SAXSdb — 1wyg

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1wyg
沉积日期 deposition_date	2005-02-14
结构标题 title	Crystal Structure of a Rat Xanthine Dehydrogenase Triple Mutant (C535A, C992R and C1324S)
关键词 keywords	DEHYDROGENASE TO OXIDASE CONVERSION, OXIDOREDUCTASE; OXIDOREDUCTASE
实验方法 method	X-RAY DIFFRACTION

▼

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

回转半径 Rg (Guinier) rg_guinier	32.04 Å
回转半径 Rg (电子) rg_electron	31.36 Å
零角强度 I(0) i0	326663000.00
分子量 molecular_weight	144510.0 kDa
排除体积 excluded_volume	180610 Å³
包络体积 envelope_volume	214450 Å³
水化壳体积 shell_volume	53916 Å³
包络直径 envelope_diameter	109.7 Å
壳层 Rg shell_rg	40.52 Å
包络 Rg envelope_rg	31.64 Å
形状 Rg shape_rg	31.38 Å
总 Rg total_rg	31.97 Å
总原子数 total_atoms	10124
残基数 n_residues	1297
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

▼

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

最大尺寸 Dmax dmax	102.4 Å
Rg (实空间) rg_real	31.85 Å
Rg 误差 (实空间) rg_real_error	0.41 Å
I(0) (实空间) i0_real	3.2670e+08
I(0) 误差 (实空间) i0_real_error	3.8510e+06
Rg (倒空间) rg_reciprocal	31.94 Å
I(0) (倒空间) i0_reciprocal	326700000.0000
解质量估计 total_estimate	0.6826
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	39.7 Å
偏度 Skewness skewness	0.202
峰度 Kurtosis kurtosis	-0.375
角度范围 angular_range	— – 0.2450 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	105200000.0000
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: 0.872; Stabil: 1.000; Sysdev: 0.096; Positv: 1.000; Valcen: 0.985; Smooth: 0.981

▶

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

▶

5. 实体与聚合体信息 (8)

Entity 1 polymer

描述 description	Xanthine dehydrogenase/oxidase
分子量 formula_weight	146420.3 kDa
EC 编号 ec_number	1.1.1.204, 1.1.3.22
突变 mutation	C535A, C992R, C1324S
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	10330

MTADELVFFVNGKKVVEKNADPETTLLVYLRRKLGLCGTKLGCGEGGCGACTVMISKYDRLQNKIVHFSVNACLAPICSLHHVAVTTVEGIGNTQKLHPVQERIARSHGSQCGFCTPGIVMSMYTLLRNQPEPTVEEIENAFQGNLCRCTGYRPILQGFRTFAKDGGCCGGSGNNPNCCMNQTKDQTVSLSPSLFNPEDFKPLDPTQEPIFPPELLRLKDTPQKKLRFEGERVTWIQASTMEELLDLKAQHPDAKLVVGNTEIGIEMKFKNMLFPLIVCPAWIPELNSVVHGPEGISFGASCPLSLVESVLAEEIAKLPEQKTEVFRGVMEQLRWFAGKQVKSVASIGGNIITASPISDLNPVFMASGAKLTLVSRGTRRTVRMDHTFFPGYRKTLLRPEEILLSIEIPYSKEGEFFSAFKQASRREDDIAKVTSGMRVLFKPGTIEVQELSLCFGGMADRTISALKTTPKQLSKSWNEELLQSVCAGLAEELQLAPDAPGGMVEFRRTLTLSFFFKFYLTVLQKLGRADLEDMAGKLDPTFASATLLFQKDPPANVQLFQEVPKDQSEEDMVGRPLPHLAANMQASGEAVYCDDIPRYENELSLRLVTSTRAHAKITSIDTSEAKKVPGFVCFLTAEDVPNSNATGLFNDETVFAKDEVTCVGHIIGAVVADTPEHAQRAARGVKITYEDLPAIITIQDAINNNSFYGSEIKIEKGDLKKGFSEADNVVSGELYIGGQEHFYLETNCTIAVPKGEAGEMELFVSTQNTMKTQSFVAKMLGVPDNRIVVRVKRMGGGFGGKETRSTVVSTALALAAHKTGRPVRCMLDRDEDMLITGGRHPFLAKYKVGFMKTGTVVALEVAHFSNGGNTEDLSRSIMERALFHMDNAYKIPNIRGTGRICKTNLPSNTAFRGFGGPQGMLIAEYWMSEVAITCGLPAEEVRRKNMYKEGDLTHFNQKLEGFTLPRCWDECIASSQYLARKREVEKFNRENRWKKRGLCIIPTKFGISFTLPFLNQGGALVHVYTDGSVLLTHGGTEMGQGLHTKMVQVASRALKIPTSKIHISETSTNTVPNTSPTAASASADLNGQGVYEACQTILKRLEPFKKKKPTGPWEAWVMDAYTSAVSLSATGFYKTPNLGYSFETNSGNPFHYFSYGVACSEVEIDCLTGDHKNLRTDIVMDVGSSLNPAIDIGQVEGAFVQGLGLFTMEELHYSPEGSLHTRGPSTYKIPAFGSIPIEFRVSLLRDCPNKRAIYASKAVGEPPLFLASSIFFAIKDAIRAARAQHGDNAKQLFQLDSPATPEKIRNACVDQFTTLCVTGVPENSKSWSVRI

