1zhs

Crystal structure of MVL bound to Man3GlcNAc2

Method: X-RAY DIFFRACTION D_max: 114.5 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	1zhs
沉积日期 deposition_date	2005-04-26
结构标题 title	Crystal structure of MVL bound to Man3GlcNAc2
关键词 keywords	MVL, HIV-1, carbohydrate binding, SUGAR BINDING PROTEIN; SUGAR BINDING PROTEIN
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	34.66 Å
回转半径 Rg (电子) rg_electron	34.13 Å
零角强度 I(0) i0	201841000.00
分子量 molecular_weight	114300.0 kDa
排除体积 excluded_volume	142900 Å³
包络体积 envelope_volume	178250 Å³
水化壳体积 shell_volume	43778 Å³
包络直径 envelope_diameter	118.7 Å
壳层 Rg shell_rg	40.56 Å
包络 Rg envelope_rg	33.71 Å
形状 Rg shape_rg	34.12 Å
总 Rg total_rg	34.62 Å
总原子数 total_atoms	8026
残基数 n_residues	904
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	114.5 Å
Rg (实空间) rg_real	34.65 Å
Rg 误差 (实空间) rg_real_error	0.88 Å
I(0) (实空间) i0_real	2.0180e+08
I(0) 误差 (实空间) i0_real_error	3.0600e+06
Rg (倒空间) rg_reciprocal	34.66 Å
I(0) (倒空间) i0_reciprocal	201800000.0000
解质量估计 total_estimate	0.8871
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	34.9 Å
偏度 Skewness skewness	0.305
峰度 Kurtosis kurtosis	-0.435
角度范围 angular_range	— – 0.2300 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	63760000.0000
实空间数据点数 n_real_points	47
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.882; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.885

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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	mannan-binding lectin
分子量 formula_weight	12244.7 kDa
来源方法 src_method	man
拷贝数 entity_count	8

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H
原子数 atom_count	8669

ASYKVNIPAGPLWSNAEAQQVGPKIAAAHQGNFTGQWTTVVESAMSVVEVELQVENTGIHEFKTDVLAGPLWSNDEAQKLGPQIAASYGAEFTGQWRTIVEGVMSVIQIKYTF

来源 Source

来源生物 organism	Microcystis viridis
NCBI 分类编号 ncbi_taxonomy_id	44822
宿主生物 host_organism	Escherichia coli

Entity 2 branched

描述 description	;alpha-D-mannopyranose-(1-3)-[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	910.8 kDa
来源方法 src_method	man
拷贝数 entity_count	16

Entity 3 non-polymer

描述 description	1,2-ETHANEDIOL
分子量 formula_weight	62.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	26

Entity 4 non-polymer

描述 description	PHOSPHATE ION
分子量 formula_weight	95.0 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	643

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6. 折叠分类 (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

结构域编号 domain_id	d1zhsa1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.230 — Dodecin subunit-like
超家族 Superfamily superfamily	d.230.7 — Oligosaccharide binding protein
家族 Family family	d.230.7.1 — Oligomannose binding protein MVL-like

结构域编号 domain_id	d1zhsa2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.230 — Dodecin subunit-like
超家族 Superfamily superfamily	d.230.7 — Oligosaccharide binding protein
家族 Family family	d.230.7.1 — Oligomannose binding protein MVL-like

结构域编号 domain_id	d1zhsb1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.230 — Dodecin subunit-like
超家族 Superfamily superfamily	d.230.7 — Oligosaccharide binding protein
家族 Family family	d.230.7.1 — Oligomannose binding protein MVL-like

结构域编号 domain_id	d1zhsb2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.230 — Dodecin subunit-like
超家族 Superfamily superfamily	d.230.7 — Oligosaccharide binding protein
家族 Family family	d.230.7.1 — Oligomannose binding protein MVL-like

结构域编号 domain_id	d1zhsc1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.230 — Dodecin subunit-like
超家族 Superfamily superfamily	d.230.7 — Oligosaccharide binding protein
家族 Family family	d.230.7.1 — Oligomannose binding protein MVL-like

结构域编号 domain_id	d1zhsc2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.230 — Dodecin subunit-like
超家族 Superfamily superfamily	d.230.7 — Oligosaccharide binding protein
家族 Family family	d.230.7.1 — Oligomannose binding protein MVL-like

结构域编号 domain_id	d1zhsd1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.230 — Dodecin subunit-like
超家族 Superfamily superfamily	d.230.7 — Oligosaccharide binding protein
家族 Family family	d.230.7.1 — Oligomannose binding protein MVL-like

结构域编号 domain_id	d1zhsd2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.230 — Dodecin subunit-like
超家族 Superfamily superfamily	d.230.7 — Oligosaccharide binding protein
家族 Family family	d.230.7.1 — Oligomannose binding protein MVL-like

结构域编号 domain_id	d1zhse1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.230 — Dodecin subunit-like
超家族 Superfamily superfamily	d.230.7 — Oligosaccharide binding protein
家族 Family family	d.230.7.1 — Oligomannose binding protein MVL-like

