SAXSdb — 8qhc

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8qhc
沉积日期 deposition_date	2023-09-07
结构标题 title	Cryo-EM structure of SidH from Legionella pneumophila in complex with LubX
关键词 keywords	SidH, Legionella, tRNA-binding, EF-Tu-binding, RNA BINDING PROTEIN; RNA BINDING 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	45.89 Å
回转半径 Rg (电子) rg_electron	46.33 Å
零角强度 I(0) i0	730720000.00
分子量 molecular_weight	211490.0 kDa
排除体积 excluded_volume	259740 Å³
包络体积 envelope_volume	381320 Å³
水化壳体积 shell_volume	69812 Å³
包络直径 envelope_diameter	160.4 Å
壳层 Rg shell_rg	49.28 Å
包络 Rg envelope_rg	46.08 Å
形状 Rg shape_rg	46.36 Å
总 Rg total_rg	46.34 Å
总原子数 total_atoms	14821
残基数 n_residues	1819
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	153.2 Å
Rg (实空间) rg_real	45.84 Å
Rg 误差 (实空间) rg_real_error	1.55 Å
I(0) (实空间) i0_real	7.3070e+08
I(0) 误差 (实空间) i0_real_error	1.4420e+07
Rg (倒空间) rg_reciprocal	45.89 Å
I(0) (倒空间) i0_reciprocal	730800000.0000
解质量估计 total_estimate	0.8926
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	54.1 Å
偏度 Skewness skewness	0.253
峰度 Kurtosis kurtosis	-0.485
角度范围 angular_range	— – 0.1700 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	40710000.0000
实空间数据点数 n_real_points	35
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.911; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.868

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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	Elongation factor Tu
分子量 formula_weight	43370.5 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C
原子数 atom_count	14829

MSKEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDNAPEEKARGITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALEGDAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVGEEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIKPHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMVVTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLS

Entity 2 polymer

描述 description	t-RNA
分子量 formula_weight	24620.8 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	B

GCCCGGAUAGCUCAGUCGGUAGAGCAGGGGAUUGAAAAUCCCCGUGXCCUUGGUUCGAUUCCGAGUCCGGGCACCA

Entity 3 polymer

描述 description	Protein SidH
分子量 formula_weight	255113.7 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

