SAXSdb — 1kbu

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1kbu
沉积日期 deposition_date	2001-11-06
结构标题 title	CRE RECOMBINASE BOUND TO A LOXP HOLLIDAY JUNCTION
关键词 keywords	;SITE-SPECIFIC RECOMBINASE, HOLLIDAY JUNCTION COMPLEX, DNA-PROTEIN CO-CRYSTAL, INT RECOMBINASE MECHANISM, 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	33.53 Å
回转半径 Rg (电子) rg_electron	32.36 Å
零角强度 I(0) i0	184862000.00
分子量 molecular_weight	92858.0 kDa
排除体积 excluded_volume	109800 Å³
包络体积 envelope_volume	155810 Å³
水化壳体积 shell_volume	40439 Å³
包络直径 envelope_diameter	129.0 Å
壳层 Rg shell_rg	38.64 Å
包络 Rg envelope_rg	32.79 Å
形状 Rg shape_rg	32.31 Å
总 Rg total_rg	32.93 Å
总原子数 total_atoms	6436
残基数 n_residues	709
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	121.0 Å
Rg (实空间) rg_real	33.57 Å
Rg 误差 (实空间) rg_real_error	1.13 Å
I(0) (实空间) i0_real	1.8490e+08
I(0) 误差 (实空间) i0_real_error	3.0990e+06
Rg (倒空间) rg_reciprocal	33.55 Å
I(0) (倒空间) i0_reciprocal	184900000.0000
解质量估计 total_estimate	0.8512
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	41.2 Å
偏度 Skewness skewness	0.388
峰度 Kurtosis kurtosis	-0.152
角度范围 angular_range	— – 0.2350 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	28750000.0000
实空间数据点数 n_real_points	48
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.747; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.872; Smooth: 0.948

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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
分子量 formula_weight	10510.8 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	C
原子数 atom_count	6837

ATAAGTTCGTATAATGTATGCTATACGAAGTTAT

Entity 2 polymer

描述 description	LOXP
分子量 formula_weight	10399.8 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

ATAACTTCGTATAGCATACATTATACGAACTTAT

Entity 3 polymer

描述 description	CRE RECOMBINASE
分子量 formula_weight	39424.0 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

MHHHHHHSNLLTVHQNLPALPVDATSDEVRKNLMDMFRDRQAFSEHTWKMLLSVCRSWAAWCKLNNRKWFPAEPEDVRDYLLYLQARGLAVKTIQQHLGQLNMLHRRSGLPRPSDSNAVSLVMRRIRKENVDAGERAKQALAFERTDFDQVRSLMENSDRCQDIRNLAFLGIAYNTLLRIAEIARIRVKDISRTDGGRMLIHIGRTKTLVSTAGVEKALSLGVTKLVERWISVSGVADDPNNYLFCRVRKNGVAAPSATSQLSTRALEGIFEATHRLIYGAKDDSGQRYLAWSGHSARVGAARDMARAGVSIPEIMQAGGWTNVNIVMNYIRNLDSETGAMVRLLEDGD

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	237

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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	d1kbua1
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	d1kbua2
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	d1kbub1
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	d1kbub2
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	1kbuA01
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	1kbuA02
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	1kbuB01
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	1kbuB02
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

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7. 引用文献 (3)

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晶胞边长 a length_a	107.170 Å
晶胞边长 b length_b	121.600 Å
晶胞边长 c length_c	179.310 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	2.200 Å
最低分辨率 resolution_low	5.000 Å
R 因子 r_factor	0.2310
R_work r_work	0.2310
R_free r_free	0.2790

fit	/app/data/saxs_computation/kb/1kbu/1kbu.fit
pddf	/app/data/pr_computation/kb/1kbu/1kbu.pr.out
profile	/app/data/saxs_computation/kb/1kbu/1kbu.dat

CRE RECOMBINASE BOUND TO A LOXP HOLLIDAY JUNCTION

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 (3)

8. 文件与曲线 (10)

Files (7)

Curves (3)