SAXSdb — 9efk

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9efk
沉积日期 deposition_date	2024-11-20
结构标题 title	Cryo-EM structure of the portal-tail complex of LME-1 phage
关键词 keywords	LME-1, legionella pneumophila, phage, portal, tail, podovirus, podophage, 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	80.44 Å
回转半径 Rg (电子) rg_electron	79.83 Å
零角强度 I(0) i0	45531100000.00
分子量 molecular_weight	1838200.0 kDa
排除体积 excluded_volume	2303800 Å³
包络体积 envelope_volume	3254100 Å³
水化壳体积 shell_volume	312730 Å³
包络直径 envelope_diameter	262.3 Å
壳层 Rg shell_rg	92.35 Å
包络 Rg envelope_rg	78.86 Å
形状 Rg shape_rg	79.83 Å
总 Rg total_rg	79.93 Å
总原子数 total_atoms	129576
残基数 n_residues	16542
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	296.6 Å
Rg (实空间) rg_real	83.47 Å
Rg 误差 (实空间) rg_real_error	1.69 Å
I(0) (实空间) i0_real	4.5530e+10
I(0) 误差 (实空间) i0_real_error	9.2450e+08
Rg (倒空间) rg_reciprocal	81.46 Å
I(0) (倒空间) i0_reciprocal	45660000000.0000
解质量估计 total_estimate	0.8789
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	93.7 Å
偏度 Skewness skewness	0.527
峰度 Kurtosis kurtosis	0.390
角度范围 angular_range	— – 0.0950 Å⁻¹
当前正则化参数 α current_alpha	0.9002
最高正则化参数 α highest_alpha	4720000000.0000
实空间数据点数 n_real_points	20
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.646; Stabil: 0.906; Sysdev: 1.000; Positv: 1.000; Valcen: 0.972; Smooth: 0.872

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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	orf12
分子量 formula_weight	62743.1 kDa
来源方法 src_method	nat
拷贝数 entity_count	12

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,I,J,K,L
原子数 atom_count	129576

MVDVKKLLGKRDNSKLYEEIRKETKPKLDVNRLCRMRNDAKSDLDMWRSILQTAYHYAMPDYNPFENYGLAGFLTPGQQYNADIYDLTLPIAHKRLADKMLMNMVPQGQQWVKFTPGDEFGEPGTPLYQRALDATQRMTDHFFKIIDRSNFYLAVGESLQDVLISTGIIAINEGNRKRPVRYEAVPPAQVMFQGDAEGQVDAIFRDWYQVRIENIKSMWPKAEVAKLNKKPEDKVDIWECAWIDYEAPEKERYQYVVMTSSKDVLLEQSNSSWPWVVYRMRRLTGEIRGRGPSLSAYPTAATINQALEDELVAAAFQANPMYMAASDSAFNQQTFTPRPGSIVPVQMVQGEWPIKPFEQSGNIQFNALLVNDFRQQINELLYAFPLGAVNSPTRTATEAEIRYTENLESFSAMVPRLQNEFFIPVIQRTLWVINKVLPETFANIPDDIRNKMISVDGQILGLSFDTPLMTAKGQVKTAALLGFYQAAASLLGPEAATASLDPVEVLTNLADNQGIDVRNIKTREELEQLLQAAGQIAQQEAAQQGVIIGSEQPQ

Entity 2 polymer

描述 description	orf18
分子量 formula_weight	89922.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	M,N,O,P,Q,R

MPIRSISNTFNRGELDPTLFARDDLDIYDKGARKLRNMIALWTGAARIAPGTIYIDMMVDRENGNAVIQDPLMVKGFDFTYDADAEITYTIIIRKSGTNIAFDIYYADTLQTTVTSTAYLATQIQDIHVAAAHDRVLILHENVQIRQLKRGASHSSWSLTTFNPRVYPTYDFSVIGEAINYQSFTFTLSATTGSITITSSSAVFTHNHVGGLFRSLGGTARITAVASTTSASATVLDNFTGTSCAGNLSSLAEKLWNSDTTTAPVSANRGWPARGVFYLNRLILGRSLAVKNLVNLSTAGVYDNFDDADLDGLVAFSVTFNGKGEQSVQSIVADDSILFTTANKLFAQSPLVESPITINNVYFAPQSQSPATSIEAASIDNQTLFVSSDRTKVMQAMYSTADGKYITLPATMLSNSIVDYINSNGTWEPAGISTRLYLATQDNGTMLLYSTLQTQNVAGWSLRTTTGKFRQVIGEGRQSHVIVEREINIGASFEQTLDYAYLSDPTFKARYDVTEFFASSPMTSAIGVLENQNDYILIGNQAPFTALDIDFNLVASSDCQLQFEYLDGNGFWDVFTPTDNTSGFTVDGTITWTFDDVLNWAPYQVNAIENQYWIRIKRLAETVNTAPVIGQVLINTGNRIYLERQSFDEYMDSTQIVTSDSNGLVTGLTHLAGQQVYAITEDGATIGSSFVDASGETSVKNVNTTLTVGMQYKPELIPMPLYAPTQMGDSLYAEKYVQDLYVDYVDSLYLQAGFRPQLTDIPNMHLGNYTLGQSVPPQTGIYRICPRGDWEPRQEFVITQSQPGPMTIIGVGYNVEVA

Entity 3 polymer

描述 description	orf22
分子量 formula_weight	68819.8 kDa
来源方法 src_method	nat
拷贝数 entity_count	18

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	AE,AF,AG,AN,AO,AP,AW,AX,AY,BF,BG,BH,BO,BP,BQ,BX,BY,BZ

MSNIKINDVFQRIQYAASAGQTQFTIPFPFFDNEYVLVWQNGVQLVMGGAPGQYGISGAGSPSGGLITLVTPAALNDIITIQGDMPIDRTSIYSATISNLTGSDLNGDFNREVVMMKQIQTTQALLQLQYAPWLEVSQDPDVTKDRYLPLLGSGQVWRMNDSGTGIEAYTIDETPAPSSSPFIIYQADATLSNAQNLGALTSGILKQTVGGGSSTLSIAQNAVDYWAPGDELTRSQAPVSPDDVVNKAYADSIASGFTFINPVNAASTANFNSTYNNGSSGVGATLTATSNGAFSLDGQAGVLNKSYLMKDQTNTFENGIYILTQVGDGSTPAILTRATYFDQPSEIQPGDLVPVLAGTVNNGTLWLQTDTVSAVGTDPITFIAFLPAFSNIVTISGNQTITGDKTFTGTTTLDNFIFVGSNIQHLGDTGNQIIFGTATQINTINNNTISDLSSSGLRLGAANARVSTILDEDDMASDSATALATQQSIKAYVDNFRAAGAILQTVSTNMTNTFSASLAAGSGFSDVTGFNVSITPSATANKVFIKVDMLLASDTVDIVVVVRLKRNGTPIDIGNAAGSRIQITTGSTNAKALDGLQAVSFSFLDSPATTSAITYQVDIGQRTSGSAVGIVVNRSGADVDSSSYTRGASTITAQEIKG

Entity 4 polymer

描述 description	orf17
分子量 formula_weight	22792.1 kDa
来源方法 src_method	nat
拷贝数 entity_count	12

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	T,AC,AD,S,X,U,V,W,Y,Z,AA,AB

MIELTSAPTTKIEIISAAISMVGKQQTVNTIDGGGALAIDAEKLYDTLVSAELGSNRWRFAQAFQQISIITTLNPTFDGWLYECQIPADCIMVQYLYPNIQYIVFGDKILTKSNQTFTLIYSRNVPVSKWPPPFSLYIVYHLASMLGISVTNSDRMLARISQGMEMWESRALFADAQSSVTLPFRHNPYVDVRYRYKTRGY

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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	triclinic

分辨率 resolution	1.90 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	88530

fit	/app/data/saxs_computation/ef/9efk/9efk.fit
pddf	/app/data/pr_computation/ef/9efk/9efk.pr.out
profile	/app/data/saxs_computation/ef/9efk/9efk.dat

Cryo-EM structure of the portal-tail complex of LME-1 phage

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

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 polymer

聚合体 Polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)