SAXSdb — 1naa

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1naa
沉积日期 deposition_date	2002-11-27
结构标题 title	Cellobiose Dehydrogenase Flavoprotein Fragment in Complex with Cellobionolactam
关键词 keywords	GMC oxidoreductase, alpha/beta structure, rossmann fold, PHBH fold, product analogue complex, 6-hydroxylated FAD, 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	30.59 Å
回转半径 Rg (电子) rg_electron	29.58 Å
零角强度 I(0) i0	223240000.00
分子量 molecular_weight	118310.0 kDa
排除体积 excluded_volume	147530 Å³
包络体积 envelope_volume	171020 Å³
水化壳体积 shell_volume	45935 Å³
包络直径 envelope_diameter	91.8 Å
壳层 Rg shell_rg	38.67 Å
包络 Rg envelope_rg	29.32 Å
形状 Rg shape_rg	29.59 Å
总 Rg total_rg	30.32 Å
总原子数 total_atoms	8358
残基数 n_residues	1082
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	92.5 Å
Rg (实空间) rg_real	30.41 Å
Rg 误差 (实空间) rg_real_error	0.43 Å
I(0) (实空间) i0_real	2.2320e+08
I(0) 误差 (实空间) i0_real_error	3.3260e+06
Rg (倒空间) rg_reciprocal	30.49 Å
I(0) (倒空间) i0_reciprocal	223300000.0000
解质量估计 total_estimate	0.9108
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	37.4 Å
偏度 Skewness skewness	0.125
峰度 Kurtosis kurtosis	-0.623
角度范围 angular_range	— – 0.2600 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	125100000.0000
实空间数据点数 n_real_points	53
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.959; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.969

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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	Cellobiose dehydrogenase
分子量 formula_weight	57545.0 kDa
EC 编号 ec_number	1.1.99.18
来源方法 src_method	nat
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	9365

TPYDYIIVGAGPGGIIAADRLSEAGKKVLLLERGGPSTKQTGGTYVAPWATSSGLTKFDIPGLFESLFTDSNPFWWCKDITVFAGCLVGGGTSVNGALYWYPNDGDFSSSVGWPSSWTNHAPYTSKLSSRLPSTDHPSTDGQRYLEQSFNVVSQLLKGQGYNQATINDNPNYKDHVFGYSAFDFLNGKRAGPVATYLQTALARPNFTFKTNVMVSNVVRNGSQILGVQTNDPTLGPNGFIPVTPKGRVILSAGAFGTSRILFQSGIGPTDMIQTVQSNPTAAAALPPQNQWINLPVGMNAQDNPSINLVFTHPSIDAYENWADVWSNPRPADAAQYLANQSGVFAGASPKLNFWRAYSGSDGFTRYAQGTVRPGAASVNSSLPYNASQIFTITVYLSTGIQSRGRIGIDAALRGTVLTPPWLVNPVDKTVLLQALHDVVSNIGSIPGLTMITPDVTQTLEEYVDAYDPATMNSNHWVSSTTIGSSPQSAVVDSNVKVFGTNNLFIVDAGIIPHLPTGNPQGTLMSAAEQAAAKILALAGGP

Entity 2 non-polymer

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	221.2 kDa
来源方法 src_method	man
拷贝数 entity_count	5

Entity 3 non-polymer

描述 description	6-HYDROXY-FLAVIN-ADENINE DINUCLEOTIDE
分子量 formula_weight	801.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	(2R,3R,4R,5R)-4,5-dihydroxy-2-(hydroxymethyl)-6-oxopiperidin-3-yl beta-D-glucopyranoside
分子量 formula_weight	339.3 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	1007

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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	d1naaa1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.3 — FAD/NAD(P)-binding domain
超家族 Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
家族 Family family	c.3.1.2 — FAD-linked reductases, N-terminal domain

结构域编号 domain_id	d1naaa2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.16 — FAD-linked reductases, C-terminal domain
超家族 Superfamily superfamily	d.16.1 — FAD-linked reductases, C-terminal domain
家族 Family family	d.16.1.1 — GMC oxidoreductases

结构域编号 domain_id	d1naab1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.3 — FAD/NAD(P)-binding domain
超家族 Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
家族 Family family	c.3.1.2 — FAD-linked reductases, N-terminal domain

结构域编号 domain_id	d1naab2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.16 — FAD-linked reductases, C-terminal domain
超家族 Superfamily superfamily	d.16.1 — FAD-linked reductases, C-terminal domain
家族 Family family	d.16.1.1 — GMC oxidoreductases

CATH v4.4 (4 domains)

结构域编号 domain_id	1naaA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	50 — FAD/NAD(P)-binding domain
同源超家族 H-superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

结构域编号 domain_id	1naaA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	410 — Cholesterol Oxidase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Cholesterol Oxidase; domain 2

结构域编号 domain_id	1naaB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	50 — FAD/NAD(P)-binding domain
同源超家族 H-superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

结构域编号 domain_id	1naaB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	410 — Cholesterol Oxidase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Cholesterol Oxidase; domain 2

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7. 引用文献 (2)

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晶胞边长 a length_a	185.952 Å
晶胞边长 b length_b	185.952 Å
晶胞边长 c length_c	81.438 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	120.00 °
晶胞分子数 Z z_pdb	18

空间群 space_group	H 3
空间群编号 int_tables_number	146
晶系 crystal_system	—

分辨率 resolution	1.800 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	0.1460
R_work r_work	0.1460
R_free r_free	0.1850

fit	/app/data/saxs_computation/na/1naa/1naa.fit
pddf	/app/data/pr_computation/na/1naa/1naa.pr.out
profile	/app/data/saxs_computation/na/1naa/1naa.dat

Cellobiose Dehydrogenase Flavoprotein Fragment in Complex with Cellobionolactam

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