SAXSdb — 9c6o

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9c6o
沉积日期 deposition_date	2024-06-07
结构标题 title	Merbecovirus MOW15-22 Spike glycoprotein RBD bound to the P. davyi ACE2
关键词 keywords	;Merbecovirus, MERS-related coronaviruses, MOW15-22 Spike glycoprotein, fusion protein, P. davyi ACE2, Structural Genomics, Seattle Structural Genomics Center for Infectious Disease, SSGCID, VIRAL PROTEIN ;; VIRAL PROTEIN
实验方法 method	ELECTRON MICROSCOPY

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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	32.22 Å
回转半径 Rg (电子) rg_electron	31.33 Å
零角强度 I(0) i0	115689000.00
分子量 molecular_weight	86069.0 kDa
排除体积 excluded_volume	107790 Å³
包络体积 envelope_volume	143300 Å³
水化壳体积 shell_volume	38949 Å³
包络直径 envelope_diameter	107.1 Å
壳层 Rg shell_rg	37.64 Å
包络 Rg envelope_rg	31.46 Å
形状 Rg shape_rg	31.33 Å
总 Rg total_rg	31.87 Å
总原子数 total_atoms	6086
残基数 n_residues	777
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	106.4 Å
Rg (实空间) rg_real	32.26 Å
Rg 误差 (实空间) rg_real_error	0.79 Å
I(0) (实空间) i0_real	1.1570e+08
I(0) 误差 (实空间) i0_real_error	1.8960e+06
Rg (倒空间) rg_reciprocal	32.24 Å
I(0) (倒空间) i0_reciprocal	115700000.0000
解质量估计 total_estimate	0.8787
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	39.1 Å
偏度 Skewness skewness	0.389
峰度 Kurtosis kurtosis	-0.282
角度范围 angular_range	— – 0.2450 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	15280000.0000
实空间数据点数 n_real_points	50
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.846; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.886

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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	MOW15-22 RBD
分子量 formula_weight	34898.0 kDa
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	B
原子数 atom_count	6086

MGILPSPGMPALLSLVSLLSVLLMGCVAETGTYSVSSFEAKPQGSFIESVYEGNECDFTKLFIGQVPQPYEFGRLVFTNCNYNFTKLLSYFQVNTFQCQKVTPESIATGCYSSLTVDWFAYRVEDKSDLLPGSSSDLQRFNYKPTYSNPTCLISAYTNLVPLGGVNPTNYTTLTNCYGCVDKDPANPWGDQICIPEFVTEVEPGFRPKPSCARVGLEGHISGNDTYSAIVTNGELDSTGDPIWRKGVALTKQPIDSSRADLAFFVSVQIDAQSSSVCPLGAPKLVPRGSSSGGSGLNDIFEAQKIEWHEGGSHHHHHHHH

来源 Source

来源生物 organism	Merbecovirus
NCBI 分类编号 ncbi_taxonomy_id	2509494
宿主生物 host_organism	Homo sapiens

Entity 2 polymer

描述 description	Pteronotus davyi ACE2 ectodomain
分子量 formula_weight	89589.0 kDa
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

MPMGSLQPLATLYLLGMLVASVLAQILTEDEKAKEFLEKFDLEAEKLYHQSSLASWNYNTNITEENVKKMNEADREWSTFYENMTKIAKNYNLSQITDDKVKRQLQALQQNGLSEDENKRLNNILNEMSTIYSTGKVCKPNNPQQCLLLATGLEDIMQYSKDYDERLWAWEGWRSQVGKQLRPLYEKYVDLKNEMAREKNYEDYGDYWRGDYETDGKEDYAYSRNQLIDDVERTFEEIKPLYEHLHAYVRTKLMDAYPSRISPTGCLPAHLLGDMWGRFWTNLYDLTVPYGEKPTIDVTAAMINQSWDAEKIFKEAEKFFMSVGLFNMTQGFWNNSMLTKPDDGREVVCHPTAWDLGNNDFRIKMCTKVTMDDFLTAHHEMGHIQYDMAYAKQPFLLRNGANEGFHEAVGEIMSLSAATPKHLKDLGLLAQNYPEDYETEINFLLKQALNIVGTLPFTYMLEKWRWMVFKGQIPKDQWTKKWWEMKRDIVGVVEPVPHDETYCDAASLFHVANDYSFIRYYTRTIFQFQFQEALCRTAQHTGPLHKCDISNSTAAGEKLLKMLELGKSQPWTFALENIVGERKINVRPLLDYFRPLFNWLKEQNSNSFVGWRTDWSPYVDQSIKVRISLKSALGDKAYEWNDNEMYFFQSSVAYAMRVYFSNFKNQTTPFGVENVQVRNLKPRVSFNFFVTSPKNVSDIIPRSEVVEAIRMSRGRINDAFRLDDNSLEFLGLVPRGSSSGGSGLNDIFEAQKIEWHEGGSHHHHHHHH

来源 Source

来源生物 organism	Pteronotus davyi
NCBI 分类编号 ncbi_taxonomy_id	94956
宿主生物 host_organism	Homo sapiens

Entity 3 branched

描述 description	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	586.5 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 4 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	syn
拷贝数 entity_count	1

Entity 5 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	syn
拷贝数 entity_count	7

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7. 引用文献 (1)

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分辨率 resolution	2.77 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	705956

fit	/app/data/saxs_computation/c6/9c6o/9c6o.fit
pddf	/app/data/pr_computation/c6/9c6o/9c6o.pr.out
profile	/app/data/saxs_computation/c6/9c6o/9c6o.dat

Merbecovirus MOW15-22 Spike glycoprotein RBD bound to the P. davyi ACE2

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

冷冻电镜 EM 3D

5. 实体与聚合体信息 (5)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 branched

Entity 4 branched

Entity 5 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)