1jrp

Crystal Structure of Xanthine Dehydrogenase inhibited by alloxanthine from Rhodobacter capsulatus

Method: X-RAY DIFFRACTION Dmax: 228.7 Å Quality: GOOD

SAXS 散射曲线 SAXS Profile

SAXS profile for 1jrp

P(r) 距离分布 P(r) Distribution

P(r) distribution for 1jrp
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1. 结构基本信息 1. Structure Basics

条目编号 entry_id1jrp
沉积日期 deposition_date2001-08-14
结构标题 titleCrystal Structure of Xanthine Dehydrogenase inhibited by alloxanthine from Rhodobacter capsulatus
关键词 keywordsPartial Beta-Barrel; xdh; xo, OXIDOREDUCTASE; OXIDOREDUCTASE
实验方法 methodX-RAY DIFFRACTION

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier63.51
回转半径 Rg (电子) rg_electron64.11
零角强度 I(0) i04148910000.00
分子量 molecular_weight524580.0 kDa
排除体积 excluded_volume648900 ų
包络体积 envelope_volume864630 ų
水化壳体积 shell_volume114850 ų
包络直径 envelope_diameter225.9
壳层 Rg shell_rg62.62
包络 Rg envelope_rg63.26
形状 Rg shape_rg64.13
总 Rg total_rg64.02
总原子数 total_atoms36748
残基数 n_residues4840
球谐函数阶数 n_harmonics20
q 范围 q_range— – 0.5000 −1
数据点数 n_points101
壳层类型 shell_typedirectional
溶剂电子密度 solvent_density0.3340 e/ų
壳层衬度 contrast_shell0.0300 e/ų
CRYSOL 版本 crysol_version4.1.3

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax228.7
Rg (实空间) rg_real63.96
Rg 误差 (实空间) rg_real_error3.07
I(0) (实空间) i0_real4.1490e+09
I(0) 误差 (实空间) i0_real_error8.9370e+07
Rg (倒空间) rg_reciprocal63.07
I(0) (倒空间) i0_reciprocal4142000000.0000
解质量估计 total_estimate0.8402
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks1
主峰位置 r_peak_primary64.0
偏度 Skewness skewness0.437
峰度 Kurtosis kurtosis-0.445
角度范围 angular_range— – 0.1250 −1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha387700000.0000
实空间数据点数 n_real_points26
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.753; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.961; Smooth: 0.699

4. 晶体学与实验 4. Crystallography & Experiment

5. 实体与聚合体信息 (8)

6. 折叠分类 (SCOP + CATH) 62 domains

SCOP 2.08 (24 domains)

结构域编号 domain_idd1jrpa1
类 Class classa — All alpha proteins
折叠类型 Fold folda.56 — CO dehydrogenase ISP C-domain like
超家族 Superfamily superfamilya.56.1 — CO dehydrogenase ISP C-domain like
家族 Family familya.56.1.1 — CO dehydrogenase ISP C-domain like
结构域编号 domain_idd1jrpa2
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.15 — beta-Grasp (ubiquitin-like)
超家族 Superfamily superfamilyd.15.4 — 2Fe-2S ferredoxin-like
家族 Family familyd.15.4.2 — 2Fe-2S ferredoxin domains from multidomain proteins
结构域编号 domain_idd1jrpa3
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.87 — CO dehydrogenase flavoprotein C-domain-like
超家族 Superfamily superfamilyd.87.2 — CO dehydrogenase flavoprotein C-terminal domain-like
家族 Family familyd.87.2.1 — CO dehydrogenase flavoprotein C-terminal domain-like
结构域编号 domain_idd1jrpa4
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.145 — FAD-binding/transporter-associated domain-like
超家族 Superfamily superfamilyd.145.1 — FAD-binding/transporter-associated domain-like
家族 Family familyd.145.1.3 — CO dehydrogenase flavoprotein N-terminal domain-like
结构域编号 domain_idd1jrpb1
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.41 — alpha/beta-Hammerhead
超家族 Superfamily superfamilyd.41.1 — CO dehydrogenase molybdoprotein N-domain-like
家族 Family familyd.41.1.1 — CO dehydrogenase molybdoprotein N-domain-like
结构域编号 domain_idd1jrpb2
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.133 — Molybdenum cofactor-binding domain
超家族 Superfamily superfamilyd.133.1 — Molybdenum cofactor-binding domain
家族 Family familyd.133.1.1 — Molybdenum cofactor-binding domain
结构域编号 domain_idd1jrpc1
类 Class classa — All alpha proteins
折叠类型 Fold folda.56 — CO dehydrogenase ISP C-domain like
超家族 Superfamily superfamilya.56.1 — CO dehydrogenase ISP C-domain like
家族 Family familya.56.1.1 — CO dehydrogenase ISP C-domain like
结构域编号 domain_idd1jrpc2
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.15 — beta-Grasp (ubiquitin-like)
超家族 Superfamily superfamilyd.15.4 — 2Fe-2S ferredoxin-like
家族 Family familyd.15.4.2 — 2Fe-2S ferredoxin domains from multidomain proteins
结构域编号 domain_idd1jrpc3
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.87 — CO dehydrogenase flavoprotein C-domain-like
超家族 Superfamily superfamilyd.87.2 — CO dehydrogenase flavoprotein C-terminal domain-like
家族 Family familyd.87.2.1 — CO dehydrogenase flavoprotein C-terminal domain-like
结构域编号 domain_idd1jrpc4
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.145 — FAD-binding/transporter-associated domain-like
超家族 Superfamily superfamilyd.145.1 — FAD-binding/transporter-associated domain-like
家族 Family familyd.145.1.3 — CO dehydrogenase flavoprotein N-terminal domain-like
结构域编号 domain_idd1jrpd1
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.41 — alpha/beta-Hammerhead
超家族 Superfamily superfamilyd.41.1 — CO dehydrogenase molybdoprotein N-domain-like
家族 Family familyd.41.1.1 — CO dehydrogenase molybdoprotein N-domain-like
结构域编号 domain_idd1jrpd2
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.133 — Molybdenum cofactor-binding domain
超家族 Superfamily superfamilyd.133.1 — Molybdenum cofactor-binding domain
家族 Family familyd.133.1.1 — Molybdenum cofactor-binding domain
结构域编号 domain_idd1jrpe1
类 Class classa — All alpha proteins
折叠类型 Fold folda.56 — CO dehydrogenase ISP C-domain like
超家族 Superfamily superfamilya.56.1 — CO dehydrogenase ISP C-domain like
家族 Family familya.56.1.1 — CO dehydrogenase ISP C-domain like
结构域编号 domain_idd1jrpe2
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.15 — beta-Grasp (ubiquitin-like)
超家族 Superfamily superfamilyd.15.4 — 2Fe-2S ferredoxin-like
家族 Family familyd.15.4.2 — 2Fe-2S ferredoxin domains from multidomain proteins
结构域编号 domain_idd1jrpe3
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.87 — CO dehydrogenase flavoprotein C-domain-like
超家族 Superfamily superfamilyd.87.2 — CO dehydrogenase flavoprotein C-terminal domain-like
家族 Family familyd.87.2.1 — CO dehydrogenase flavoprotein C-terminal domain-like
结构域编号 domain_idd1jrpe4
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.145 — FAD-binding/transporter-associated domain-like
超家族 Superfamily superfamilyd.145.1 — FAD-binding/transporter-associated domain-like
家族 Family familyd.145.1.3 — CO dehydrogenase flavoprotein N-terminal domain-like
结构域编号 domain_idd1jrpf1
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.41 — alpha/beta-Hammerhead
超家族 Superfamily superfamilyd.41.1 — CO dehydrogenase molybdoprotein N-domain-like
家族 Family familyd.41.1.1 — CO dehydrogenase molybdoprotein N-domain-like
结构域编号 domain_idd1jrpf2
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.133 — Molybdenum cofactor-binding domain
超家族 Superfamily superfamilyd.133.1 — Molybdenum cofactor-binding domain
家族 Family familyd.133.1.1 — Molybdenum cofactor-binding domain
结构域编号 domain_idd1jrpg1
类 Class classa — All alpha proteins
折叠类型 Fold folda.56 — CO dehydrogenase ISP C-domain like
超家族 Superfamily superfamilya.56.1 — CO dehydrogenase ISP C-domain like
家族 Family familya.56.1.1 — CO dehydrogenase ISP C-domain like
结构域编号 domain_idd1jrpg2
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.15 — beta-Grasp (ubiquitin-like)
超家族 Superfamily superfamilyd.15.4 — 2Fe-2S ferredoxin-like
家族 Family familyd.15.4.2 — 2Fe-2S ferredoxin domains from multidomain proteins
结构域编号 domain_idd1jrpg3
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.87 — CO dehydrogenase flavoprotein C-domain-like
超家族 Superfamily superfamilyd.87.2 — CO dehydrogenase flavoprotein C-terminal domain-like
家族 Family familyd.87.2.1 — CO dehydrogenase flavoprotein C-terminal domain-like
结构域编号 domain_idd1jrpg4
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.145 — FAD-binding/transporter-associated domain-like
超家族 Superfamily superfamilyd.145.1 — FAD-binding/transporter-associated domain-like
家族 Family familyd.145.1.3 — CO dehydrogenase flavoprotein N-terminal domain-like
结构域编号 domain_idd1jrph1
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.41 — alpha/beta-Hammerhead
超家族 Superfamily superfamilyd.41.1 — CO dehydrogenase molybdoprotein N-domain-like
家族 Family familyd.41.1.1 — CO dehydrogenase molybdoprotein N-domain-like
结构域编号 domain_idd1jrph2
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.133 — Molybdenum cofactor-binding domain
超家族 Superfamily superfamilyd.133.1 — Molybdenum cofactor-binding domain
家族 Family familyd.133.1.1 — Molybdenum cofactor-binding domain

CATH v4.4 (38 domains)

结构域编号 domain_id1jrpA01
类 Class class3 — Alpha Beta
架构 Architecture architecture10 — Roll
拓扑 Topology topology20 — Ubiquitin-like (UB roll)
同源超家族 H-superfamily homologous superfamily30 — Beta-grasp domain
结构域编号 domain_id1jrpA02
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology150 — DNA polymerase; domain 1
同源超家族 H-superfamily homologous superfamily120 — [2Fe-2S]-binding domain
结构域编号 domain_id1jrpA04
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology390 — Enolase-like; domain 1
同源超家族 H-superfamily homologous superfamily50 — CO dehydrogenase flavoprotein, C-terminal domain
结构域编号 domain_id1jrpB01
类 Class class3 — Alpha Beta
架构 Architecture architecture90 — Alpha-Beta Complex
拓扑 Topology topology1170 — Aldehyde Oxidoreductase; domain 3
同源超家族 H-superfamily homologous superfamily50 — Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead
结构域编号 domain_id1jrpB02
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology365 — Aldehyde Oxidoreductase; domain 4
同源超家族 H-superfamily homologous superfamily10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain
结构域编号 domain_id1jrpB03
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology365 — Aldehyde Oxidoreductase; domain 4
同源超家族 H-superfamily homologous superfamily10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain
结构域编号 domain_id1jrpB04
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology365 — Aldehyde Oxidoreductase; domain 4
同源超家族 H-superfamily homologous superfamily10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain
结构域编号 domain_id1jrpB05
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology365 — Aldehyde Oxidoreductase; domain 4
同源超家族 H-superfamily homologous superfamily10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain
结构域编号 domain_id1jrpC01
类 Class class3 — Alpha Beta
架构 Architecture architecture10 — Roll
拓扑 Topology topology20 — Ubiquitin-like (UB roll)
同源超家族 H-superfamily homologous superfamily30 — Beta-grasp domain
结构域编号 domain_id1jrpC02
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology150 — DNA polymerase; domain 1
同源超家族 H-superfamily homologous superfamily120 — [2Fe-2S]-binding domain
结构域编号 domain_id1jrpC03
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology43 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2
同源超家族 H-superfamily homologous superfamily10 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2
结构域编号 domain_id1jrpC04
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology465 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3
同源超家族 H-superfamily homologous superfamily10
结构域编号 domain_id1jrpC05
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology390 — Enolase-like; domain 1
同源超家族 H-superfamily homologous superfamily50 — CO dehydrogenase flavoprotein, C-terminal domain
结构域编号 domain_id1jrpD01
类 Class class3 — Alpha Beta
架构 Architecture architecture90 — Alpha-Beta Complex
拓扑 Topology topology1170 — Aldehyde Oxidoreductase; domain 3
同源超家族 H-superfamily homologous superfamily50 — Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead
结构域编号 domain_id1jrpD02
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology365 — Aldehyde Oxidoreductase; domain 4
同源超家族 H-superfamily homologous superfamily10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain
结构域编号 domain_id1jrpD03
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology365 — Aldehyde Oxidoreductase; domain 4
同源超家族 H-superfamily homologous superfamily10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain
结构域编号 domain_id1jrpD04
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology365 — Aldehyde Oxidoreductase; domain 4
同源超家族 H-superfamily homologous superfamily10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain
结构域编号 domain_id1jrpD05
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology365 — Aldehyde Oxidoreductase; domain 4
同源超家族 H-superfamily homologous superfamily10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain
结构域编号 domain_id1jrpE01
类 Class class3 — Alpha Beta
架构 Architecture architecture10 — Roll
拓扑 Topology topology20 — Ubiquitin-like (UB roll)
同源超家族 H-superfamily homologous superfamily30 — Beta-grasp domain
结构域编号 domain_id1jrpE02
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology150 — DNA polymerase; domain 1
同源超家族 H-superfamily homologous superfamily120 — [2Fe-2S]-binding domain
结构域编号 domain_id1jrpE03
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology43 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2
同源超家族 H-superfamily homologous superfamily10 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2
结构域编号 domain_id1jrpE04
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology465 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3
同源超家族 H-superfamily homologous superfamily10
结构域编号 domain_id1jrpE05
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology390 — Enolase-like; domain 1
同源超家族 H-superfamily homologous superfamily50 — CO dehydrogenase flavoprotein, C-terminal domain
结构域编号 domain_id1jrpF01
类 Class class3 — Alpha Beta
架构 Architecture architecture90 — Alpha-Beta Complex
拓扑 Topology topology1170 — Aldehyde Oxidoreductase; domain 3
同源超家族 H-superfamily homologous superfamily50 — Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead
结构域编号 domain_id1jrpF02
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology365 — Aldehyde Oxidoreductase; domain 4
同源超家族 H-superfamily homologous superfamily10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain
结构域编号 domain_id1jrpF03
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology365 — Aldehyde Oxidoreductase; domain 4
同源超家族 H-superfamily homologous superfamily10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain
结构域编号 domain_id1jrpF04
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology365 — Aldehyde Oxidoreductase; domain 4
同源超家族 H-superfamily homologous superfamily10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain
结构域编号 domain_id1jrpF05
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology365 — Aldehyde Oxidoreductase; domain 4
同源超家族 H-superfamily homologous superfamily10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain
结构域编号 domain_id1jrpG01
类 Class class3 — Alpha Beta
架构 Architecture architecture10 — Roll
拓扑 Topology topology20 — Ubiquitin-like (UB roll)
同源超家族 H-superfamily homologous superfamily30 — Beta-grasp domain
结构域编号 domain_id1jrpG02
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology150 — DNA polymerase; domain 1
同源超家族 H-superfamily homologous superfamily120 — [2Fe-2S]-binding domain
结构域编号 domain_id1jrpG03
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology43 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2
同源超家族 H-superfamily homologous superfamily10 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2
结构域编号 domain_id1jrpG04
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology465 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3
同源超家族 H-superfamily homologous superfamily10
结构域编号 domain_id1jrpG05
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology390 — Enolase-like; domain 1
同源超家族 H-superfamily homologous superfamily50 — CO dehydrogenase flavoprotein, C-terminal domain
结构域编号 domain_id1jrpH01
类 Class class3 — Alpha Beta
架构 Architecture architecture90 — Alpha-Beta Complex
拓扑 Topology topology1170 — Aldehyde Oxidoreductase; domain 3
同源超家族 H-superfamily homologous superfamily50 — Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead
结构域编号 domain_id1jrpH02
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology365 — Aldehyde Oxidoreductase; domain 4
同源超家族 H-superfamily homologous superfamily10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain
结构域编号 domain_id1jrpH03
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology365 — Aldehyde Oxidoreductase; domain 4
同源超家族 H-superfamily homologous superfamily10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain
结构域编号 domain_id1jrpH04
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology365 — Aldehyde Oxidoreductase; domain 4
同源超家族 H-superfamily homologous superfamily10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain
结构域编号 domain_id1jrpH05
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology365 — Aldehyde Oxidoreductase; domain 4
同源超家族 H-superfamily homologous superfamily10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain

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