MGSSHHHHHHSSGLVPRGSMKRTIETYIIYLKEDLKIADTCKTIKDGLLKSITDKTHFSEELATYFERDNPNAPFKVNTTDPTQVAVLKKLLNALENAEKSFRAIENIDISRDRYTAMIAKDAVMVSYKAVHEIYAALQLINHSNSDIQDIVGPHIQKLLPQMALASKALGNFAPEHPEESAGAVLAGVVNMLPTEKPTESESLGKLSNLIFELPHYFEELQKLIATGASGIATKSITSAEDYQSAMIKKANETKYYFEQLSSKSGLLAIPSYLSIVKRLIAHSTDLVNAGAPLTKQAYLDAVAKLEDIKHNILPQLISELEMVEESMGLKPGLLTDPALEQMNKYYTQLAEQVDNIAKAAGVLDTVSDYSDSIGGKIVRFLAGDSKKLDVGPKLTPAPDLGVLMDDVFIQKRRSNQESRLNEARLSSEDKSVLAAANRFFDKIGSYNSIHKAWSKWSLANISQSEKDALIKEYKQFQPHFAALYPDIDKLVVDALTQPTGSNIVSRLYSSDYKQLWSSDHFKQVLSCKDSVLSSIQQSLAQSEFKAKLIEKTMSHSEETAYSMNNKTTNLTTRVQPFEPLKFTLEDDKPVEYYHKRVIAASNQILELERAQKGVAEFFNYIQKKYPHENPSFDSLDESDKEFLRKAYKTFQPQLLALKHDDINTRLVSSLTSSKPTDPPLRLTDLVSLKSGINDYLNEKISDLNQDKTTLLDKEEEAREEQYAKNPLVAKGAELEKQTLFGQMSKLKLSKSVDDFFNKKFQTYLKDNLSPEVWKQLSSNGETLDFDKIPYLEFHKDSPEVAMYKQLINSMHYMKNGLEKLESLNDYGDPNNIYHRTRFVMTTFNALVMNICFSKYYVMEAGNNPGLKAIVQEGLDLLKPLEGMPLIGDYLKTTEKQEPPKQNIITAWKKQQAVVESGLSKGPKPKTDQQLISEQLGKIQEAIDNFDGDLEVSDSAREKIKTQIGEFAKGISGLSFGPGSVKKILAALTKLETQLSNLDKESPEVTLGKLKDIHSELNAQFRAAAEYTEYHSGQKFGSYSNNISTIVSNFCNGLVSNLPLKQEPAPKVKAPEKPVTPVITGTTNPHEVVFGTKHEEFNSVYQPYLLLKRITDEFRDQNNPYKPSFDELKEEAVSYYDKIQPLLESVDPKFDKNFIAKHKESSTLLKAIDEVMSMRQRINNPESSFAKLKDLHLEGDFEKEENKEKFRQLYKEIQPYLHKIDSTYDQTQFLEGLKTAKDFSGALQRIMNEENALQQSTSLKDTSYLQLIAESLYQIPVKLNKLKAEPDTPEPSKEEIDANVKAFVEGLNGLSFGPGSVKKILSTAAKLQMQLSDIGKEGRELTMGRLKEIQAEFGTILMAAADNAEFHLGLKPGTYSRTVSERFEKFYSSLIVNLPLEKDQTGLELLIDTTSTQKRLAREMERLESVKEDTSAIDTKKSIFGTEHEQFSTLYQPYASLRHIAKDIEDGVHMNLYERTLEELKEEASNEYKKIQPYLAKINPEFTEDYISKTDGEYSLLHAIDRVFEERHKINKPSSPFDKLRDLYLDGDFEKEENKEQFLQLYAELQPHLIKINYQYDLAYFLRELQTPEDFKAATERIINDESKLQELITGLDDTKRLKVKLCEERIGYFIDLLKKQELEVGPEKIQAFKEKIFFNYIHANVNSALDAKIGSHAEQFLQFIEKDFLDKKNEILEKITIDQDMEEEIAKAIDRIAPDIINNKIESFKKLLFDSYIQSDIKNSLHNELGIYTSLFIDKISPEIHLHQSEILGNVAFDSKMGAEIGSKINAITPGILLNNNPLKEAYVDLNNTLKEINTLLDEENKKTRDNPCRNEKIAKLTSLKDRLSDLDSIPKENTVEFLKKMQEETRSSLKSLESNDALINIYDVLNSLKETIENGSDLPEIKKDKLQMISDVQNILSNFDKNPAERLNLAVQILNDSNPEVLSKTKGNFLIGEAFKGQVFTNYINTKISEQLNNELGPYGKVFLKQIMPDFIAKKSEIIKEIAIDNMETGLETQFKIHAPAIFEKNKELKAAYEQLNVHLKEVQSLIEAEEKKPKGNPCREEKIAALRSHQSQLMNTQRIPDHETLRFLQEQNKSAKSFMGKLEKYDTMISVYDSLTEIREHVSNHKSLSKEIKDEKIQEISKMEDMLKTTSKEPSIRLAEVKAHGLSDQCKNVLLKNSDNFLVSFFKTLFSKLFNIKNENETLVSSFKQRLQNIKGPEPVATPMETPENEAPLVNANITRF

来源 Source

来源生物 organism	Legionella pneumophila
NCBI 分类编号 ncbi_taxonomy_id	446
宿主生物 host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 4 polymer

描述 description	E3 ubiquitin--protein ligase
分子量 formula_weight	30506.8 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	D

MHHHHHHSAGLEVLFQGPMGYRIEMATRNPFDIDHKSKYLREAALEANLSHPETTPTMLTCPIDSGFLKDPVITPEGFVYNKSSILKWLETKKEDPQSRKPLTAKDLQPFPELLIIVNRFVETQTNYEKLKNRLVQNARVAARQKEYTEIPDIFLCPISKTLIKTPVITAQGKVYDQEALSNFLIATGNKDETGKKLSIDDVVVFDELYQQIKVYNFYRKREMQKNQIQPSVSSGFGFFSLNFLTSWLWGTEEKKEKTSSDMTY

来源 Source

来源生物 organism	Legionella pneumophila
NCBI 分类编号 ncbi_taxonomy_id	446
宿主生物 host_organism	Escherichia coli

Entity 5 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 6 non-polymer

描述 description	GUANOSINE-5'-TRIPHOSPHATE
分子量 formula_weight	523.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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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	3.10 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	255829

fit	/app/data/saxs_computation/qh/8qhc/8qhc.fit
pddf	/app/data/pr_computation/qh/8qhc/8qhc.pr.out
profile	/app/data/saxs_computation/qh/8qhc/8qhc.dat

Cryo-EM structure of SidH from Legionella pneumophila in complex with LubX

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 (6)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

来源 Source

Entity 4 polymer

聚合体 Polymer

来源 Source

Entity 5 non-polymer

Entity 6 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)