1flo

FLP Recombinase-Holliday Junction Complex I

Method: X-RAY DIFFRACTION D_max: 125.3 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	1flo
沉积日期 deposition_date	2000-08-14
结构标题 title	FLP Recombinase-Holliday Junction Complex I
关键词 keywords	Tyrosine recombinase, protein-DNA complex, Holliday-junction, domain-swapping, ligase, lyase-DNA COMPLEX; ligase, lyase/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	40.79 Å
回转半径 Rg (电子) rg_electron	40.20 Å
零角强度 I(0) i0	888773000.00
分子量 molecular_weight	227280.0 kDa
排除体积 excluded_volume	276920 Å³
包络体积 envelope_volume	388720 Å³
水化壳体积 shell_volume	77033 Å³
包络直径 envelope_diameter	126.6 Å
壳层 Rg shell_rg	48.84 Å
包络 Rg envelope_rg	39.02 Å
形状 Rg shape_rg	40.21 Å
总 Rg total_rg	40.60 Å
总原子数 total_atoms	15871
残基数 n_residues	1752
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	125.3 Å
Rg (实空间) rg_real	40.54 Å
Rg 误差 (实空间) rg_real_error	0.90 Å
I(0) (实空间) i0_real	8.8880e+08
I(0) 误差 (实空间) i0_real_error	1.5740e+07
Rg (倒空间) rg_reciprocal	40.79 Å
I(0) (倒空间) i0_reciprocal	889000000.0000
解质量估计 total_estimate	0.8233
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	54.6 Å
偏度 Skewness skewness	0.028
峰度 Kurtosis kurtosis	-0.532
角度范围 angular_range	— – 0.1950 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	133500000.0000
实空间数据点数 n_real_points	40
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.909; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.972; Smooth: 0.000

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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	SYMMETRIZED FRT DNA SITES
分子量 formula_weight	3916.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	E,G,I,K
原子数 atom_count	16064

TAAGTTCCTATTC

Entity 2 polymer

描述 description	SYMMETRIZED FRT DNA SITES
分子量 formula_weight	6165.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	F,H,J,L

TTTAAAAGAATAGGAACTTC

Entity 3 polymer

描述 description	FLP RECOMBINASE
分子量 formula_weight	48611.7 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D

PQFDILCKTPPKVLVRQFVERFERPSGEKIALCAAELTYLCWMITHNGTAIKRATFMSYNTIISNSLSFDIVNKSLQFKYKTQKATILEASLKKLIPAWEFTIIPYYGQKHQSDITDIVSSLQLQFESSEEADKGNSHSKKMLKALLSEGESIWEITEKILNSFEYTSRFTKTKTLYQFLFLATFINCGRFSDIKNVDPKSFKLVQNKYLGVIIQCLVTETKTSVSRHIYFFSARGRIDPLVYLDEFLRNSEPVLKRVNRTGNSSSNKQEYQLLKDNLVRSYNKALKKNAPYSIFAIKNGPKSHIGRHLMTSFLSMKGLTELTNVVGNWSDKRASAVARTTYTHQITAIPDHYFALVSRYYAYDPISKEMIALKDETNPIEEWQHIEQLKGSAEGSIRYPAWNGIISQEVLDYLSSYINRRI

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI 分类编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Entity 4 non-polymer

描述 description	PHOSPHONIC ACID
分子量 formula_weight	82.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

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	193

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6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1floa1
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	d1floa2
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	d1flob1
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	d1flob2
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	d1floc1
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	d1floc2
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	d1flod1
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	d1flod2
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 (8 domains)

结构域编号 domain_id	1floA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	300 — GMP Synthetase; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	80 — FLP Recombinase, lambda integrase-like, N-terminal domain (domain 1)

结构域编号 domain_id	1floA02
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	1floB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	300 — GMP Synthetase; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	80 — FLP Recombinase, lambda integrase-like, N-terminal domain (domain 1)

结构域编号 domain_id	1floB02
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	1floC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	300 — GMP Synthetase; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	80 — FLP Recombinase, lambda integrase-like, N-terminal domain (domain 1)

结构域编号 domain_id	1floC02
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	1floD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	300 — GMP Synthetase; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	80 — FLP Recombinase, lambda integrase-like, N-terminal domain (domain 1)

结构域编号 domain_id	1floD02
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	81.480 Å
晶胞边长 b length_b	180.180 Å
晶胞边长 c length_c	98.600 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	97.02 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	2.650 Å
最低分辨率 resolution_low	15.000 Å
R 因子 r_factor	0.2540
R_work r_work	0.2490
R_free r_free	0.2970

fit	/app/data/saxs_computation/fl/1flo/1flo.fit
pddf	/app/data/pr_computation/fl/1flo/1flo.pr.out
profile	/app/data/saxs_computation/fl/1flo/1flo.dat

FLP Recombinase-Holliday Junction Complex I

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

6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)