SAXSdb — 8qfs

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8qfs
沉积日期 deposition_date	2023-09-04
结构标题 title	Cryo-EM structure of SidH from Legionella pneumophila
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	42.49 Å
回转半径 Rg (电子) rg_electron	42.52 Å
零角强度 I(0) i0	607818000.00
分子量 molecular_weight	189850.0 kDa
排除体积 excluded_volume	232210 Å³
包络体积 envelope_volume	325990 Å³
水化壳体积 shell_volume	64596 Å³
包络直径 envelope_diameter	138.3 Å
壳层 Rg shell_rg	46.98 Å
包络 Rg envelope_rg	42.04 Å
形状 Rg shape_rg	42.57 Å
总 Rg total_rg	42.60 Å
总原子数 total_atoms	13294
残基数 n_residues	1631
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	135.1 Å
Rg (实空间) rg_real	42.39 Å
Rg 误差 (实空间) rg_real_error	1.35 Å
I(0) (实空间) i0_real	6.0780e+08
I(0) 误差 (实空间) i0_real_error	1.1660e+07
Rg (倒空间) rg_reciprocal	42.49 Å
I(0) (倒空间) i0_reciprocal	607900000.0000
解质量估计 total_estimate	0.8931
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	51.1 Å
偏度 Skewness skewness	0.193
峰度 Kurtosis kurtosis	-0.530
角度范围 angular_range	— – 0.1850 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	36340000.0000
实空间数据点数 n_real_points	38
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.952; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.752

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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	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	13294

MSKEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDNAPEEKARGITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALEGDAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVGEEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIKPHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMVVTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLS

Entity 2 polymer

描述 description	tRNA
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	255821.6 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

MKHHHHHHHHHHSAGLEVLFQGPMKRTIETYIIYLKEDLKIADTCKTIKDGLLKSITDKTHFSEELATYFERDNPNAPFKVNTTDPTQVAVLKKLLNALENAEKSFRAIENIDISRDRYTAMIAKDAVMVSYKAVHEIYAALQLINHSNSDIQDIVGPHIQKLLPQMALASKALGNFAPEHPEESAGAVLAGVVNMLPTEKPTESESLGKLSNLIFELPHYFEELQKLIATGASGIATKSITSAEDYQSAMIKKANETKYYFEQLSSKSGLLAIPSYLSIVKRLIAHSTDLVNAGAPLTKQAYLDAVAKLEDIKHNILPQLISELEMVEESMGLKPGLLTDPALEQMNKYYTQLAEQVDNIAKAAGVLDTVSDYSDSIGGKIVRFLAGDSKKLDVGPKLTPAPDLGVLMDDVFIQKRRSNQESRLNEARLSSEDKSVLAAANRFFDKIGSYNSIHKAWSKWSLANISQSEKDALIKEYKQFQPHFAALYPDIDKLVVDALTQPTGSNIVSRLYSSDYKQLWSSDHFKQVLSCKDSVLSSIQQSLAQSEFKAKLIEKTMSHSEETAYSMNNKTTNLTTRVQPFEPLKFTLEDDKPVEYYHKRVIAASNQILELERAQKGVAEFFNYIQKKYPHENPSFDSLDESDKEFLRKAYKTFQPQLLALKHDDINTRLVSSLTSSKPTDPPLRLTDLVSLKSGINDYLNEKISDLNQDKTTLLDKEEEAREEQYAKNPLVAKGAELEKQTLFGQMSKLKLSKSVDDFFNKKFQTYLKDNLSPEVWKQLSSNGETLDFDKIPYLEFHKDSPEVAMYKQLINSMHYMKNGLEKLESLNDYGDPNNIYHRTRFVMTTFNALVMNICFSKYYVMEAGNNPGLKAIVQEGLDLLKPLEGMPLIGDYLKTTEKQEPPKQNIITAWKKQQAVVESGLSKGPKPKTDQQLISEQLGKIQEAIDNFDGDLEVSDSAREKIKTQIGEFAKGISGLSFGPGSVKKILAALTKLETQLSNLDKESPEVTLGKLKDIHSELNAQFRAAAEYTEYHSGQKFGSYSNNISTIVSNFCNGLVSNLPLKQEPAPKVKAPEKPVTPVITGTTNPHEVVFGTKHEEFNSVYQPYLLLKRITDEFRDQNNPYKPSFDELKEEAVSYYDKIQPLLESVDPKFDKNFIAKHKESSTLLKAIDEVMSMRQRINNPESSFAKLKDLHLEGDFEKEENKEKFRQLYKEIQPYLHKIDSTYDQTQFLEGLKTAKDFSGALQRIMNEENALQQSTSLKDTSYLQLIAESLYQIPVKLNKLKAEPDTPEPSKEEIDANVKAFVEGLNGLSFGPGSVKKILSTAAKLQMQLSDIGKEGRELTMGRLKEIQAEFGTILMAAADNAEFHLGLKPGTYSRTVSERFEKFYSSLIVNLPLEKDQTGLELLIDTTSTQKRLAREMERLESVKEDTSAIDTKKSIFGTEHEQFSTLYQPYASLRHIAKDIEDGVHMNLYERTLEELKEEASNEYKKIQPYLAKINPEFTEDYISKTDGEYSLLHAIDRVFEERHKINKPSSPFDKLRDLYLDGDFEKEENKEQFLQLYAELQPHLIKINYQYDLAYFLRELQTPEDFKAATERIINDESKLQELITGLDDTKRLKVKLCEERIGYFIDLLKKQELEVGPEKIQAFKEKIFFNYIHANVNSALDAKIGSHAEQFLQFIEKDFLDKKNEILEKITIDQDMEEEIAKAIDRIAPDIINNKIESFKKLLFDSYIQSDIKNSLHNELGIYTSLFIDKISPEIHLHQSEILGNVAFDSKMGAEIGSKINAITPGILLNNNPLKEAYVDLNNTLKEINTLLDEENKKTRDNPCRNEKIAKLTSLKDRLSDLDSIPKENTVEFLKKMQEETRSSLKSLESNDALINIYDVLNSLKETIENGSDLPEIKKDKLQMISDVQNILSNFDKNPAERLNLAVQILNDSNPEVLSKTKGNFLIGEAFKGQVFTNYINTKISEQLNNELGPYGKVFLKQIMPDFIAKKSEIIKEIAIDNMETGLETQFKIHAPAIFEKNKELKAAYEQLNVHLKEVQSLIEAEEKKPKGNPCREEKIAALRSHQSQLMNTQRIPDHETLRFLQEQNKSAKSFMGKLEKYDTMISVYDSLTEIREHVSNHKSLSKEIKDEKIQEISKMEDMLKTTSKEPSIRLAEVKAHGLSDQCKNVLLKNSDNFLVSFFKTLFSKLFNIKNENETLVSSFKQRLQNIKGPEPVATPMETPENEAPLVNANITRF

来源 Source

来源生物 organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;
NCBI 分类编号 ncbi_taxonomy_id	866768
宿主生物 host_organism	Legionella pneumophila

Entity 4 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 5 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	triclinic

分辨率 resolution	2.70 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	367741

fit	/app/data/saxs_computation/qf/8qfs/8qfs.fit
pddf	/app/data/pr_computation/qf/8qfs/8qfs.pr.out
profile	/app/data/saxs_computation/qf/8qfs/8qfs.dat

Cryo-EM structure of SidH from Legionella pneumophila

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 (5)

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 non-polymer

Entity 5 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)