S, C455S

Method: X-RAY DIFFRACTION D_max: 132.8 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

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9pi6
沉积日期 deposition_date	2025-07-10
结构标题 title	Single stranded DNA-binding protein (ICP8) from Herpes simplex virus-1, apo form.Mutations: K166A, E167A, C254S, C455S
关键词 keywords	Mutation apoprotein, DNA BINDING PROTEIN; DNA BINDING 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	41.16 Å
回转半径 Rg (电子) rg_electron	40.38 Å
零角强度 I(0) i0	800978000.00
分子量 molecular_weight	230250.0 kDa
排除体积 excluded_volume	287230 Å³
包络体积 envelope_volume	378870 Å³
水化壳体积 shell_volume	75218 Å³
包络直径 envelope_diameter	138.4 Å
壳层 Rg shell_rg	48.08 Å
包络 Rg envelope_rg	40.02 Å
形状 Rg shape_rg	40.42 Å
总 Rg total_rg	40.63 Å
总原子数 total_atoms	16190
残基数 n_residues	2122
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	132.8 Å
Rg (实空间) rg_real	41.04 Å
Rg 误差 (实空间) rg_real_error	0.93 Å
I(0) (实空间) i0_real	8.0100e+08
I(0) 误差 (实空间) i0_real_error	1.2700e+07
Rg (倒空间) rg_reciprocal	41.16 Å
I(0) (倒空间) i0_reciprocal	801100000.0000
解质量估计 total_estimate	0.8825
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	52.4 Å
偏度 Skewness skewness	0.249
峰度 Kurtosis kurtosis	-0.357
角度范围 angular_range	— – 0.1900 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	131500000.0000
实空间数据点数 n_real_points	39
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.884; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.839

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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 (5)

Entity 1 polymer

描述 description	Major DNA-binding protein
分子量 formula_weight	122115.6 kDa
突变 mutation	K166A, E167A, C254S, C455S
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	16294

METKPKTATTIKVPPGPLGYVYARACPSEGIELLALLSARSGDADVAVAPLVVGLTVESGFEANVAVVVGSRTTGLGGTAVSLKLTPSHYSSSVYVFHGGRHLDPSTQAPNLTRLCERARRHFGFSDYTPRPGDLKHETTGEALCERLGLDPDRALLYLVVTEGFAAAVCINNTFLHLGGSDKVTIGGAEVHRIPVYPLQLFMPDFSRVIAEPFNANHRSIGENFTYPLPFFNRPLNRLLFEAVVGPAAVALRSRNVDAVARAAAHLAFDENHEGAALPADITFTAFEASQGKTPRGGRDGGGKGPAGGFEQRLASVMAGDAALALESIVSMAVFDEPPTDISAWPLCEGQDTAAARANAVGAYLARAAGLVGAMVFSTNSALHLTEVDDAGPADPKDHSKPSFYRFFLVPGTHVAANPQVDREGHVVPGFEGRPTAPLVGGTQEFAGEHLAMLSGFSPALLAKMLFYLERCDGGVIVGRQEMDVFRYVADSNQTDVPCNLCTFDTRHACVHTTLMRLRARHPKFASAARGAIGVFGTMNSMYSDCDVLGNYAAFSALKRADGSETARTIMQETYRAATERVMAELETLQYVDQAVPTAMGRLETIITNREALHTVVNNVRQVVDREVEQLMRNLVEGRNFKFRDGLGEANHAMSLTLDPYACGPCPLLQLLGRRSNLAVYQDLALSQCHGVFAGQSVEGRNFRNQFQPVLRRRVMDMFNNGFLSAKTLTVALSEGAAICAPSLTAGQTAPAESSFEGDVARVTLGFPKELRVKSRVLFAGASANASEAAKARVASLQSAYQKPDKRVDILLGPLGFLLKQFHAAIFPNGKPPGSNQPNPQWFWTALQRNQLPARLLSREDIETIAFIKKFSLDYGAINFINLAPNNVSELAMYYMANQILRYCDHSTYFINTLTAIIAGSRRPPSVQAAAAWSAQGGAGLEAGARALMDAVDAHPGAWTSMFASCNLLRPVMAARPMVVLGLSISKYYGMAGNDRVFQAGNWASLMGGKNACPLLIFDRTRKFVLACPRAGFVCAASNLGGGAHESSLCEQLRGIISEGGAAVASSVFVATVKSLGPRTQQLQIEDWLALLEDEYLSEEMMELTARALERGNGEWSTDAALEVAHEAEALVSQLG

来源 Source

来源生物 organism	Human alphaherpesvirus 1
通用名 common_name	Herpes simplex virus type 1
NCBI 分类编号 ncbi_taxonomy_id	10298
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 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	104

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7. 引用文献 (1)

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晶胞边长 a length_a	90.348 Å
晶胞边长 b length_b	139.779 Å
晶胞边长 c length_c	98.869 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	111.09 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	2.750 Å
最低分辨率 resolution_low	92.417 Å
R 因子 r_factor	—
R_work r_work	0.1771
R_free r_free	0.2609

fit	/app/data/saxs_computation/pi/9pi6/9pi6.fit
pddf	/app/data/pr_computation/pi/9pi6/9pi6.pr.out
profile	/app/data/saxs_computation/pi/9pi6/9pi6.dat

Single stranded DNA-binding protein (ICP8) from Herpes simplex virus-1, apo form.Mutations: K166A, E167A, C254S, C455S

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