9ncr

;Isoreticular, Porous co-crystal of Replication Initiator Protein REPE54 and symmetrical expanded duplex (31mer) containing the cognate REPE54 sequence and additional G/C rich expansion sequence ;

Method: X-RAY DIFFRACTION D_max: 105.1 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	9ncr
沉积日期 deposition_date	2025-02-17
最后修订 last_revision	2026-02-18
结构标题 title	;Isoreticular, Porous co-crystal of Replication Initiator Protein REPE54 and symmetrical expanded duplex (31mer) containing the cognate REPE54 sequence and additional G/C rich expansion sequence ;
关键词 keywords	DNA, Protein, DNA Binding Protein, DNA BINDING PROTEIN-DNA complex; 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	27.29 Å
回转半径 Rg (电子) rg_electron	25.71 Å
零角强度 I(0) i0	51875700.00
分子量 molecular_weight	44031.0 kDa
排除体积 excluded_volume	49779 Å³
包络体积 envelope_volume	66995 Å³
水化壳体积 shell_volume	23696 Å³
包络直径 envelope_diameter	109.8 Å
壳层 Rg shell_rg	30.02 Å
包络 Rg envelope_rg	26.23 Å
形状 Rg shape_rg	25.58 Å
总 Rg total_rg	26.37 Å
总原子数 total_atoms	3026
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	105.1 Å
Rg (实空间) rg_real	27.62 Å
Rg 误差 (实空间) rg_real_error	1.09 Å
I(0) (实空间) i0_real	5.1880e+07
I(0) 误差 (实空间) i0_real_error	8.0530e+05
Rg (倒空间) rg_reciprocal	27.52 Å
I(0) (倒空间) i0_reciprocal	51870000.0000
解质量估计 total_estimate	0.7965
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	29.0 Å
偏度 Skewness skewness	0.666
峰度 Kurtosis kurtosis	0.304
角度范围 angular_range	— – 0.2900 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	3523000.0000
实空间数据点数 n_real_points	59
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.589; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.630; Smooth: 0.953

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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	DNA (31-MER)
分子量 formula_weight	9459.1 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	3060

GCCGGACCTGTGACAAATTGCCCTCAGCCCG

Entity 2 polymer

描述 description	DNA (31-MER)
分子量 formula_weight	9610.2 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

CCGGGCTGAGGGCAATTTGTCACAGGTCCGG

Entity 3 polymer

描述 description	Replication initiation protein
分子量 formula_weight	30749.1 kDa
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
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

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	2

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7. 引用文献 (1)

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晶胞边长 a length_a	76.032 Å
晶胞边长 b length_b	124.855 Å
晶胞边长 c length_c	139.093 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	91.85 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	I 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	monoclinic

分辨率 resolution	3.240 Å
最低分辨率 resolution_low	34.760 Å
R 因子 r_factor	0.2214
R_work r_work	0.2203
R_free r_free	0.2310

fit	/app/data/saxs_computation/nc/9ncr/9ncr.fit
pddf	/app/data/pr_computation/nc/9ncr/9ncr.pr.out
profile	/app/data/saxs_computation/nc/9ncr/9ncr.dat

;Isoreticular, Porous co-crystal of Replication Initiator Protein REPE54 and symmetrical expanded duplex (31mer) containing the cognate REPE54 sequence and additional G/C rich expansion sequence ;

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 (4)

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

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)