SAXSdb — 1mu9

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1mu9
沉积日期 deposition_date	2002-09-23
结构标题 title	Crystal Structure of a Human Tyrosyl-DNA Phosphodiesterase (Tdp1)-Vanadate Complex
关键词 keywords	PLD Superfamily, Protein-Vanadate Complex, HYDROLASE; HYDROLASE
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	32.30 Å
回转半径 Rg (电子) rg_electron	31.72 Å
零角强度 I(0) i0	136403000.00
分子量 molecular_weight	96958.0 kDa
排除体积 excluded_volume	122710 Å³
包络体积 envelope_volume	146050 Å³
水化壳体积 shell_volume	38809 Å³
包络直径 envelope_diameter	116.5 Å
壳层 Rg shell_rg	37.94 Å
包络 Rg envelope_rg	31.77 Å
形状 Rg shape_rg	31.71 Å
总 Rg total_rg	32.27 Å
总原子数 total_atoms	6863
残基数 n_residues	859
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	110.7 Å
Rg (实空间) rg_real	32.46 Å
Rg 误差 (实空间) rg_real_error	1.23 Å
I(0) (实空间) i0_real	1.3640e+08
I(0) 误差 (实空间) i0_real_error	2.1300e+06
Rg (倒空间) rg_reciprocal	32.40 Å
I(0) (倒空间) i0_reciprocal	136400000.0000
解质量估计 total_estimate	0.8526
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	31.6 Å
偏度 Skewness skewness	0.452
峰度 Kurtosis kurtosis	-0.398
角度范围 angular_range	— – 0.2450 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	46970000.0000
实空间数据点数 n_real_points	50
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.731; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.927; Smooth: 0.964

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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	Tyrosyl-DNA Phosphodiesterase
分子量 formula_weight	54731.2 kDa
突变 mutation	D322N,M328T,F548L
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
原子数 atom_count	7146

MGSSHHHHHHSSGLVPRGSHMLEDPGEGQDIWDMLDKGNPFQFYLTRVSGVKPKYNSGALHIKDILSPLFGTLVSSAQFNYCFDVDWLVKQYPPEFRKKPILLVHGDKREAKAHLHAQAKPYENISLCQAKLDIAFGTHHTKMMLLLYEEGLRVVIHTSNLIHADWHQKTQGIWLSPLYPRIADGTHKSGESPTHFKANLISYLTAYNAPSLKEWIDVIHKHDLSETNVYLIGSTPGRFQGSQKDNWGHFRLKKLLKDHASSMPNAESWPVVGQFSSVGSLGADESKWLCSEFKESMLTLGKESKTPGKSSVPLYLIYPSVENVRTSLEGYPAGGSLPYSIQTAEKQNWLHSYFHKWSAETSGRSNAMPHIKTYMRPSPDFSKIAWFLVTSANLSKAAWGALEKNGTQLMIRSYELGVLFLPSALGLDSFKVKQKFFAGSQEPMATFPVPYDLPPELYGSKDRPWIWNIPYVKAPDTHGNMWVPS

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 BL21

Entity 2 non-polymer

描述 description	VANADATE ION
分子量 formula_weight	114.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 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	2

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	283

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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	d1mu9a1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.136 — Phospholipase D/nuclease
超家族 Superfamily superfamily	d.136.1 — Phospholipase D/nuclease
家族 Family family	d.136.1.3 — Tyrosyl-DNA phosphodiesterase TDP1

结构域编号 domain_id	d1mu9a2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.136 — Phospholipase D/nuclease
超家族 Superfamily superfamily	d.136.1 — Phospholipase D/nuclease
家族 Family family	d.136.1.3 — Tyrosyl-DNA phosphodiesterase TDP1

结构域编号 domain_id	d1mu9b1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.136 — Phospholipase D/nuclease
超家族 Superfamily superfamily	d.136.1 — Phospholipase D/nuclease
家族 Family family	d.136.1.3 — Tyrosyl-DNA phosphodiesterase TDP1

结构域编号 domain_id	d1mu9b2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.136 — Phospholipase D/nuclease
超家族 Superfamily superfamily	d.136.1 — Phospholipase D/nuclease
家族 Family family	d.136.1.3 — Tyrosyl-DNA phosphodiesterase TDP1

CATH v4.4 (4 domains)

结构域编号 domain_id	1mu9A01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	870 — Endonuclease; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Endonuclease Chain A

结构域编号 domain_id	1mu9A02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	870 — Endonuclease; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Endonuclease Chain A

结构域编号 domain_id	1mu9B01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	870 — Endonuclease; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Endonuclease Chain A

结构域编号 domain_id	1mu9B02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	870 — Endonuclease; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Endonuclease Chain A

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7. 引用文献 (2)

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晶胞边长 a length_a	50.028 Å
晶胞边长 b length_b	104.980 Å
晶胞边长 c length_c	194.297 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	8

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	2.050 Å
最低分辨率 resolution_low	19.970 Å
R 因子 r_factor	0.2050
R_work r_work	0.1990
R_free r_free	0.2140

fit	/app/data/saxs_computation/mu/1mu9/1mu9.fit
pddf	/app/data/pr_computation/mu/1mu9/1mu9.pr.out
profile	/app/data/saxs_computation/mu/1mu9/1mu9.dat

Crystal Structure of a Human Tyrosyl-DNA Phosphodiesterase (Tdp1)-Vanadate Complex

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