SAXSdb — 8poh

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8poh
沉积日期 deposition_date	2023-07-04
最后修订 last_revision	2024-02-21
结构标题 title	Influenza A/H7N9 polymerase symmetric dimer bound to the promoter (PA K289A/C489R)
关键词 keywords	Viral polymerase, 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	53.97 Å
回转半径 Rg (电子) rg_electron	54.68 Å
零角强度 I(0) i0	1355010000.00
分子量 molecular_weight	295740.0 kDa
排除体积 excluded_volume	365620 Å³
包络体积 envelope_volume	531320 Å³
水化壳体积 shell_volume	84839 Å³
包络直径 envelope_diameter	189.1 Å
壳层 Rg shell_rg	53.14 Å
包络 Rg envelope_rg	53.70 Å
形状 Rg shape_rg	54.70 Å
总 Rg total_rg	54.53 Å
总原子数 total_atoms	20693
残基数 n_residues	2517
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	176.7 Å
Rg (实空间) rg_real	54.41 Å
Rg 误差 (实空间) rg_real_error	1.89 Å
I(0) (实空间) i0_real	1.3550e+09
I(0) 误差 (实空间) i0_real_error	2.6560e+07
Rg (倒空间) rg_reciprocal	53.59 Å
I(0) (倒空间) i0_reciprocal	1353000000.0000
解质量估计 total_estimate	0.5648
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	54.8 Å
偏度 Skewness skewness	0.580
峰度 Kurtosis kurtosis	-0.313
角度范围 angular_range	— – 0.1450 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	106500000.0000
实空间数据点数 n_real_points	30
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.725; Stabil: 0.998; Sysdev: 0.017; Positv: 1.000; Valcen: 0.977; Smooth: 0.139

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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	Polymerase acidic protein
分子量 formula_weight	84394.1 kDa
突变 mutation	K289A; C489R
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,E
原子数 atom_count	20729

MHHHHHHHHGSGSMEDFVRQCFNPMIVELAEKAMKEYGEDPKIETNKFASICTHLEVCFMYSDFHFIDERGESTIIESGDPNVLLKHRFEIIEGRDRTMAWTVVNSICNTTGVEKPKFLPDLYDYKENRFIEIGVTRREVHIYYLEKANKIKSEKTHIHIFSFTGEEMATKADYTLDEESRARIKTRLFTIRQEMASRGLWDSFRQSERGEETIEERFEITGTMRRLADQSLPPNFSSLENFRAYVDGFEPNGCIEGKLSQMSKEVNARIEPFLRTTPRPLRLPDGPPCSQRSKFLLMDALALSIEDPSHEGEGIPLYDAIKCMKTFFGWKEPNIIKPHEKGINPNYLLTWKQVLAELQDIENEEKIPRTKNMKKTSQLKWALGENMAPEKVDFEDCKDVNDLKQYDSDEPEPRSLACWIQSEFNKACELTDSSWVELDEIGEDVAPIEHIASMRRNYFTAEVSHCRATEYIMKGVYINTALLNASCAAMDDFQLIPMISKRRTKEGRRKTNLYGFIIKGRSHLRNDTDVVNFVSMEFSLTDPRLEPHKWEKYCVLEIGDMLLRTAVGQVSRPMFLYVRTNGTSKIKMKWGMEMRRCLLQSLQQIESMIEAESSVKEKDLTKEFFENKSETWPIGESPKGVEEGSIGKVCRTLLAKSVFNSLYASPQLEGFSAESRKLLLIVQALRDNLEPGTFDLEGLYEAIEECLINDPWVLLNASWFNSFLTHALR

来源 Source

来源生物 organism	Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9))
NCBI 分类编号 ncbi_taxonomy_id	1318616
宿主生物 host_organism	Trichoplusia ni

Entity 2 polymer

描述 description	RNA-directed RNA polymerase catalytic subunit
分子量 formula_weight	86496.2 kDa
EC 编号 ec_number	2.7.7.48
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B,F

