SAXSdb — 1urj

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1urj
沉积日期 deposition_date	2003-10-30
结构标题 title	Single stranded DNA-binding protein(ICP8) from Herpes simplex virus-1
关键词 keywords	DNA-BINDING PROTEIN, SSB, ICP8, HSV-1, DNA-BINDING, DNA REPLICATION, ZINC-FINGER, NUCLEAR PROTEIN., 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	42.61 Å
回转半径 Rg (电子) rg_electron	42.01 Å
零角强度 I(0) i0	768772000.00
分子量 molecular_weight	224710.0 kDa
排除体积 excluded_volume	279250 Å³
包络体积 envelope_volume	374720 Å³
水化壳体积 shell_volume	72296 Å³
包络直径 envelope_diameter	144.5 Å
壳层 Rg shell_rg	48.84 Å
包络 Rg envelope_rg	41.61 Å
形状 Rg shape_rg	42.05 Å
总 Rg total_rg	42.17 Å
总原子数 total_atoms	15703
残基数 n_residues	2060
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	139.5 Å
Rg (实空间) rg_real	42.54 Å
Rg 误差 (实空间) rg_real_error	1.57 Å
I(0) (实空间) i0_real	7.6880e+08
I(0) 误差 (实空间) i0_real_error	1.4790e+07
Rg (倒空间) rg_reciprocal	42.61 Å
I(0) (倒空间) i0_reciprocal	768800000.0000
解质量估计 total_estimate	0.8809
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	52.8 Å
偏度 Skewness skewness	0.311
峰度 Kurtosis kurtosis	-0.297
角度范围 angular_range	— – 0.1850 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	96300000.0000
实空间数据点数 n_real_points	38
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.878; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.824

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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 (4)

Entity 1 polymer

描述 description	MAJOR DNA-BINDING PROTEIN
分子量 formula_weight	122267.8 kDa
突变 mutation	YES
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	15798

METKPKTATTIKVPPGPLGYVYARACPSEGIELLALLSARSGDSDVAVAPLVVGLTVESGFEANVAVVVGSRTTGLGGTAVSLKLTPSHYSSSVYVFHGGRHLDPSTQAPNLTRLCERARRHFGFSDYTPRPGDLKHETTGEALCERLGLDPDRALLYLVVTEGFKEAVCINNTFLHLGGSDKVTIGGAEVHRIPVYPLQLFMPDFSRVIAEPFNANHRSIGEKFTYPLPFFNRPLNRLLFEAVVGPAAVALRSRNVDAVARAAAHLAFDENHEGAALPADITFTAFEASQGKTPRGGRDGGGKGAAGGFEQRLASVMAGDAALALESIVSMAVFDEPPTDISAWPLFEGQDTAAARANAVGAYLARAAGLVGAMVFSTNSALHLTEVDDAGPADPKDHSKPSFYRFFLVPGTHVAANPQVDREGHVVPGFEGRPTAPLVGGTQEFAGEHLAMLSGFSPALLAKMLFYLERCDGAVIVGRQEMDVFRYVADSNQTDVPCNLCTFDTRHACVHTTLMRLRARHPKFASAARGAIGVFGTMNSMYSDCDVLGNYAAFSALKRADGSETARTIMQETYRAATERVMAELETLQYVDQAVPTAMGRLETIITNREALHTVVNNVRQVVDREVEQLMRNLVEGRNFKFRDGLGEANHAMSLTLDPYACGPCPLLQLLGRRSNLAVYQDLALSQCHGVFAGQSVEGRNFRNQFQPVLRRRVMDMFNNGFLSAKTLTVALSEGAAICAPSLTAGQTAPAESSFEGDVARVTLGFPKELRVKSRVLFAGASANASEAAKARVASLQSAYQKPDKRVDILLGPLGFLLKQFHAAIFPNGKPPGSNQPNPQWFWTALQRNQLPARLLSREDIETIAFIKKFSLDYGAINFINLAPNNVSELAMYYMANQILRYCDHSTYFINTLTAIIAGSRRPPSVQAAAAWSAQGGAGLEAGARALMDAVDAHPGAWTSMFASCNLLRPVMAARPMVVLGLSISKYYGMAGNDRVFQAGNWASLMGGKNACPLLIFDRTRKFVLACPRAGFVCAASSLGGGAHESSLCEQLRGIISEGGAAVASSVFVATVKSLGPRTQQLQIEDWLALLEDEYLSEEMMELTARALERGNGEWSTDAALEVAHEAEALVSQLG

来源 Source

来源生物 organism	HUMAN HERPESVIRUS 1
通用名 common_name	HERPES VIRUS
NCBI 分类编号 ncbi_taxonomy_id	10298
宿主生物 host_organism	Trichoplusia ni

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	MERCURY (II) ION
分子量 formula_weight	200.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

Entity 4 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	95

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6. 折叠分类 (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1urja_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.58 — Viral ssDNA binding protein
超家族 Superfamily superfamily	e.58.1 — Viral ssDNA binding protein
家族 Family family	e.58.1.1 — Viral ssDNA binding protein

结构域编号 domain_id	d1urjb_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.58 — Viral ssDNA binding protein
超家族 Superfamily superfamily	e.58.1 — Viral ssDNA binding protein
家族 Family family	e.58.1.1 — Viral ssDNA binding protein

CATH v4.4 (4 domains)

结构域编号 domain_id	1urjA02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	190 — Delta-Endotoxin; domain 1
同源超家族 H-superfamily homologous superfamily	40 — Viral ssDNA binding protein, head domain

结构域编号 domain_id	1urjA03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	150 — DNA polymerase; domain 1
同源超家族 H-superfamily homologous superfamily	560 —

结构域编号 domain_id	1urjB02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	190 — Delta-Endotoxin; domain 1
同源超家族 H-superfamily homologous superfamily	40 — Viral ssDNA binding protein, head domain

结构域编号 domain_id	1urjB03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	150 — DNA polymerase; domain 1
同源超家族 H-superfamily homologous superfamily	560 —

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7. 引用文献 (1)

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晶胞边长 a length_a	100.910 Å
晶胞边长 b length_b	145.370 Å
晶胞边长 c length_c	162.030 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	8

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	3.000 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.2350
R_work r_work	0.2350
R_free r_free	0.2857

fit	/app/data/saxs_computation/ur/1urj/1urj.fit
pddf	/app/data/pr_computation/ur/1urj/1urj.pr.out
profile	/app/data/saxs_computation/ur/1urj/1urj.dat

Single stranded DNA-binding protein(ICP8) from Herpes simplex virus-1

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