SAXSdb — 2a9d

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2a9d
沉积日期 deposition_date	2005-07-11
结构标题 title	Crystal structure of recombinant chicken sulfite oxidase with Arg at residue 161
关键词 keywords	sulfite oxidase; Molybdopterin; Molybdenum, 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	27.14 Å
回转半径 Rg (电子) rg_electron	26.27 Å
零角强度 I(0) i0	111741000.00
分子量 molecular_weight	81090.0 kDa
排除体积 excluded_volume	100530 Å³
包络体积 envelope_volume	118610 Å³
水化壳体积 shell_volume	36681 Å³
包络直径 envelope_diameter	88.8 Å
壳层 Rg shell_rg	34.46 Å
包络 Rg envelope_rg	26.30 Å
形状 Rg shape_rg	26.28 Å
总 Rg total_rg	27.03 Å
总原子数 total_atoms	5709
残基数 n_residues	728
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	84.2 Å
Rg (实空间) rg_real	27.00 Å
Rg 误差 (实空间) rg_real_error	0.58 Å
I(0) (实空间) i0_real	1.1170e+08
I(0) 误差 (实空间) i0_real_error	1.5730e+06
Rg (倒空间) rg_reciprocal	27.05 Å
I(0) (倒空间) i0_reciprocal	111700000.0000
解质量估计 total_estimate	0.9022
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	33.4 Å
偏度 Skewness skewness	0.184
峰度 Kurtosis kurtosis	-0.525
角度范围 angular_range	— – 0.2900 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	51340000.0000
实空间数据点数 n_real_points	59
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.936; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.926

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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 (5)

Entity 1 polymer

描述 description	Sulfite Oxidase
分子量 formula_weight	40734.0 kDa
EC 编号 ec_number	1.8.3.1
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	6539

DPFAGDPPRHPGLRVNSQKPFNAEPPAELLAERFLTPNELFFTRNHLPVPAVEPSSYRLRVDGPGGRTLSLSLAELRSRFPKHEVTATLQCAGNRRSEMSRVRPVKGLPWDIGAISTARWGGARLRDVLLHAGFPEELQGEWHVCFEGLDADPGGAPYGASIPYGRALSPAADVLLAYEMNGTELPRDHGFPVRVVVPGVVGARSVKWLRRVAVSPDESPSHWQQNDYKGFSPCVDWDTVDYRTAPAIQELPVQSAVTQPRPGAAVPPGELTVKGYAWSGGGREVVRVDVSLDGGRTWKVARLMGDKAPPGRAWAWALWELTVPVEAGTELEIVCKAVDSSYNVQPDSVAPIWNLRGVLSTAWHRVRVSVQD

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	4

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 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	824

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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	d2a9da1
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	d2a9da2
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	d2a9db1
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	d2a9db2
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	2a9dA01
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	2a9dA02
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	2a9dB01
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	2a9dB02
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	56.137 Å
晶胞边长 b length_b	123.102 Å
晶胞边长 c length_c	55.129 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	94.31 °
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	1.701 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	0.1570
R_work r_work	0.1550
R_free r_free	0.1870

fit	/app/data/saxs_computation/a9/2a9d/2a9d.fit
pddf	/app/data/pr_computation/a9/2a9d/2a9d.pr.out
profile	/app/data/saxs_computation/a9/2a9d/2a9d.dat

Crystal structure of recombinant chicken sulfite oxidase with Arg at residue 161

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