SAXSdb — 1v7w

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1v7w
沉积日期 deposition_date	2003-12-24
结构标题 title	Crystal structure of Vibrio proteolyticus chitobiose phosphorylase in complex with GlcNAc
关键词 keywords	beta-sandwich, (alpha/alpha)6 barrel, 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	28.54 Å
回转半径 Rg (电子) rg_electron	27.46 Å
零角强度 I(0) i0	131312000.00
分子量 molecular_weight	88572.0 kDa
排除体积 excluded_volume	109550 Å³
包络体积 envelope_volume	125610 Å³
水化壳体积 shell_volume	37352 Å³
包络直径 envelope_diameter	92.7 Å
壳层 Rg shell_rg	35.68 Å
包络 Rg envelope_rg	27.70 Å
形状 Rg shape_rg	27.44 Å
总 Rg total_rg	28.27 Å
总原子数 total_atoms	6256
残基数 n_residues	779
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	89.2 Å
Rg (实空间) rg_real	28.47 Å
Rg 误差 (实空间) rg_real_error	0.50 Å
I(0) (实空间) i0_real	1.3130e+08
I(0) 误差 (实空间) i0_real_error	1.9430e+06
Rg (倒空间) rg_reciprocal	28.50 Å
I(0) (倒空间) i0_reciprocal	131300000.0000
解质量估计 total_estimate	0.8992
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	33.5 Å
偏度 Skewness skewness	0.297
峰度 Kurtosis kurtosis	-0.436
角度范围 angular_range	— – 0.2800 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	32230000.0000
实空间数据点数 n_real_points	57
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.929; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.898

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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	chitobiose phosphorylase
分子量 formula_weight	91286.0 kDa
EC 编号 ec_number	2.4.1.-
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	7168

MKYGYFDNDNREYVITRPDVPAPWTNYLGTEKFCTVISHNAGGYSFYNSPEYNRVTKFRPNATFDRPGHYVYLRDDDSGDYWSISWQPVAKSLDEAQYQIRHGLSYSKFQCDYNGIHARKTLFVPKGEDAEIWDVVIKNTSDQVRTISAFSFVEFSFSHIQSDNQNHQMSLYSAGTAYRPGLIEYDLYYNTDDFEGFYYLASTFDPDSYDGQRDRFLGLYRDEANPLAVEQGRCSNSAQTCYNHCGSLHKQFTLQPGEEIRFAYILGIGKGNGERLREHYQDVANIDAAFAAIKAHWDERCAKFQVKSPNQGLDTMINAWTLYQAETCVVWSRFASFIEVGGRTGLGYRDTAQDAISVPHANPEMTRKRIVDLLRGQVKAGYGLHLFDPDWFDPEKEDVAPSKSPTVVPTPSDEDKIHGIKDTCSDDHLWLIPTICKYVMETGETSFFDQMIPYADGGEASVYEHMKAALDFSAEYVGQTGICKGLRADWNDCLNLGGGESSMVSFLHFWALQEFIDLAKFLGKDQDVNTYTEMAANVREACETHLWDDEGGWYIRGLTKNGDKIGTAQQQEGRVHLESNTLAVLSGLASQERGEQAMDAVDEHLFSPYGLHLNAPSFSTPNDDIGFVTRVYQGVKENGAIFSHPNPWAWVAETKLGRGDRAMKFYDALNPYNQNDIIEKRIAEPYSYVQFIMGRDHQDHGRANHPWLTGTSGWAYFAVTNYILGVQSGFTGLSVDPCIPSDWPGFEVTRQWRGATYHIQVENPDHVSKGVKSITLNGAPIQGRIPPQAQGSDNQVVVVLGHHHHHH

来源 Source

来源生物 organism	Vibrio proteolyticus
NCBI 分类编号 ncbi_taxonomy_id	671
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	2-acetamido-2-deoxy-alpha-D-glucopyranose
分子量 formula_weight	221.2 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 3 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	1

Entity 4 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 5 non-polymer

描述 description	CHLORIDE ION
分子量 formula_weight	35.5 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	912

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6. 折叠分类 (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1v7wa1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.102 — alpha/alpha toroid
超家族 Superfamily superfamily	a.102.1 — Six-hairpin glycosidases
家族 Family family	a.102.1.4 — Glycosyltransferase family 36 C-terminal domain

结构域编号 domain_id	d1v7wa2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.30 — Supersandwich
超家族 Superfamily superfamily	b.30.5 — Galactose mutarotase-like
家族 Family family	b.30.5.3 — Glycosyltransferase family 36 N-terminal domain

CATH v4.4 (3 domains)

结构域编号 domain_id	1v7wA01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	70 — Distorted Sandwich
拓扑 Topology topology	98 — Beta-galactosidase; Chain A, domain 5
同源超家族 H-superfamily homologous superfamily	40 — Glycoside hydrolase, family 65, N-terminal domain

结构域编号 domain_id	1v7wA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	420 — Maltose phosphorylase, domain 3
同源超家族 H-superfamily homologous superfamily	10 — Maltose phosphorylase, domain 3

结构域编号 domain_id	1v7wA03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	50 — Alpha/alpha barrel
拓扑 Topology topology	10 — Glycosyltransferase
同源超家族 H-superfamily homologous superfamily	10 —

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7. 引用文献 (2)

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晶胞边长 a length_a	141.064 Å
晶胞边长 b length_b	70.729 Å
晶胞边长 c length_c	80.410 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	98.41 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	1.600 Å
最低分辨率 resolution_low	38.870 Å
R 因子 r_factor	0.1570
R_work r_work	0.1570
R_free r_free	0.1790

fit	/app/data/saxs_computation/v7/1v7w/1v7w.fit
pddf	/app/data/pr_computation/v7/1v7w/1v7w.pr.out
profile	/app/data/saxs_computation/v7/1v7w/1v7w.dat

Crystal structure of Vibrio proteolyticus chitobiose phosphorylase in complex with GlcNAc

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution