1xdy

Structural and Biochemical Identification of a Novel Bacterial Oxidoreductase, W-containing cofactor

Method: X-RAY DIFFRACTION D_max: 193.6 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	1xdy
沉积日期 deposition_date	2004-09-08
结构标题 title	Structural and Biochemical Identification of a Novel Bacterial Oxidoreductase, W-containing cofactor
关键词 keywords	Bioinformatics, sequence analysis, electron transfer, oxidoreductase, molybdoenzymes, molybdopterin; OXIDOREDUCTASE
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	61.48 Å
回转半径 Rg (电子) rg_electron	62.34 Å
零角强度 I(0) i0	1244630000.00
分子量 molecular_weight	300810.0 kDa
排除体积 excluded_volume	377450 Å³
包络体积 envelope_volume	544570 Å³
水化壳体积 shell_volume	77441 Å³
包络直径 envelope_diameter	212.4 Å
壳层 Rg shell_rg	56.23 Å
包络 Rg envelope_rg	60.87 Å
形状 Rg shape_rg	62.34 Å
总 Rg total_rg	62.19 Å
总原子数 total_atoms	21147
残基数 n_residues	2625
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	193.6 Å
Rg (实空间) rg_real	62.17 Å
Rg 误差 (实空间) rg_real_error	1.72 Å
I(0) (实空间) i0_real	1.2450e+09
I(0) 误差 (实空间) i0_real_error	2.3780e+07
Rg (倒空间) rg_reciprocal	60.84 Å
I(0) (倒空间) i0_reciprocal	1242000000.0000
解质量估计 total_estimate	0.8135
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	59.6 Å
偏度 Skewness skewness	0.491
峰度 Kurtosis kurtosis	-0.518
角度范围 angular_range	— – 0.1300 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	30720000.0000
实空间数据点数 n_real_points	27
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.873; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.952; Smooth: 0.001

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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	Bacterial Sulfite Oxidase
分子量 formula_weight	33666.3 kDa
来源方法 src_method	man
拷贝数 entity_count	10

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H,I,J
原子数 atom_count	21369

DLLSWFKGNDRPPAPAGKALEFSKPAAWQNNLPLTPADKVSGYNNFYEFGLDKADPAANAGSLKTDPWTLKISGEVAKPLTLDHDDLTRRFPLEERIYRMRCVEAWSMVVPWIGFPLHKLLALAEPTSNAKYVAFETIYAPEQMPGQQDRFIGGGLKYPYVEGLRLDEAMHPLTLMTVGVYGKALPPQNGAPVRLIVPWKYGFKGIKSIVSIKLTRERPPTTWNLAAPDEYGFYANVNPYVDHPRWSQATERFIGSGGILDVQRQPTLLFNGYADQVASLYRGLDLRENFLEHHHHHH

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	TUNGSTEN ION
分子量 formula_weight	183.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	10

Entity 3 non-polymer

描述 description	PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER
分子量 formula_weight	395.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	10

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	222

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6. 折叠分类 (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

结构域编号 domain_id	d1xdya_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.176 — Oxidoreductase molybdopterin-binding domain
超家族 Superfamily superfamily	d.176.1 — Oxidoreductase molybdopterin-binding domain
家族 Family family	d.176.1.1 — Oxidoreductase molybdopterin-binding domain

结构域编号 domain_id	d1xdyb_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.176 — Oxidoreductase molybdopterin-binding domain
超家族 Superfamily superfamily	d.176.1 — Oxidoreductase molybdopterin-binding domain
家族 Family family	d.176.1.1 — Oxidoreductase molybdopterin-binding domain

结构域编号 domain_id	d1xdyc_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.176 — Oxidoreductase molybdopterin-binding domain
超家族 Superfamily superfamily	d.176.1 — Oxidoreductase molybdopterin-binding domain
家族 Family family	d.176.1.1 — Oxidoreductase molybdopterin-binding domain