MDVNPTLLFLKVPVQNAISTTFPYTGDPPYSHGTGTGYTMDTVNRTHKYSEKGKWTTNTETGAPQLNPIDGPLPEDNEPSGYAQTDCVLEAMAFLEESHPGIFENSCLETMEIVQQTRVDKLTQGRQTYDWTLNRNQPAATALANTIEVFRSNGLTANESGRLIDFLKDVMDSMDKEEMEITTHFQRKRRVRDNMTKKMVTQRTIGKKKQRLNKRSYLIRALTLNTMTKDAERGKLKRRAIATPGMQIRGFVYFVEALARSICEKLEQSGLPVGGNEKKAKLANVVRKMMTNSQDTELSFTITGDNTKWNENQNPRMFLAMITYITRNQPEWFRNVLSIAPIMFSNKMARLGKGYMFESKSMKLRTQVPAEMLANIDLKYFNKSTREKIEKIRPLLIDGTASLSPGMMMGMFNMLSTVLGVSILNLGQKKYTKTTYWWDGLQSSDDFALIVNAPNHEGIQAGVDRFYRTCKLVGINMSKKKSYINRTGTFEFTSFFYRYGFVANFSMELPSFGVSGINESADMSVGVTVIKNNMINNDLGPATAQMALQLFIKDYRYTYRCHRGDTQIQTRRAFELKKLWEQTRSKAGLLVSDGGPNLYNIRNLHIPEVCLKWELMDEDYQGRLCNPMNPFVSHKEIDSVNNAVVMPAHGPAKSMEYDAVATTHSWIPKRNRSILNTSQRGILEDEQMYQKCCNLFEKFFPSSSYRRPVGISSMVEAMVSRARIDARIDFESGRIKKEEFAEIMKICSTIEELRRQK

来源 Source

来源生物 organism	Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9))
NCBI 分类编号 ncbi_taxonomy_id	1318616
宿主生物 host_organism	Trichoplusia ni

Entity 3 polymer

描述 description	Polymerase basic protein 2
分子量 formula_weight	88937.4 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C,G

MERIKELRDLMSQSRTREILTKTTVDHMAIIKKYTSGRQEKNPALRMKWMMAMKYPITADKRIMEMIPERNEQGQTLWSKTNDAGSDRVMVSPLAVTWWNRNGPTTSTVHYPKVYKTYFEKVERLKHGTFGPVHFRNQVKIRRRVDINPGHADLSAKEAQDVIMEVVFPNEVGARILTSESQLTITKEKKKELQDCKIAPLMVAYMLERELVRKTRFLPVAGGTSSVYIEVLHLTQGTCWEQMYTPGGEVRNDDVDQSLIIAARNIVRRATVSADPLASLLEMCHSTQIGGVRMVDILRQNPTEEQAVDICKAAMGLRISSSFSFGGFTFKRTSGSSVKREEEVLTGNLQTLKIRVHEGYEEFTMVGRRATAILRKATRRLIQLIVSGKDEQSIAEAIIVAMVFSQEDCMIKAVRGDLNFVNRANQRLNPMHQLLRHFQKDAKVLFQNWGIEPIDNVMGMIGILPDMTPSTEMSLRGVRVSKMGVDEYSSTERVVVSIDRFLRVRDQRGNVLLSPEEVSETQGTEKLTITYSSSMMWEINGPESVLVNTYQWIIRNWENVKIQWSQDPTMLYNKMEFEPFQSLVPKAARGQYSGFVRVLFQQMRDVLGTFDTVQIIKLLPFAAAPPEQSRMQFSSLTVNVRGSGMRIVVRGNSPVFNYNKATKRLTVLGKDAGALMEDPDEGTAGVESAVLRGFLILGKENKRYGPALSINELSNLAKGEKANVLIGQGDVVLVMKRKRDSSILTDSQTATKRIRMAINGWSHPQFEKGGGSGGGSGGSAWSHPQFEK

来源 Source

来源生物 organism	Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9))
NCBI 分类编号 ncbi_taxonomy_id	1318616
宿主生物 host_organism	Trichoplusia ni

Entity 4 polymer

描述 description	51-mer vRNA loop (v51_mut_S)
分子量 formula_weight	16093.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	R,V,S,U

AGUAGAAACAAGGGUGUAUUUUCCCCUCUUUUUGUUUCCCCUGCUUUUGCU

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

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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	3.30 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	278761

fit	/app/data/saxs_computation/po/8poh/8poh.fit
pddf	/app/data/pr_computation/po/8poh/8poh.pr.out
profile	/app/data/saxs_computation/po/8poh/8poh.dat

Influenza A/H7N9 polymerase symmetric dimer bound to the promoter (PA K289A/C489R)

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

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 polymer

聚合体 Polymer

来源 Source

Entity 4 polymer

聚合体 Polymer

Entity 5 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)