SAXSdb — 1s4n

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1s4n
沉积日期 deposition_date	2004-01-16
结构标题 title	Crystal structure of yeast alpha1,2-mannosyltransferase Kre2p/Mnt1p
关键词 keywords	ALPHA/BETA FOLD, NUCLEOTIDE-BINDING DOMAIN, ROSSMANN FOLD, 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	26.83 Å
回转半径 Rg (电子) rg_electron	25.82 Å
零角强度 I(0) i0	105291000.00
分子量 molecular_weight	82280.0 kDa
排除体积 excluded_volume	103140 Å³
包络体积 envelope_volume	119720 Å³
水化壳体积 shell_volume	37111 Å³
包络直径 envelope_diameter	89.4 Å
壳层 Rg shell_rg	34.40 Å
包络 Rg envelope_rg	25.97 Å
形状 Rg shape_rg	25.79 Å
总 Rg total_rg	26.76 Å
总原子数 total_atoms	5823
残基数 n_residues	672
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	85.3 Å
Rg (实空间) rg_real	26.68 Å
Rg 误差 (实空间) rg_real_error	0.48 Å
I(0) (实空间) i0_real	1.0530e+08
I(0) 误差 (实空间) i0_real_error	1.3130e+06
Rg (倒空间) rg_reciprocal	26.73 Å
I(0) (倒空间) i0_reciprocal	105300000.0000
解质量估计 total_estimate	0.8937
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	33.2 Å
偏度 Skewness skewness	0.204
峰度 Kurtosis kurtosis	-0.423
角度范围 angular_range	— – 0.2950 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	28330000.0000
实空间数据点数 n_real_points	60
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.881; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.975

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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	Glycolipid 2-alpha-mannosyltransferase
分子量 formula_weight	41349.2 kDa
EC 编号 ec_number	2.4.1.131
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	6494

EFADAPIDTKTTMDYITPSFANKAGKPKACYVTLVRNKELKGLLSSIKYVENKINKKFPYPWVFLNDEPFTEEFKEAVTKAVSSEVKFGILPKEHWSYPEWINQTKAAEIRADAATKYIYGGSESYRHMCRYQSGFFWRHELLEEYDWYWRVEPDIKLYCDINYDVFKWMQENEKVYGFTVSIHEYEVTIPTLWQTSMDFIKKNPEYLDENNLMSFLSNDNGKTYNLCHFWSNFEIANLNLWRSPAYREYFDTLDHQGGFFYERWGDAPVHSIAAALFLPKDKIHYFSDIGYHHPPYDNCPLDKEVYNSNNCECDQGNDFTFQGYSCGKEYYDAQGLVKPKNWKKFRE

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI 分类编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Pichia pastoris

Entity 2 branched

描述 description	;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-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	1397.2 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 3 branched

描述 description	2-acetamido-2-deoxy-alpha-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	1

Entity 4 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	2

Entity 5 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

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	671

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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	d1s4na_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.68 — Nucleotide-diphospho-sugar transferases
超家族 Superfamily superfamily	c.68.1 — Nucleotide-diphospho-sugar transferases
家族 Family family	c.68.1.16 — Glycolipid 2-alpha-mannosyltransferase

结构域编号 domain_id	d1s4nb_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.68 — Nucleotide-diphospho-sugar transferases
超家族 Superfamily superfamily	c.68.1 — Nucleotide-diphospho-sugar transferases
家族 Family family	c.68.1.16 — Glycolipid 2-alpha-mannosyltransferase

CATH v4.4 (2 domains)

结构域编号 domain_id	1s4nA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

结构域编号 domain_id	1s4nB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

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7. 引用文献 (1)

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晶胞边长 a length_a	60.694 Å
晶胞边长 b length_b	101.068 Å
晶胞边长 c length_c	62.036 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	98.81 °
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	2.010 Å
最低分辨率 resolution_low	19.960 Å
R 因子 r_factor	0.1800
R_work r_work	0.1800
R_free r_free	0.2320

fit	/app/data/saxs_computation/s4/1s4n/1s4n.fit
pddf	/app/data/pr_computation/s4/1s4n/1s4n.pr.out
profile	/app/data/saxs_computation/s4/1s4n/1s4n.dat

Crystal structure of yeast alpha1,2-mannosyltransferase Kre2p/Mnt1p

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution