SAXSdb — 1rfi

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1rfi
沉积日期 deposition_date	2003-11-10
结构标题 title	Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, pentapeptide KLNYK, and tetranucleotide AGTC
关键词 keywords	Protein-DNA complex, vanadate complex, transition state mimic., HYDROLASE-DNA COMPLEX; HYDROLASE/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	32.42 Å
回转半径 Rg (电子) rg_electron	31.84 Å
零角强度 I(0) i0	144162000.00
分子量 molecular_weight	99221.0 kDa
排除体积 excluded_volume	125320 Å³
包络体积 envelope_volume	148610 Å³
水化壳体积 shell_volume	39226 Å³
包络直径 envelope_diameter	116.4 Å
壳层 Rg shell_rg	38.26 Å
包络 Rg envelope_rg	31.91 Å
形状 Rg shape_rg	31.82 Å
总 Rg total_rg	32.42 Å
总原子数 total_atoms	7015
残基数 n_residues	868
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	111.2 Å
Rg (实空间) rg_real	32.58 Å
Rg 误差 (实空间) rg_real_error	1.01 Å
I(0) (实空间) i0_real	1.4420e+08
I(0) 误差 (实空间) i0_real_error	2.3190e+06
Rg (倒空间) rg_reciprocal	32.52 Å
I(0) (倒空间) i0_reciprocal	144200000.0000
解质量估计 total_estimate	0.8520
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	31.8 Å
偏度 Skewness skewness	0.435
峰度 Kurtosis kurtosis	-0.460
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	54990000.0000
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: 0.729; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.913; Smooth: 0.977

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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	5'-D(APGPTPC)-3'
分子量 formula_weight	1190.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	D,F
原子数 atom_count	7258

AGTC

Entity 2 polymer

描述 description	Tyrosyl-DNA phosphodiesterase 1
分子量 formula_weight	54731.2 kDa
EC 编号 ec_number	3.1.4.-
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

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 3 polymer

描述 description	Topoisomerase I-Derived Peptide
分子量 formula_weight	666.8 kDa
突变 mutation	L724K
来源方法 src_method	syn
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C,E

KLNYK

Entity 4 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 5 non-polymer

描述 description	SPERMINE
分子量 formula_weight	202.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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	243

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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	d1rfia1
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	d1rfia2
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	d1rfib1
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	d1rfib2
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	1rfiA01
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	1rfiA02
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	1rfiB01
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	1rfiB02
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 (4)

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晶胞边长 a length_a	49.820 Å
晶胞边长 b length_b	104.832 Å
晶胞边长 c length_c	193.539 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	2.200 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	0.1898
R_work r_work	0.1878
R_free r_free	0.2270

fit	/app/data/saxs_computation/rf/1rfi/1rfi.fit
pddf	/app/data/pr_computation/rf/1rfi/1rfi.pr.out
profile	/app/data/saxs_computation/rf/1rfi/1rfi.dat

Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, pentapeptide KLNYK, and tetranucleotide AGTC

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 (6)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 polymer

聚合体 Polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 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 (4)

8. 文件与曲线 (10)

Files (7)

Curves (3)