SAXSdb — 2a9c

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2a9c
沉积日期 deposition_date	2005-07-11
结构标题 title	Crystal structure of R138Q mutant of recombinant chicken sulfite oxidase with the bound product, sulfate, at the active site
关键词 keywords	sulfite oxidase; Molybdopterin; Molybdenum; CSO; sulfate; R138Q; R160Q, OXIDOREDUCTASE; 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	26.96 Å
回转半径 Rg (电子) rg_electron	26.06 Å
零角强度 I(0) i0	107438000.00
分子量 molecular_weight	79664.0 kDa
排除体积 excluded_volume	98858 Å³
包络体积 envelope_volume	116990 Å³
水化壳体积 shell_volume	36402 Å³
包络直径 envelope_diameter	87.2 Å
壳层 Rg shell_rg	34.26 Å
包络 Rg envelope_rg	26.14 Å
形状 Rg shape_rg	26.06 Å
总 Rg total_rg	26.84 Å
总原子数 total_atoms	5610
残基数 n_residues	718
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	82.8 Å
Rg (实空间) rg_real	26.81 Å
Rg 误差 (实空间) rg_real_error	0.45 Å
I(0) (实空间) i0_real	1.0740e+08
I(0) 误差 (实空间) i0_real_error	1.4680e+06
Rg (倒空间) rg_reciprocal	26.86 Å
I(0) (倒空间) i0_reciprocal	107400000.0000
解质量估计 total_estimate	0.9068
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	81.4 Å
偏度 Skewness skewness	0.169
峰度 Kurtosis kurtosis	-0.535
角度范围 angular_range	— – 0.2950 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	51230000.0000
实空间数据点数 n_real_points	60
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.943; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.960

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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	Sulfite Oxidase
分子量 formula_weight	40604.8 kDa
EC 编号 ec_number	1.8.3.1
突变 mutation	R138Q
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	6142

DPFAGDPPRHPGLRVNSQKPFNAEPPAELLAERFLTPNELFFTQNHLPVPAVEPSSYRLRVDGPGGGTLSLSLAELRSRFPKHEVTATLQCAGNRRSEMSRVRPVKGLPWDIGAISTARWGGARLRDVLLHAGFPEELQGEWHVCFEGLDADPGGAPYGASIPYGRALSPAADVLLAYEMNGTELPRDHGFPVRVVVPGVVGARSVKWLRRVAVSPDESPSHWQQNDYKGFSPCVDWDTVDYRTAPAIQELPVQSAVTQPRPGAAVPPGELTVKGYAWSGGGREVVRVDVSLDGGRTWKVARLMGDKAPPGRAWAWALWELTVPVEAGTELEIVCKAVDSSYNVQPDSVAPIWNLRGVLSTAWHRVRVSVQD

来源 Source

来源生物 organism	Gallus gallus
通用名 common_name	chicken
NCBI 分类编号 ncbi_taxonomy_id	9031
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	2

Entity 4 non-polymer

描述 description	MOLYBDENUM ATOM
分子量 formula_weight	95.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 5 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	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	532

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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	d2a9ca1
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	d2a9ca2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.18 — E set domains
家族 Family family	b.1.18.6 — Molybdenum-containing oxidoreductases-like dimerisation domain

结构域编号 domain_id	d2a9cb1
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	d2a9cb2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.18 — E set domains
家族 Family family	b.1.18.6 — Molybdenum-containing oxidoreductases-like dimerisation domain

CATH v4.4 (4 domains)

结构域编号 domain_id	2a9cA01
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	2a9cA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	650 —

结构域编号 domain_id	2a9cB01
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	2a9cB02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	650 —

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7. 引用文献 (1)

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晶胞边长 a length_a	53.905 Å
晶胞边长 b length_b	122.572 Å
晶胞边长 c length_c	55.180 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	94.97 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

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	2.505 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	0.1600
R_work r_work	0.1560
R_free r_free	0.2370

fit	/app/data/saxs_computation/a9/2a9c/2a9c.fit
pddf	/app/data/pr_computation/a9/2a9c/2a9c.pr.out
profile	/app/data/saxs_computation/a9/2a9c/2a9c.dat

Crystal structure of R138Q mutant of recombinant chicken sulfite oxidase with the bound product, sulfate, at the active site

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution