2c5r

The structure of phage phi29 replication organizer protein p16.7 in complex with double stranded DNA

Method: X-RAY DIFFRACTION D_max: 82.9 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	2c5r
沉积日期 deposition_date	2005-10-31
结构标题 title	The structure of phage phi29 replication organizer protein p16.7 in complex with double stranded DNA
关键词 keywords	DNA-BINDING PROTEIN-DNA COMPLEX, DNA-BINDING PROTEIN, COMPLEX (DNA-BINDING PROTEIN-DNA); 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	24.66 Å
回转半径 Rg (电子) rg_electron	23.68 Å
零角强度 I(0) i0	48468900.00
分子量 molecular_weight	49766.0 kDa
排除体积 excluded_volume	60685 Å³
包络体积 envelope_volume	78606 Å³
水化壳体积 shell_volume	27505 Å³
包络直径 envelope_diameter	82.9 Å
壳层 Rg shell_rg	30.93 Å
包络 Rg envelope_rg	23.83 Å
形状 Rg shape_rg	23.66 Å
总 Rg total_rg	24.59 Å
总原子数 total_atoms	3484
残基数 n_residues	400
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	82.9 Å
Rg (实空间) rg_real	24.53 Å
Rg 误差 (实空间) rg_real_error	0.44 Å
I(0) (实空间) i0_real	4.8470e+07
I(0) 误差 (实空间) i0_real_error	7.2800e+05
Rg (倒空间) rg_reciprocal	24.56 Å
I(0) (倒空间) i0_reciprocal	48470000.0000
解质量估计 total_estimate	0.8752
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	31.6 Å
偏度 Skewness skewness	0.224
峰度 Kurtosis kurtosis	-0.281
角度范围 angular_range	— – 0.3200 Å⁻¹
当前正则化参数 α current_alpha	0.0002
最高正则化参数 α highest_alpha	7864000.0000
实空间数据点数 n_real_points	64
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.793; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.995

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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	EARLY PROTEIN P16.7
分子量 formula_weight	7938.0 kDa
来源方法 src_method	man
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F
原子数 atom_count	3535

KTVNLSACEVAVLDLYEQSNIRIPSDIIEDLVNQRLQSEQEVLNYIETQRTYWKLENQKKLYRGSLK

来源 Source

来源生物 organism	BACILLUS PHAGE PHI29
NCBI 分类编号 ncbi_taxonomy_id	10756
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 polymer

描述 description	5'-D(TPCPCPAPCPCPGPGP)-3'
分子量 formula_weight	2387.6 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	Y

TCCACCGG

Entity 3 polymer

描述 description	5'-D(CPCPGPGPTPGPGPAP)-3'
分子量 formula_weight	2467.6 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	Z

CCGGTGGA

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	51

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6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d2c5ra1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.251 — Phage replication organizer domain
超家族 Superfamily superfamily	a.251.1 — Phage replication organizer domain
家族 Family family	a.251.1.1 — Phage replication organizer domain

结构域编号 domain_id	d2c5rb_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.251 — Phage replication organizer domain
超家族 Superfamily superfamily	a.251.1 — Phage replication organizer domain
家族 Family family	a.251.1.1 — Phage replication organizer domain

结构域编号 domain_id	d2c5rc_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.251 — Phage replication organizer domain
超家族 Superfamily superfamily	a.251.1 — Phage replication organizer domain
家族 Family family	a.251.1.1 — Phage replication organizer domain

结构域编号 domain_id	d2c5rd_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.251 — Phage replication organizer domain
超家族 Superfamily superfamily	a.251.1 — Phage replication organizer domain
家族 Family family	a.251.1.1 — Phage replication organizer domain

结构域编号 domain_id	d2c5re_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.251 — Phage replication organizer domain
超家族 Superfamily superfamily	a.251.1 — Phage replication organizer domain
家族 Family family	a.251.1.1 — Phage replication organizer domain

结构域编号 domain_id	d2c5rf_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.251 — Phage replication organizer domain
超家族 Superfamily superfamily	a.251.1 — Phage replication organizer domain
家族 Family family	a.251.1.1 — Phage replication organizer domain

CATH v4.4 (6 domains)

结构域编号 domain_id	2c5rA00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily	600 — Phage phi29 replication organiser protein p16.7-like

结构域编号 domain_id	2c5rB00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily	600 — Phage phi29 replication organiser protein p16.7-like

结构域编号 domain_id	2c5rC00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily	600 — Phage phi29 replication organiser protein p16.7-like

结构域编号 domain_id	2c5rD00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily	600 — Phage phi29 replication organiser protein p16.7-like

结构域编号 domain_id	2c5rE00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily	600 — Phage phi29 replication organiser protein p16.7-like

结构域编号 domain_id	2c5rF00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily	600 — Phage phi29 replication organiser protein p16.7-like

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7. 引用文献 (1)

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晶胞边长 a length_a	65.505 Å
晶胞边长 b length_b	72.111 Å
晶胞边长 c length_c	127.360 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	24

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	2.900 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	0.2540
R_work r_work	0.2510
R_free r_free	0.2920

fit	/app/data/saxs_computation/c5/2c5r/2c5r.fit
pddf	/app/data/pr_computation/c5/2c5r/2c5r.pr.out
profile	/app/data/saxs_computation/c5/2c5r/2c5r.dat

The structure of phage phi29 replication organizer protein p16.7 in complex with double stranded DNA

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

来源 Source

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

Entity 4 water

6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)