8tip

;Isoreticular, interpenetrating co-crystal of Replication Initiator Protein REPE54 and symmetrical expanded duplex (31mer) containing the cognate REPE54 sequence and an additional G-C rich sequence with blunt ends and 5' terminal phosphates. ;

Method: X-RAY DIFFRACTION D_max: 102.8 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	8tip
沉积日期 deposition_date	2023-07-20
结构标题 title	;Isoreticular, interpenetrating co-crystal of Replication Initiator Protein REPE54 and symmetrical expanded duplex (31mer) containing the cognate REPE54 sequence and an additional G-C rich sequence with blunt ends and 5' terminal phosphates. ;
关键词 keywords	Replication Initiator RepE Complex Co-Crystal, DNA BINDING PROTEIN-DNA complex, DNA BINDING PROTEIN; DNA BINDING PROTEIN/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	27.65 Å
回转半径 Rg (电子) rg_electron	25.97 Å
零角强度 I(0) i0	53393300.00
分子量 molecular_weight	44611.0 kDa
排除体积 excluded_volume	50420 Å³
包络体积 envelope_volume	69632 Å³
水化壳体积 shell_volume	24222 Å³
包络直径 envelope_diameter	104.4 Å
壳层 Rg shell_rg	30.43 Å
包络 Rg envelope_rg	26.60 Å
形状 Rg shape_rg	25.80 Å
总 Rg total_rg	26.73 Å
总原子数 total_atoms	3061
残基数 n_residues	279
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	102.8 Å
Rg (实空间) rg_real	27.99 Å
Rg 误差 (实空间) rg_real_error	1.08 Å
I(0) (实空间) i0_real	5.3390e+07
I(0) 误差 (实空间) i0_real_error	8.3400e+05
Rg (倒空间) rg_reciprocal	27.88 Å
I(0) (倒空间) i0_reciprocal	53390000.0000
解质量估计 total_estimate	0.5954
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	30.7 Å
偏度 Skewness skewness	0.648
峰度 Kurtosis kurtosis	0.225
角度范围 angular_range	— – 0.2850 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	3538000.0000
实空间数据点数 n_real_points	58
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.666; Stabil: 1.000; Sysdev: 0.075; Positv: 1.000; Valcen: 0.668; Smooth: 0.845

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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	;DNA (5'-D(ACPCPCPGPGPAPCPCPTPGPTPGPAPCPAPAPAPTPTPGPCPCPCPTPCPAPGPAPCPGP*G)-3')\| ;
分子量 formula_weight	9796.3 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	A
原子数 atom_count	3128

ACCCGGACCTGTGACAAATTGCCCTCAGACGG

Entity 2 polymer

描述 description	;DNA (5'-D(ACPCPGPTPCPTPGPAPGPGPGPCPAPAPTPTPTPGPTPCPAPCPAPGPGPTPCPCPGPGP*G)-3') ;
分子量 formula_weight	9898.4 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

ACCGTCTGAGGGCAATTTGTCACAGGTCCGGG

Entity 3 polymer

描述 description	Replication initiation protein
分子量 formula_weight	30749.1 kDa
突变 mutation	R118P
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	C

MRGSHHHHHHGSMAETAVINHKKRKNSPRIVQSNDLTEAAYSLSRDQKRMLYLFVDQIRKSDGTLQEHDGICEIHVAKYAEIFGLTSAEASKDIRQALKSFAGKEVVFYRPEEDAGDEKGYESFPWFIKPAHSPSRGLYSVHINPYLIPFFIGLQNRFTQFRLSETKEITNPYAMRLYESLCQYRKPDGSGIVSLKIDWIIERYQLPQSYQRMPDFRRRFLQVCVNEINSRTPMRLSYIEKKKGRQTTHIVFSFRDITSMTTG

来源 Source

来源生物 organism	Escherichia coli K-12
NCBI 分类编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	Escherichia coli

Entity 4 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	5

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	16

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7. 引用文献 (3)

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晶胞边长 a length_a	74.850 Å
晶胞边长 b length_b	132.913 Å
晶胞边长 c length_c	136.374 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	I 2 2 2
空间群编号 int_tables_number	23
晶系 crystal_system	orthorhombic

分辨率 resolution	2.790 Å
最低分辨率 resolution_low	38.850 Å
R 因子 r_factor	0.1974
R_work r_work	0.1925
R_free r_free	0.2400

fit	/app/data/saxs_computation/ti/8tip/8tip.fit
pddf	/app/data/pr_computation/ti/8tip/8tip.pr.out
profile	/app/data/saxs_computation/ti/8tip/8tip.dat

;Isoreticular, interpenetrating co-crystal of Replication Initiator Protein REPE54 and symmetrical expanded duplex (31mer) containing the cognate REPE54 sequence and an additional G-C rich sequence with blunt ends and 5' terminal phosphates. ;

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 (5)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

来源 Source

Entity 4 non-polymer

Entity 5 water

7. 引用文献 (3)

8. 文件与曲线 (10)

Files (7)

Curves (3)