结构域编号 domain_id	d1xdyd_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.176 — Oxidoreductase molybdopterin-binding domain
超家族 Superfamily superfamily	d.176.1 — Oxidoreductase molybdopterin-binding domain
家族 Family family	d.176.1.1 — Oxidoreductase molybdopterin-binding domain

结构域编号 domain_id	d1xdye_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.176 — Oxidoreductase molybdopterin-binding domain
超家族 Superfamily superfamily	d.176.1 — Oxidoreductase molybdopterin-binding domain
家族 Family family	d.176.1.1 — Oxidoreductase molybdopterin-binding domain

结构域编号 domain_id	d1xdyf_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.176 — Oxidoreductase molybdopterin-binding domain
超家族 Superfamily superfamily	d.176.1 — Oxidoreductase molybdopterin-binding domain
家族 Family family	d.176.1.1 — Oxidoreductase molybdopterin-binding domain

结构域编号 domain_id	d1xdyg_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.176 — Oxidoreductase molybdopterin-binding domain
超家族 Superfamily superfamily	d.176.1 — Oxidoreductase molybdopterin-binding domain
家族 Family family	d.176.1.1 — Oxidoreductase molybdopterin-binding domain

结构域编号 domain_id	d1xdyh_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.176 — Oxidoreductase molybdopterin-binding domain
超家族 Superfamily superfamily	d.176.1 — Oxidoreductase molybdopterin-binding domain
家族 Family family	d.176.1.1 — Oxidoreductase molybdopterin-binding domain

结构域编号 domain_id	d1xdyi_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.176 — Oxidoreductase molybdopterin-binding domain
超家族 Superfamily superfamily	d.176.1 — Oxidoreductase molybdopterin-binding domain
家族 Family family	d.176.1.1 — Oxidoreductase molybdopterin-binding domain

结构域编号 domain_id	d1xdyj_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.176 — Oxidoreductase molybdopterin-binding domain
超家族 Superfamily superfamily	d.176.1 — Oxidoreductase molybdopterin-binding domain
家族 Family family	d.176.1.1 — Oxidoreductase molybdopterin-binding domain

CATH v4.4 (10 domains)

结构域编号 domain_id	1xdyA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	420 — Sulfite Oxidase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Oxidoreductase, molybdopterin-binding domain

结构域编号 domain_id	1xdyB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	420 — Sulfite Oxidase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Oxidoreductase, molybdopterin-binding domain

结构域编号 domain_id	1xdyC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	420 — Sulfite Oxidase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Oxidoreductase, molybdopterin-binding domain

结构域编号 domain_id	1xdyD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	420 — Sulfite Oxidase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Oxidoreductase, molybdopterin-binding domain

结构域编号 domain_id	1xdyE00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	420 — Sulfite Oxidase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Oxidoreductase, molybdopterin-binding domain

结构域编号 domain_id	1xdyF00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	420 — Sulfite Oxidase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Oxidoreductase, molybdopterin-binding domain

结构域编号 domain_id	1xdyG00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	420 — Sulfite Oxidase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Oxidoreductase, molybdopterin-binding domain

结构域编号 domain_id	1xdyH00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	420 — Sulfite Oxidase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Oxidoreductase, molybdopterin-binding domain

结构域编号 domain_id	1xdyI00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	420 — Sulfite Oxidase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Oxidoreductase, molybdopterin-binding domain

结构域编号 domain_id	1xdyJ00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	420 — Sulfite Oxidase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Oxidoreductase, molybdopterin-binding domain

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7. 引用文献 (1)

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晶胞边长 a length_a	84.842 Å
晶胞边长 b length_b	177.513 Å
晶胞边长 c length_c	104.214 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	109.73 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	20

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	2.200 Å
最低分辨率 resolution_low	38.960 Å
R 因子 r_factor	0.2260
R_work r_work	0.2260
R_free r_free	0.2580

fit	/app/data/saxs_computation/xd/1xdy/1xdy.fit
pddf	/app/data/pr_computation/xd/1xdy/1xdy.pr.out
profile	/app/data/saxs_computation/xd/1xdy/1xdy.dat