1kre

STRUCTURE OF P. CITRINUM ALPHA 1,2-MANNOSIDASE REVEALS THE BASIS FOR DIFFERENCES IN SPECIFICITY OF THE ER AND GOLGI CLASS I ENZYMES

Method: X-RAY DIFFRACTION D_max: 95.2 Å Quality: GOOD

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1kre
沉积日期 deposition_date	2002-01-09
结构标题 title	STRUCTURE OF P. CITRINUM ALPHA 1,2-MANNOSIDASE REVEALS THE BASIS FOR DIFFERENCES IN SPECIFICITY OF THE ER AND GOLGI CLASS I ENZYMES
关键词 keywords	(ALPHA/ALPHA)7-BARREL, 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	30.45 Å
回转半径 Rg (电子) rg_electron	29.73 Å
零角强度 I(0) i0	191762000.00
分子量 molecular_weight	109090.0 kDa
排除体积 excluded_volume	135660 Å³
包络体积 envelope_volume	161870 Å³
水化壳体积 shell_volume	44286 Å³
包络直径 envelope_diameter	98.0 Å
壳层 Rg shell_rg	38.13 Å
包络 Rg envelope_rg	29.47 Å
形状 Rg shape_rg	29.71 Å
总 Rg total_rg	30.50 Å
总原子数 total_atoms	7706
残基数 n_residues	950
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	95.2 Å
Rg (实空间) rg_real	30.37 Å
Rg 误差 (实空间) rg_real_error	0.48 Å
I(0) (实空间) i0_real	1.9180e+08
I(0) 误差 (实空间) i0_real_error	2.6240e+06
Rg (倒空间) rg_reciprocal	30.41 Å
I(0) (倒空间) i0_reciprocal	191800000.0000
解质量估计 total_estimate	0.8979
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	36.6 Å
偏度 Skewness skewness	0.280
峰度 Kurtosis kurtosis	-0.455
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	77630000.0000
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: 0.919; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.913

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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	Mannosyl-oligosaccharide alpha-1,2-mannosidase
分子量 formula_weight	56626.6 kDa
EC 编号 ec_number	3.2.1.113
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	7904

MRLPVSFPLTVLSLLGSTIAHPYGETEAVLRSEPKSNQAKADAVKEAFQHAWNGYMKYAFPHDELTPVSNGHADSRNGWGASAVDALSTAVIMGKADVVNAILEHVADIDFSKTSDTVSLFETTIRYLAGMLSGYDLLQGPAKNLVDNQDLIDGLLDQSRNLADVLKFAFDTPSGVPYNNINITSHGNDGATTNGLAVTGTLVLEWTRLSDLTGDEEYAKLSQKAESYLLKPQPSSSEPFPGLVGSSININDGQFADSRVSWNGGDDSFYEYLIKMYVYDPKRFETYKDRWVLAAESTIKHLKSHPKSRPDLTFLSSYSNRNYDLSSQHLTCFDGGSFLLGGTVLDRQDFIDFGLELVDGCEATYNSTLTKIGPDSWGWDPKKVPSDQKEFYEKAGFYISSGSYVLRPEVIESFYYAHRVTGKEIYRDWVWNAFVAINSTCRTDSGFAAVSDVNKANGGSKYDNQESFLFAEVMKYSYLAHSEDAAWQVQKGGKNTFVYNTEAHPISVARN

来源 Source

来源生物 organism	Penicillium citrinum
NCBI 分类编号 ncbi_taxonomy_id	5077
宿主生物 host_organism	Aspergillus oryzae

Entity 2 branched

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	424.4 kDa
来源方法 src_method	man
拷贝数 entity_count	4

Entity 3 branched

描述 description	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	910.8 kDa
来源方法 src_method	man
拷贝数 entity_count	2

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	2

Entity 5 non-polymer

描述 description	1-DEOXYMANNOJIRIMYCIN
分子量 formula_weight	163.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	198

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6. 折叠分类 (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1krea_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.102 — alpha/alpha toroid
超家族 Superfamily superfamily	a.102.2 — Seven-hairpin glycosidases
家族 Family family	a.102.2.1 — Class I alpha-1;2-mannosidase, catalytic domain

结构域编号 domain_id	d1kreb_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.102 — alpha/alpha toroid
超家族 Superfamily superfamily	a.102.2 — Seven-hairpin glycosidases
家族 Family family	a.102.2.1 — Class I alpha-1;2-mannosidase, catalytic domain

CATH v4.4 (2 domains)

结构域编号 domain_id	1kreA00
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 —

结构域编号 domain_id	1kreB00
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 (1)

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晶胞边长 a length_a	56.487 Å
晶胞边长 b length_b	110.997 Å
晶胞边长 c length_c	86.235 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	99.17 °
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	2.200 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	0.2021
R_work r_work	0.1981
R_free r_free	0.2429

fit	/app/data/saxs_computation/kr/1kre/1kre.fit
pddf	/app/data/pr_computation/kr/1kre/1kre.pr.out
profile	/app/data/saxs_computation/kr/1kre/1kre.dat