SAXSdb — 2av6

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2av6
沉积日期 deposition_date	2005-08-29
结构标题 title	X-Ray studies on maltodextrin phosphorylase complexes: recognition of substrates and cathalitic mechanism of phosphorylase family
关键词 keywords	;maltopentaose, carbohydrate recognition, phosphorylase mechanism, ternary complexes with natural and inhibitory substrates, Transferase ;; TRANSFERASE
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	38.93 Å
回转半径 Rg (电子) rg_electron	38.76 Å
零角强度 I(0) i0	491095000.00
分子量 molecular_weight	183070.0 kDa
排除体积 excluded_volume	229750 Å³
包络体积 envelope_volume	283260 Å³
水化壳体积 shell_volume	60107 Å³
包络直径 envelope_diameter	133.2 Å
壳层 Rg shell_rg	45.18 Å
包络 Rg envelope_rg	38.70 Å
形状 Rg shape_rg	38.74 Å
总 Rg total_rg	39.18 Å
总原子数 total_atoms	12928
残基数 n_residues	1592
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	129.3 Å
Rg (实空间) rg_real	38.98 Å
Rg 误差 (实空间) rg_real_error	0.92 Å
I(0) (实空间) i0_real	4.9110e+08
I(0) 误差 (实空间) i0_real_error	7.7560e+06
Rg (倒空间) rg_reciprocal	38.96 Å
I(0) (倒空间) i0_reciprocal	491100000.0000
解质量估计 total_estimate	0.8831
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	41.0 Å
偏度 Skewness skewness	0.361
峰度 Kurtosis kurtosis	-0.476
角度范围 angular_range	— – 0.2050 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	204900000.0000
实空间数据点数 n_real_points	42
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.869; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.878

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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	Maltodextrin phosphorylase
分子量 formula_weight	90547.1 kDa
EC 编号 ec_number	2.4.1.1
突变 mutation	H261A, T262F, A263E
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	14073

SQPIFNDKQFQEALSRQWQRYGLNSAAEMTPRQWWLAVSEALAEMLRAQPFAKPVANQRHVNYISMEFLIGRLTGNNLLNLGWYQDVQDSLKAYDINLTDLLEEEIDPALGNGGLGRLAACFLDSMATVGQSATGYGLNYQYGLFRQSFVDGKQVEAPDDWHRSNYPWFRHNEALDVQVGIGGKVTKDGRWEPEFTITGQAWDLPVVGYRNGVAQPLRLWQATHAHPFDLTKFNDGDFLRAEQQGINAEKLTKVLYPNDNAFEGKKLRLMQQYFQCACSVADILRRHHLAGRKLHELADYEVIQLNDTHPTIAIPELLRVLIDEHQMSWDDAWAITSKTFAYTNHTLMPEALERWDVKLVKGLLPRHMQIINEINTRFKTLVEKTWPGDEKVWAKLAVVHDKQVHMANLCVVGGFAVNGVAALHSDLVVKDLFPEYHQLWPNKFHNVTNGITPRRWIKQCNPALAALLDKSLQKEWANDLDQLINLEKFADDAKFRQQYREIKQANKVRLAEFVKVRTGIEINPQAIFDIQIKRLHEYKRQHLNLLHILALYKEIRENPQADRVPRVFLFGAKAAPGYYLAKNIIFAINKVADVINNDPLVGDKLKVVFLPDYCVSAAEKLIPAADISEQISTAGKEASGTGNMKLALNGALTVGTLDGANVEIAEKVGEENIFIFGHTVEQVKAILAKGYDPVKWRKKDKVLDAVLKELESGKYSDGDKHAFDQMLHSIGKQGGDPYLVMADFAAYVEAQKQVDVLYRDQEAWTRAAILNTARCGMFSSDRSIRDYQARIWQAKR

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 branched

描述 description	;alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose ;
分子量 formula_weight	828.7 kDa
来源方法 src_method	man
拷贝数 entity_count	2

Entity 3 non-polymer

描述 description	NITRATE ION
分子量 formula_weight	62.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	PYRIDOXAL-5'-PHOSPHATE
分子量 formula_weight	247.1 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	1145

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6. 折叠分类 (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d2av6a_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.87 — UDP-Glycosyltransferase/glycogen phosphorylase
超家族 Superfamily superfamily	c.87.1 — UDP-Glycosyltransferase/glycogen phosphorylase
家族 Family family	c.87.1.4 — Oligosaccharide phosphorylase

结构域编号 domain_id	d2av6b_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.87 — UDP-Glycosyltransferase/glycogen phosphorylase
超家族 Superfamily superfamily	c.87.1 — UDP-Glycosyltransferase/glycogen phosphorylase
家族 Family family	c.87.1.4 — Oligosaccharide phosphorylase

CATH v4.4 (4 domains)

结构域编号 domain_id	2av6A01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	2000 — Glycogen Phosphorylase B;

结构域编号 domain_id	2av6A02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	2000 — Glycogen Phosphorylase B;

结构域编号 domain_id	2av6B01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	2000 — Glycogen Phosphorylase B;

结构域编号 domain_id	2av6B02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	2000 — Glycogen Phosphorylase B;

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7. 引用文献 (1)

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晶胞边长 a length_a	74.957 Å
晶胞边长 b length_b	105.614 Å
晶胞边长 c length_c	218.629 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	8

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	2.010 Å
最低分辨率 resolution_low	15.000 Å
R 因子 r_factor	0.1927
R_work r_work	0.1900
R_free r_free	0.2439

fit	/app/data/saxs_computation/av/2av6/2av6.fit
pddf	/app/data/pr_computation/av/2av6/2av6.pr.out
profile	/app/data/saxs_computation/av/2av6/2av6.dat

X-Ray studies on maltodextrin phosphorylase complexes: recognition of substrates and cathalitic mechanism of phosphorylase family

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