SAXSdb — 2i66

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2i66
沉积日期 deposition_date	2006-08-28
结构标题 title	Structural Basis for the Mechanistic Understanding Human CD38 Controlled Multiple Catalysis
关键词 keywords	the catalytic pocket, reaction product, reaction intermediate, HYDROLASE; HYDROLASE
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	27.37 Å
回转半径 Rg (电子) rg_electron	26.67 Å
零角强度 I(0) i0	66861700.00
分子量 molecular_weight	60675.0 kDa
排除体积 excluded_volume	74499 Å³
包络体积 envelope_volume	93472 Å³
水化壳体积 shell_volume	29289 Å³
包络直径 envelope_diameter	103.1 Å
壳层 Rg shell_rg	33.74 Å
包络 Rg envelope_rg	27.03 Å
形状 Rg shape_rg	26.66 Å
总 Rg total_rg	27.43 Å
总原子数 total_atoms	4246
残基数 n_residues	504
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	99.6 Å
Rg (实空间) rg_real	27.41 Å
Rg 误差 (实空间) rg_real_error	0.78 Å
I(0) (实空间) i0_real	6.6860e+07
I(0) 误差 (实空间) i0_real_error	8.9470e+05
Rg (倒空间) rg_reciprocal	27.40 Å
I(0) (倒空间) i0_reciprocal	66860000.0000
解质量估计 total_estimate	0.8495
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	29.2 Å
偏度 Skewness skewness	0.394
峰度 Kurtosis kurtosis	-0.199
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	16810000.0000
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: 0.710; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.920; Smooth: 0.988

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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	ADP-ribosyl cyclase 1
分子量 formula_weight	30380.4 kDa
EC 编号 ec_number	3.2.2.5
突变 mutation	Q49T, N100D, N164D, N209D, N219D
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	4690

KREAEARWRQTWSGPGTTKRFPETVLARCVKYTEIHPEMRHVDCQSVWDAFKGAFISKHPCDITEEDYQPLMKLGTQTVPCNKILLWSRIKDLAHQFTQVQRDMFTLEDTLLGYLADDLTWCGEFDTSKINYQSCPDWRKDCSNNPVSVFWKTVSRRFAEAACDVVHVMLDGSRSKIFDKDSTFGSVEVHNLQPEKVQTLEAWVIHGGREDSRDLCQDPTIKELESIISKRNIQFSCKNIYRPDKFLQCVKNPEDSSCTSEI

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Pichia pastoris

Entity 2 non-polymer

描述 description	;[(2R,3R,4R,5R)-5-(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL [(2R,3S,4R,5S)-3,4,5-TRIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN DIPHOSPHATE ;
分子量 formula_weight	575.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 3 non-polymer

描述 description	;[(2R,3R,4R,5R)-5-(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL [(2R,3S,4S)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN DIPHOSPHATE ;
分子量 formula_weight	559.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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	444

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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	d2i66a_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.23 — Flavodoxin-like
超家族 Superfamily superfamily	c.23.14 — N-(deoxy)ribosyltransferase-like
家族 Family family	c.23.14.3 — ADP ribosyl cyclase-like

结构域编号 domain_id	d2i66b_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.23 — Flavodoxin-like
超家族 Superfamily superfamily	c.23.14 — N-(deoxy)ribosyltransferase-like
家族 Family family	c.23.14.3 — ADP ribosyl cyclase-like

CATH v4.4 (4 domains)

结构域编号 domain_id	2i66A01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	82 — ADP Ribosyl Cyclase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — ADP Ribosyl Cyclase; Chain A, domain 1

结构域编号 domain_id	2i66A02
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	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	2i66B01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	82 — ADP Ribosyl Cyclase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — ADP Ribosyl Cyclase; Chain A, domain 1

结构域编号 domain_id	2i66B02
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	720 — NAD(P)-binding Rossmann-like Domain

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7. 引用文献 (1)

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晶胞边长 a length_a	41.710 Å
晶胞边长 b length_b	52.812 Å
晶胞边长 c length_c	65.424 Å
晶胞夹角 α angle_alpha	105.93 °
晶胞夹角 β angle_beta	91.80 °
晶胞夹角 γ angle_gamma	95.22 °
晶胞分子数 Z z_pdb	2

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	1.700 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.1847
R_work r_work	0.1822
R_free r_free	0.2291

fit	/app/data/saxs_computation/i6/2i66/2i66.fit
pddf	/app/data/pr_computation/i6/2i66/2i66.pr.out
profile	/app/data/saxs_computation/i6/2i66/2i66.dat

Structural Basis for the Mechanistic Understanding Human CD38 Controlled Multiple Catalysis

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