SAXSdb — 1xns

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1xns
沉积日期 deposition_date	2004-10-05
结构标题 title	Peptide trapped Holliday junction intermediate in Cre-loxP recombination
关键词 keywords	CRE Recombinase, holliday junction, recombination, complex (recombinase-DNA), peptide inhibitor, Hydrolase, Ligase-DNA COMPLEX; Hydrolase, Ligase/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	33.10 Å
回转半径 Rg (电子) rg_electron	31.97 Å
零角强度 I(0) i0	191922000.00
分子量 molecular_weight	94004.0 kDa
排除体积 excluded_volume	110900 Å³
包络体积 envelope_volume	157270 Å³
水化壳体积 shell_volume	41206 Å³
包络直径 envelope_diameter	126.6 Å
壳层 Rg shell_rg	38.35 Å
包络 Rg envelope_rg	32.33 Å
形状 Rg shape_rg	31.92 Å
总 Rg total_rg	32.57 Å
总原子数 total_atoms	6511
残基数 n_residues	713
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	118.2 Å
Rg (实空间) rg_real	33.10 Å
Rg 误差 (实空间) rg_real_error	1.22 Å
I(0) (实空间) i0_real	1.9190e+08
I(0) 误差 (实空间) i0_real_error	3.2010e+06
Rg (倒空间) rg_reciprocal	33.10 Å
I(0) (倒空间) i0_reciprocal	191900000.0000
解质量估计 total_estimate	0.8599
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	36.9 Å
偏度 Skewness skewness	0.338
峰度 Kurtosis kurtosis	-0.292
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	32030000.0000
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: 0.764; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.936; Smooth: 0.946

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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	loxP DNA
分子量 formula_weight	10775.0 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	C
原子数 atom_count	6807

TATAACTTCGTATAATGTATGCTATACGAAGTTAT

Entity 2 polymer

描述 description	loxP DNA
分子量 formula_weight	10439.8 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	D

ATAACTTCGTATAGCATACATTATACGAAGTTAT

Entity 3 polymer

描述 description	Recombinase CRE
分子量 formula_weight	36577.8 kDa
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

SDEVRKNLMDMFRDRQAFSEHTWKMLLSVCRSWAAWCKLNNRKWFPAEPEDVRDYLLYLQARGLAVKTIQQHLGQLNMLHRRSGLPRPSDSNAVSLVMRRIRKENVDAGERAKQALAFERTDFDQVRSLMENSDRCQDIRNLAFLGIAYNTLLRIAEIARIRVKDISRTDGGRMLIHIGRTKTLVSTAGVEKALSLGVTKLVERWISVSGVADDPNNYLFCRVRKNGVAAPSATSQLSTRALEGIFEATHRLIYGAKDDSGQRYLAWSGHSARVGAARDMARAGVSIPEIMQAGGWTNVNIVMNYIRNLDSETGAMVRLLEDGD

来源 Source

来源生物 organism	Enterobacteria phage P1
NCBI 分类编号 ncbi_taxonomy_id	10678
宿主生物 host_organism	Escherichia coli BL21(DE3)

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	296

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1xnsa1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.60 — SAM domain-like
超家族 Superfamily superfamily	a.60.9 — lambda integrase-like, N-terminal domain
家族 Family family	a.60.9.1 — lambda integrase-like, N-terminal domain

结构域编号 domain_id	d1xnsa2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.163 — DNA breaking-rejoining enzymes
超家族 Superfamily superfamily	d.163.1 — DNA breaking-rejoining enzymes
家族 Family family	d.163.1.1 — Lambda integrase-like, catalytic core

结构域编号 domain_id	d1xnsb1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.60 — SAM domain-like
超家族 Superfamily superfamily	a.60.9 — lambda integrase-like, N-terminal domain
家族 Family family	a.60.9.1 — lambda integrase-like, N-terminal domain

结构域编号 domain_id	d1xnsb2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.163 — DNA breaking-rejoining enzymes
超家族 Superfamily superfamily	d.163.1 — DNA breaking-rejoining enzymes
家族 Family family	d.163.1.1 — Lambda integrase-like, catalytic core

CATH v4.4 (4 domains)

结构域编号 domain_id	1xnsA01
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	130 — Tyrosine recombinase, N-terminal domain

结构域编号 domain_id	1xnsA02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	443 — hpI Integrase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Intergrase catalytic core

结构域编号 domain_id	1xnsB01
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	130 — Tyrosine recombinase, N-terminal domain

结构域编号 domain_id	1xnsB02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	443 — hpI Integrase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Intergrase catalytic core

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7. 引用文献 (1)

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晶胞边长 a length_a	106.078 Å
晶胞边长 b length_b	121.529 Å
晶胞边长 c length_c	177.799 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	C 2 2 21
空间群编号 int_tables_number	20
晶系 crystal_system	—

分辨率 resolution	2.800 Å
最低分辨率 resolution_low	47.670 Å
R 因子 r_factor	0.1996
R_work r_work	0.1963
R_free r_free	0.2654

fit	/app/data/saxs_computation/xn/1xns/1xns.fit
pddf	/app/data/pr_computation/xn/1xns/1xns.pr.out
profile	/app/data/saxs_computation/xn/1xns/1xns.dat

Peptide trapped Holliday junction intermediate in Cre-loxP recombination

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 water

6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)