9ii8

Crystal structure of Staphylococcus aureus DinG protein in complex with ssDNA

Method: X-RAY DIFFRACTION D_max: 98.5 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	9ii8
沉积日期 deposition_date	2024-06-19
最后修订 last_revision	2025-06-25
结构标题 title	Crystal structure of Staphylococcus aureus DinG protein in complex with ssDNA
关键词 keywords	helicase, nuclease, HYDROLASE/DNA, HYDROLASE-DNA complex; HYDROLASE/DNA
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	33.08 Å
回转半径 Rg (电子) rg_electron	32.05 Å
零角强度 I(0) i0	163516000.00
分子量 molecular_weight	105420.0 kDa
排除体积 excluded_volume	133470 Å³
包络体积 envelope_volume	174300 Å³
水化壳体积 shell_volume	44355 Å³
包络直径 envelope_diameter	108.1 Å
壳层 Rg shell_rg	39.99 Å
包络 Rg envelope_rg	31.39 Å
形状 Rg shape_rg	32.02 Å
总 Rg total_rg	32.84 Å
总原子数 total_atoms	7432
残基数 n_residues	900
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	98.5 Å
Rg (实空间) rg_real	32.83 Å
Rg 误差 (实空间) rg_real_error	0.55 Å
I(0) (实空间) i0_real	1.6350e+08
I(0) 误差 (实空间) i0_real_error	2.2130e+06
Rg (倒空间) rg_reciprocal	32.94 Å
I(0) (倒空间) i0_reciprocal	163500000.0000
解质量估计 total_estimate	0.6925
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	47.2 Å
偏度 Skewness skewness	0.032
峰度 Kurtosis kurtosis	-0.651
角度范围 angular_range	— – 0.2400 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	47860000.0000
实空间数据点数 n_real_points	49
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.967; Stabil: 1.000; Sysdev: 0.049; Positv: 1.000; Valcen: 0.992; Smooth: 0.958

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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 (2)

Entity 1 polymer

描述 description	;DNA (5'-D(PTPTPTPT)-3') ;
分子量 formula_weight	1171.8 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	B
原子数 atom_count	7432

TTTT

Entity 2 polymer

描述 description	;3'-5' exonuclease DinG ;
分子量 formula_weight	104475.5 kDa
EC 编号 ec_number	3.1.-.-
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A

MGMATYAVVDLETTGNQLDFDDIIQIGITFVRNNQIIDTYHSMIRTNLEIPPFIQALTSIEENMLQQAPYFNQVAQEIYDKIKDCIFVAHNVDFDLNFIKKAFKDCNIQYRPKKVIDTLEIFKIAFPTDKSYQLSELAEAHGITLANAHRADEDAATTAKLMILAFEKFEKLPLDTLKQLYYLSKQLKYDLYDIFFEMVRQYDAKPLDKFYEKFEQIIYRKQVDFKKPTTNYNGSLKSLYRKAVDQLGLTYRPQQLYLAETILDQLMHSEKAMIEASLGSGKSLAYLLAALMYNIETGKHVMISTNTKLLQSQLLEKDIPAMNEALNFKINALLIKSKSDYISLGLISQILKDDTSNYEVNILKMQLLIWITETPSGDIQELNLKGGQKMYFDQKIETYVPARHDVHYYNFIKRNAQNIQIGITNHAHLIHSDVENSIYQLFDDCIVDEAHRLPDYALNQVTNELSYADIKYQLGLIGKNENEKLLKAIDQLEKQRILEKLDIAPIDIFGLKASMNEIHELNEQLFSTIFTIINDSDVYDDDIHRFHNVFTFETKDILKDLHAIIDKLNKTLEIFNGISHKTVKSLRKQLLYLKDKFKNIEQSLKAGHTSFISIKNLSQKSTIRLYVKDYAVKDVLTKQVLEKFKSLIFISGTLKFNHSFEAFKQLFNKDVHFNTFEVNTSLQSAKNTSVFIPSDVASYQYKNIDEYVASIVSYIIEYTTITSSKCLVLFTSYKMMHMVQDMLNELPEFEDYVVLTQQQNQNYKIVQQFNNFDKAILLGTSTFFEGFDFQANGIKCVMIAKLPFMNKHNAKYWLMDSEFTSTFKEYVLPDAVTRFRQGLGRLIRNENDRGIIVSFDDRLINSNYKNFFEQTLENYRQKKGDIQQFGKLLRQIQKKKK

来源 Source

来源生物 organism	Staphylococcus aureus (strain NCTC 8325 / PS 47)
NCBI 分类编号 ncbi_taxonomy_id	93061
宿主生物 host_organism	Escherichia coli

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7. 引用文献 (1)

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晶胞边长 a length_a	229.170 Å
晶胞边长 b length_b	229.170 Å
晶胞边长 c length_c	128.030 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	16

空间群 space_group	I 4 2 2
空间群编号 int_tables_number	97
晶系 crystal_system	tetragonal

分辨率 resolution	3.160 Å
最低分辨率 resolution_low	111.770 Å
R 因子 r_factor	0.2699
R_work r_work	0.2687
R_free r_free	0.2930

fit	/app/data/saxs_computation/ii/9ii8/9ii8.fit
pddf	/app/data/pr_computation/ii/9ii8/9ii8.pr.out
profile	/app/data/saxs_computation/ii/9ii8/9ii8.dat

Crystal structure of Staphylococcus aureus DinG protein in complex with ssDNA

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 (2)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

来源 Source

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)