结构域编号 domain_id	d1zhse2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.230 — Dodecin subunit-like
超家族 Superfamily superfamily	d.230.7 — Oligosaccharide binding protein
家族 Family family	d.230.7.1 — Oligomannose binding protein MVL-like

结构域编号 domain_id	d1zhsf1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.230 — Dodecin subunit-like
超家族 Superfamily superfamily	d.230.7 — Oligosaccharide binding protein
家族 Family family	d.230.7.1 — Oligomannose binding protein MVL-like

结构域编号 domain_id	d1zhsf2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.230 — Dodecin subunit-like
超家族 Superfamily superfamily	d.230.7 — Oligosaccharide binding protein
家族 Family family	d.230.7.1 — Oligomannose binding protein MVL-like

结构域编号 domain_id	d1zhsg1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.230 — Dodecin subunit-like
超家族 Superfamily superfamily	d.230.7 — Oligosaccharide binding protein
家族 Family family	d.230.7.1 — Oligomannose binding protein MVL-like

结构域编号 domain_id	d1zhsg2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.230 — Dodecin subunit-like
超家族 Superfamily superfamily	d.230.7 — Oligosaccharide binding protein
家族 Family family	d.230.7.1 — Oligomannose binding protein MVL-like

结构域编号 domain_id	d1zhsh1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.230 — Dodecin subunit-like
超家族 Superfamily superfamily	d.230.7 — Oligosaccharide binding protein
家族 Family family	d.230.7.1 — Oligomannose binding protein MVL-like

结构域编号 domain_id	d1zhsh2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.230 — Dodecin subunit-like
超家族 Superfamily superfamily	d.230.7 — Oligosaccharide binding protein
家族 Family family	d.230.7.1 — Oligomannose binding protein MVL-like

CATH v4.4 (16 domains)

结构域编号 domain_id	1zhsA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1490 — Dna Ligase; domain 1
同源超家族 H-superfamily homologous superfamily	230 —

结构域编号 domain_id	1zhsA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1490 — Dna Ligase; domain 1
同源超家族 H-superfamily homologous superfamily	230 —

结构域编号 domain_id	1zhsB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1490 — Dna Ligase; domain 1
同源超家族 H-superfamily homologous superfamily	230 —

结构域编号 domain_id	1zhsB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1490 — Dna Ligase; domain 1
同源超家族 H-superfamily homologous superfamily	230 —

结构域编号 domain_id	1zhsC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1490 — Dna Ligase; domain 1
同源超家族 H-superfamily homologous superfamily	230 —

结构域编号 domain_id	1zhsC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1490 — Dna Ligase; domain 1
同源超家族 H-superfamily homologous superfamily	230 —

结构域编号 domain_id	1zhsD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1490 — Dna Ligase; domain 1
同源超家族 H-superfamily homologous superfamily	230 —

结构域编号 domain_id	1zhsD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1490 — Dna Ligase; domain 1
同源超家族 H-superfamily homologous superfamily	230 —

结构域编号 domain_id	1zhsE01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1490 — Dna Ligase; domain 1
同源超家族 H-superfamily homologous superfamily	230 —

结构域编号 domain_id	1zhsE02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1490 — Dna Ligase; domain 1
同源超家族 H-superfamily homologous superfamily	230 —

结构域编号 domain_id	1zhsF01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1490 — Dna Ligase; domain 1
同源超家族 H-superfamily homologous superfamily	230 —

结构域编号 domain_id	1zhsF02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1490 — Dna Ligase; domain 1
同源超家族 H-superfamily homologous superfamily	230 —

结构域编号 domain_id	1zhsG01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1490 — Dna Ligase; domain 1
同源超家族 H-superfamily homologous superfamily	230 —

结构域编号 domain_id	1zhsG02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1490 — Dna Ligase; domain 1
同源超家族 H-superfamily homologous superfamily	230 —

结构域编号 domain_id	1zhsH01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1490 — Dna Ligase; domain 1
同源超家族 H-superfamily homologous superfamily	230 —

结构域编号 domain_id	1zhsH02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1490 — Dna Ligase; domain 1
同源超家族 H-superfamily homologous superfamily	230 —

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7. 引用文献 (1)

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晶胞边长 a length_a	47.783 Å
晶胞边长 b length_b	73.740 Å
晶胞边长 c length_c	78.863 Å
晶胞夹角 α angle_alpha	90.45 °
晶胞夹角 β angle_beta	98.45 °
晶胞夹角 γ angle_gamma	108.91 °
晶胞分子数 Z z_pdb	8

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

分辨率 resolution	1.800 Å
最低分辨率 resolution_low	19.880 Å
R 因子 r_factor	—
R_work r_work	0.1920
R_free r_free	0.2210

fit	/app/data/saxs_computation/zh/1zhs/1zhs.fit
pddf	/app/data/pr_computation/zh/1zhs/1zhs.pr.out
profile	/app/data/saxs_computation/zh/1zhs/1zhs.dat