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI 分类编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 non-polymer

描述 description	PHOSPHATE ION
分子量 formula_weight	95.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 3 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	FE2/S2 (INORGANIC) CLUSTER
分子量 formula_weight	175.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 5 non-polymer

描述 description	FLAVIN-ADENINE DINUCLEOTIDE
分子量 formula_weight	785.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 6 non-polymer

描述 description	2-HYDROXYBENZOIC ACID
分子量 formula_weight	138.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 7 non-polymer

描述 description	ACETIC ACID
分子量 formula_weight	60.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 8 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	206

▼

6. 折叠分类 (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

结构域编号 domain_id	1wygA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	20 — Ubiquitin-like (UB roll)
同源超家族 H-superfamily homologous superfamily	30 — Beta-grasp domain

结构域编号 domain_id	1wygA02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	150 — DNA polymerase; domain 1
同源超家族 H-superfamily homologous superfamily	120 — [2Fe-2S]-binding domain

结构域编号 domain_id	1wygA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	43 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2

结构域编号 domain_id	1wygA04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	465 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1wygA05
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	390 — Enolase-like; domain 1
同源超家族 H-superfamily homologous superfamily	50 — CO dehydrogenase flavoprotein, C-terminal domain

结构域编号 domain_id	1wygA06
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	365 — Aldehyde Oxidoreductase; domain 4
同源超家族 H-superfamily homologous superfamily	10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain

结构域编号 domain_id	1wygA07
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1170 — Aldehyde Oxidoreductase; domain 3
同源超家族 H-superfamily homologous superfamily	50 — Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead

结构域编号 domain_id	1wygA08
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	365 — Aldehyde Oxidoreductase; domain 4
同源超家族 H-superfamily homologous superfamily	10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain

结构域编号 domain_id	1wygA09
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	365 — Aldehyde Oxidoreductase; domain 4
同源超家族 H-superfamily homologous superfamily	10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain

结构域编号 domain_id	1wygA10
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	365 — Aldehyde Oxidoreductase; domain 4
同源超家族 H-superfamily homologous superfamily	10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	134.253 Å
晶胞边长 b length_b	134.253 Å
晶胞边长 c length_c	523.315 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	16

空间群 space_group	I 41 2 2
空间群编号 int_tables_number	98
晶系 crystal_system	—

分辨率 resolution	2.600 Å
最低分辨率 resolution_low	25.000 Å
R 因子 r_factor	—
R_work r_work	0.2030
R_free r_free	0.2480

fit	/app/data/saxs_computation/wy/1wyg/1wyg.fit
pddf	/app/data/pr_computation/wy/1wyg/1wyg.pr.out
profile	/app/data/saxs_computation/wy/1wyg/1wyg.dat

Crystal Structure of a Rat Xanthine Dehydrogenase Triple Mutant (C535A, C992R and C1324S)

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution