SAXSdb — 9k2v

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9k2v
沉积日期 deposition_date	2024-10-18
结构标题 title	Cyanophage A4 pre-ejectosome
关键词 keywords	Cyanophage, Virus, Ejectosome, 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	73.22 Å
回转半径 Rg (电子) rg_electron	72.72 Å
零角强度 I(0) i0	12644600000.00
分子量 molecular_weight	901970.0 kDa
排除体积 excluded_volume	1108600 Å³
包络体积 envelope_volume	1973100 Å³
水化壳体积 shell_volume	216950 Å³
包络直径 envelope_diameter	219.6 Å
壳层 Rg shell_rg	84.71 Å
包络 Rg envelope_rg	67.43 Å
形状 Rg shape_rg	72.71 Å
总 Rg total_rg	72.86 Å
总原子数 total_atoms	63405
残基数 n_residues	8165
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	192.2 Å
Rg (实空间) rg_real	72.74 Å
Rg 误差 (实空间) rg_real_error	0.78 Å
I(0) (实空间) i0_real	1.2640e+10
I(0) 误差 (实空间) i0_real_error	2.3380e+08
Rg (倒空间) rg_reciprocal	74.74 Å
I(0) (倒空间) i0_reciprocal	12690000000.0000
解质量估计 total_estimate	0.8410
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	109.8 Å
偏度 Skewness skewness	-0.180
峰度 Kurtosis kurtosis	-0.655
角度范围 angular_range	— – 0.1050 Å⁻¹
当前正则化参数 α current_alpha	0.0002
最高正则化参数 α highest_alpha	1184000000.0000
实空间数据点数 n_real_points	22
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.982; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.000

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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 (4)

Entity 1 polymer

描述 description	Portal protein
分子量 formula_weight	74284.6 kDa
来源方法 src_method	nat
拷贝数 entity_count	10

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	K,M,O,G,I,F,H,J,L,N
原子数 atom_count	63405

MIRIKDFNHVITGREQPLDINEAIASYITSRYVYFKDARRVAEETWLEAWSLYSGTPEAVDHQRTQTINTVGEVNNDWRHRLNTGKAYECIETVHGYLMGALFPNREWFDLTPNNPGYANEARIIRKYLTKKFNEGKFRVSFEKYLRQLLVCGYSVMALPWRYESRPYKYNVTIKREENEYYDNSTQKANYRTVTENRVTRNAPEFECLDVFDVYLSPTSNDPNESDFIRRIKKTRADIITAIKRGYYTDIDPYDIVNMSAYEVNDRVDKLTSFQGIETNHPYCMDDIIEVVEYWGDLHLDGVSLYDVKATVIGQTLVCCEPNPFWAGKPFVVGSITELPETPYSVGLLQPNMGLLHQLNIITNQRCDNLELAIDEMWTLVQNSSLNPDEVQVAPGKVFLVDSHDDLRPIQRGGNNFVVSYQEAGLLESTIDRNTGTGNLISANASRSGERVTAAEIQAVRDAGGNRLSNIHRHIEDTSLMEILRRVYRSAQQFVTEPEMIRVSGAKPGEYLFLEVDPESLNKEYSLEPIGADFVTDATKYVRQRMDFIAFASQIPQMAERLNYEALLNDVVNHSGFDDPYSYIVKPQQPAPQPDMGATPEPQTGQAPPDEQTNPFYDIGGVSLQNAIGANIQADGANELINFTTGVNTNADQ

Entity 2 polymer

描述 description	Internal virion protein
分子量 formula_weight	40871.7 kDa
来源方法 src_method	nat
拷贝数 entity_count	10

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	V,W,X,Y,Z,v,w,x,y,z

MGGAAIGGILGGVQLVAGISQANSQANAQRQSLQAQAQTTVDASRIRQMEILQARDQSRFNSSMNELARQQNYQNQTFLIQRQLLQEQMDAETTKQQAEQQRLQTMSGIEQKDRQTEQQMVGAEVNFQQTLQQLAQQLGVVNAQSSQQLTGAEDATKELGQRLDTRDVLAMASGVGLGSSTSSQQQNADLLGTIDKVAKVLQGTQVGMEVQQRMTELASASSESERNIKLSELGSYLSDSDFMRNIANIQASATNQNVDSTMGVNAAARETAVNAINAADMMNRQTDTVNNDLAEMGYQVQTSAVNSSQNNAMSGINAQYGSIGGNTFAGLLSSGVNAFNTYQGVLGQQNALNQQKQMTYLNSGILSNGATNNNTFKGYN

Entity 3 polymer

描述 description	Internal protein
分子量 formula_weight	116336.8 kDa
来源方法 src_method	nat
拷贝数 entity_count	10

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	E,d,A,e,B,a,C,b,D,c

MTIKLIGVDNLDNSQQYNEATNSALVQSLERNQQSVSKTQQILEAGNAAIAQQAVSIGQASQQKAQANANRGSGIGGLLEGVSKAVGTYWEINQNQQLKQAQIDAKTQVIQREQAEAVARAAEKAAAEAAEANKQQALTVSEQEANAVRVELGDLYNEWRSGDKFRSEPGGMTKFRDAGLARIMSRTNITEAQKKELINLHYGNWDAEMKAYSDRTAKYAEEVSQVRRESVIKERTFRVNSVVSGLTWDADPTDAIKKVDAMVSSTVNDQNLPLLDRLQAANSMYNTAYEKVVNNATARAEVERKMKALQAYQYEAITNWNDQTKPRAEREAFDQQLQAKHGLNVDSSYMAWENSRKQYIEFQQQSRQLQDLEQNGLIDSARKVNLSDDFVGSVVQLILYGEGNTAALKERFTDNRNFEANTAGAGEVRRLLEAVPRMRRETDSLRSDNAALQVARTRLQREGVTFLMNADARTRGLLESFAQQFMVNLPKSNVGLTPEQQAEYARQTNQVQQAIEQQIIINDQRVQNNAAELAKYGLSEPEDVLRKNAATRRKLVNDTMYQLGTQAEQVRRTQTSGYGQLGITSPTTALGEGANRERLTFVAPDGYRRLRPPVVANLATVKFTGSSRNGIVPGSKVMLPFMAADAGRVRVNSDNHREARAKHTHAGEDIAAPGGTKVVSYVSGQVIKVTRQKGIGYGRYITIKGDDGMYHRFAHLSAHNVKQGQRVEAGHVIGLVGDDGSPGSYHLHWEVRDNDGYGANGTVNPLKYMGGVNFKESSAPPPQGNTNGWGYNVNNPPTARVPANAIKLPNGKFLVNNRTGALGNPTARAASEQYTVGRPVNTGKVSGSSWSGTNDYGETYGYAYLANNPEFTKKLAITATRLGISAQWLVDIMAFETGNFKKATNWSHSRTGVVGLIGFTPATARALGTTTYALAKMPPEKQLDYVYKYLSDPQLKPHLSKGVEYVAASIFGGSPLVRKMVNNRSGAMQRGDGDINLQNYLKKLGRDVGRRYDIRSMSRADRLIGSAVHTGFHEGCATCAALRSSGSDIVPHNAEFDA

Entity 4 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	5

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7. 引用文献 (1)

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晶胞边长 a length_a	1.000 Å
晶胞边长 b length_b	1.000 Å
晶胞边长 c length_c	1.000 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	—

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

分辨率 resolution	3.400 Å
最低分辨率 resolution_low	— Å
R 因子 r_factor	—
R_work r_work	—
R_free r_free	—

分辨率 resolution	3.40 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	107142

fit	/app/data/saxs_computation/k2/9k2v/9k2v.fit
pddf	/app/data/pr_computation/k2/9k2v/9k2v.pr.out
profile	/app/data/saxs_computation/k2/9k2v/9k2v.dat

Cyanophage A4 pre-ejectosome

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

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

冷冻电镜 EM 3D

5. 实体与聚合体信息 (4)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

Entity 4 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)