1zxn

Human DNA topoisomerase IIa ATPase/ADP

Method: X-RAY DIFFRACTION D_max: 162.1 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	1zxn
沉积日期 deposition_date	2005-06-08
结构标题 title	Human DNA topoisomerase IIa ATPase/ADP
关键词 keywords	GHKL nucleotide-binding fold, ISOMERASE; ISOMERASE
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	47.81 Å
回转半径 Rg (电子) rg_electron	48.14 Å
零角强度 I(0) i0	391422000.00
分子量 molecular_weight	162240.0 kDa
排除体积 excluded_volume	202030 Å³
包络体积 envelope_volume	288310 Å³
水化壳体积 shell_volume	51422 Å³
包络直径 envelope_diameter	165.9 Å
壳层 Rg shell_rg	50.07 Å
包络 Rg envelope_rg	46.91 Å
形状 Rg shape_rg	48.16 Å
总 Rg total_rg	48.18 Å
总原子数 total_atoms	11408
残基数 n_residues	1500
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	162.1 Å
Rg (实空间) rg_real	48.22 Å
Rg 误差 (实空间) rg_real_error	1.95 Å
I(0) (实空间) i0_real	3.9140e+08
I(0) 误差 (实空间) i0_real_error	7.3220e+06
Rg (倒空间) rg_reciprocal	47.82 Å
I(0) (倒空间) i0_reciprocal	391200000.0000
解质量估计 total_estimate	0.7959
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	39.3 Å
偏度 Skewness skewness	0.353
峰度 Kurtosis kurtosis	-0.793
角度范围 angular_range	— – 0.1650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	28080000.0000
实空间数据点数 n_real_points	34
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.634; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.762; Smooth: 0.677

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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 (6)

Entity 1 polymer

描述 description	DNA topoisomerase II, alpha isozyme
分子量 formula_weight	45660.5 kDa
EC 编号 ec_number	5.99.1.3
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
原子数 atom_count	11646

SVERIYQKKTQLEHILLRPDTYIGSVELVTQQMWVYDEDVGINYREVTFVPGLYKIFDEILVNAADNKQRDPKMSCIRVTIDPENNLISIWNNGKGIPVVEHKVEKMYVPALIFGQLLTSSNYDDDEKKVTGGRNGYGAKLCNIFSTKFTVETASREYKKMFKQTWMDNMGRAGEMELKPFNGEDYTCITFQPDLSKFKMQSLDKDIVALMVRRAYDIAGSTKDVKVFLNGNKLPVKGFRSYVDMYLKDKLDETGNSLKVIHEQVNHRWEVCLTMSEKGFQQISFVNSIATSKGGRHVDYVADQIVTKLVDVVKKKNKGGVAVKAHQVKNHMWIFVNALIENPTFDSQTKENMTLQPKSFGSTCQLSEKFIKAAIGCGIVESILNWVKFKAQVQLNKKCS

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 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	4

Entity 3 non-polymer

描述 description	ADENOSINE-5'-DIPHOSPHATE
分子量 formula_weight	427.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 4 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 6 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	238

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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	d1zxna1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.122 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
超家族 Superfamily superfamily	d.122.1 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
家族 Family family	d.122.1.0 — automated matches

结构域编号 domain_id	d1zxna2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.14 — Ribosomal protein S5 domain 2-like
超家族 Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
家族 Family family	d.14.1.0 — automated matches

结构域编号 domain_id	d1zxnb1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.122 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
超家族 Superfamily superfamily	d.122.1 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
家族 Family family	d.122.1.0 — automated matches

结构域编号 domain_id	d1zxnb2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.14 — Ribosomal protein S5 domain 2-like
超家族 Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
家族 Family family	d.14.1.0 — automated matches

结构域编号 domain_id	d1zxnc1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.122 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
超家族 Superfamily superfamily	d.122.1 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
家族 Family family	d.122.1.0 — automated matches

结构域编号 domain_id	d1zxnc2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.14 — Ribosomal protein S5 domain 2-like
超家族 Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
家族 Family family	d.14.1.0 — automated matches

结构域编号 domain_id	d1zxnd1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.122 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
超家族 Superfamily superfamily	d.122.1 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
家族 Family family	d.122.1.0 — automated matches

结构域编号 domain_id	d1zxnd2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.14 — Ribosomal protein S5 domain 2-like
超家族 Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
家族 Family family	d.14.1.0 — automated matches

CATH v4.4 (8 domains)

结构域编号 domain_id	1zxnA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	565 — Heat Shock Protein 90
同源超家族 H-superfamily homologous superfamily	10 — Histidine kinase-like ATPase, C-terminal domain

结构域编号 domain_id	1zxnA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	230 — Ribosomal Protein S5; domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1zxnB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	565 — Heat Shock Protein 90
同源超家族 H-superfamily homologous superfamily	10 — Histidine kinase-like ATPase, C-terminal domain

结构域编号 domain_id	1zxnB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	230 — Ribosomal Protein S5; domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1zxnC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	565 — Heat Shock Protein 90
同源超家族 H-superfamily homologous superfamily	10 — Histidine kinase-like ATPase, C-terminal domain

结构域编号 domain_id	1zxnC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	230 — Ribosomal Protein S5; domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1zxnD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	565 — Heat Shock Protein 90
同源超家族 H-superfamily homologous superfamily	10 — Histidine kinase-like ATPase, C-terminal domain

结构域编号 domain_id	1zxnD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	230 — Ribosomal Protein S5; domain 2
同源超家族 H-superfamily homologous superfamily	10 —

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7. 引用文献 (1)

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晶胞边长 a length_a	71.015 Å
晶胞边长 b length_b	90.492 Å
晶胞边长 c length_c	148.293 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	89.97 °
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	2.510 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	0.2350
R_work r_work	0.2350
R_free r_free	0.2810

fit	/app/data/saxs_computation/zx/1zxn/1zxn.fit
pddf	/app/data/pr_computation/zx/1zxn/1zxn.pr.out
profile	/app/data/saxs_computation/zx/1zxn/1zxn.dat