SAXSdb — 9ctn

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9ctn
沉积日期 deposition_date	2024-07-25
结构标题 title	Modifying region of EcPKS2 - acetylated dataset
关键词 keywords	polyketide synthase acetyltransferase ketoreductase ketosynthase dehydrogenase, BIOSYNTHETIC PROTEIN; BIOSYNTHETIC 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	56.71 Å
回转半径 Rg (电子) rg_electron	57.40 Å
零角强度 I(0) i0	1347590000.00
分子量 molecular_weight	308380.0 kDa
排除体积 excluded_volume	387010 Å³
包络体积 envelope_volume	542780 Å³
水化壳体积 shell_volume	85207 Å³
包络直径 envelope_diameter	198.5 Å
壳层 Rg shell_rg	52.46 Å
包络 Rg envelope_rg	56.81 Å
形状 Rg shape_rg	57.43 Å
总 Rg total_rg	57.14 Å
总原子数 total_atoms	43262
残基数 n_residues	2747
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	189.8 Å
Rg (实空间) rg_real	57.36 Å
Rg 误差 (实空间) rg_real_error	1.47 Å
I(0) (实空间) i0_real	1.3480e+09
I(0) 误差 (实空间) i0_real_error	2.6300e+07
Rg (倒空间) rg_reciprocal	56.16 Å
I(0) (倒空间) i0_reciprocal	1345000000.0000
解质量估计 total_estimate	0.7869
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	54.2 Å
偏度 Skewness skewness	0.627
峰度 Kurtosis kurtosis	-0.237
角度范围 angular_range	— – 0.1400 Å⁻¹
当前正则化参数 α current_alpha	0.0003
最高正则化参数 α highest_alpha	98700000.0000
实空间数据点数 n_real_points	29
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.748; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.907; Smooth: 0.075

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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 (3)

Entity 1 polymer

描述 description	Polyketide synthase 2
分子量 formula_weight	252993.6 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	A,B
原子数 atom_count	43325

MAPQEQASSSQQDDAPPKTPNVVEPYKGEVAICGLSGRYPESANVGELEYNLFNKIDMVTIDNRRWEPGYLGTPERMGKVKTITDFDAEFFGVHTKGAQTMDPMLRNLLEVVYEAIVDAGESLESMKGTRTGVYIGVSNNEVDTAYMKNWTDDDAYMVQGCHHSMYPNWISFFFDFSGPSTAYNTACSTSLVCLDAAERHLRMGVIDNAIVGGSNFIYRPATTKLFMGMNFLGSSTCKAFDESGDGFVRGEVASAILLKKADTAKRVYCTLVGSMLNNDGNQTNGILYPNSEAQEQLMTDIYSTHKIDANEVKYFECHGTGTQAGDPNETRAICNAVCKGKKDPLLIGSIKSNLGHGETASGINGISKVIITMHSRQIPPNLHFKNPNPKIPGLFDGRLKVVTETTPFDGGLIAINSFGMGGTNAHAIFRSFDKRAEPHPASDKPRLFTYCARTEEGLQKIFEEAHKHASNVEFHALCQESANTKPKSLPYRGATILNAEGEYTEIQKCPSKAREVWFVYSGMGSQWVGMGRSLMALDVFRQSIEETAAILSPFGVDLMSLLMDGTEDKLKEIMPPFICINAIQLALTDLLNSMGIVPDGLVGHSLGEVGCAYADGCLTRREAILSAFWRAKAVIDCEVKPGKMAAVELTWEEAKRLCPPGVVAACHNSQDSVTISGGAQEMTKFMAELSAQGVTVKEVNSNNISYHSSFMTEPAAYLKKGLEKEIVPKPRSKKWISTSIPEERWGNPEAQTADASYQANNLLSSVLFYEGLQKIPSNAIAIEIAPAGLLQSVIKKSLGQDCTIVALQKRKSPNNLEVFFSALGKCYSHGVPMNPLGLYPAVQFPVSIDTPMLSSMVSEAWDHSAKWRVPLVEEFEYGSGSSSDNVIDIDLSEDSPENYLLEHAVDGRMLFPATGTLVLAWKTLAKLKGVEFEQLGVQMTNVQIHQALFLNPGGKTTVSVSVMPITGEFQVRDGESLISSGVITSSEGRLLETDQHMKKGSVLDGKPDKELLFTKEIYREFLLRGYEYGAAFQGIQRASLDATDTDIRWDGRWISYLDTVLQMYLLSKPGTHQALPTLLESVTIDPRVHPAQPPEGTTEFQVLPGKWDPVLQIAAAGGVEIRSCHSIRASRRLNHDPPILEDFAFAPYVDPRPSDRSAAAVTPALRDYADACFEFSRQGMKRWLENDKNNVLPNKEEIKEALAMANKHASTPQAASNFASAKATLEALVNNKNGHRLPNHGLFEMLDIAFSEPLEGDYWDRLRMKLHDVRTYLWDDPIIAALESPDIVKLVMETVSDNVNQQVMEILEVGAARGPYYRQAIPKALEYFSIKDWQYTVADQGFVEDAAEFPVKMMQFDPLDPANFPAELTESCDLLVLKWNLQMQVDLDAAITEFSKMIKPGGFLLVLENGTRLSTFFPIKAIVSASLGGKGGPEGDRAMGCFYTDAQWSALFARHGFEQIMHIPDGIAVSMFLLRKPFEPSVAPIIINVDDLECSWLEEVQARCAELQDSHKDSRLWLVANTELSGVLGFLRSLVWEFGSEKLRCIQIDDATAGPNPPKISADSADFKELVRKDLAYNVFKNGKWGTYRGFVISDADRQKERPSEYVYADWLSAGDMSSLRWFDSPLKTGHNNGMLGSKMAHKLETETCSVYYAGLNLRDIILANGTIQRDILPEETFFKEGVLGVEFSGRNSSGKRVMGLCPPPALATTVKCPVSSLWSVPDQWTLEEAATVPLAYATAYYCLVSEGGVQKGATVFIHAGASVVGQASIAVALSYNCEIFTLTKNSDETALLKSMYPQLNDRNFCSSEDCSFEKYIRKETKGSGVDVVINTLRGKFLKASRRLLSKKGKFVDIGFKVDSNTQIAYYTREHPDLRFQLDALLESQGPEWTRLFDLVQAGIHSGVVKPLKRAVYSMDKIVDAFKTVEAEREAGKIVIKIRDEERQKVCPTPRTSFPAIHRTCFHPDKSHILVGGMGGMGLETAHWMVLRGAKKLILTSRYGITTGYQARKIAFFKQLGVEVEVLALSVNTRKAADKVFEHALKMGPVGGIFNMAMVLYNDDFLKMNREQFLKPLESKITMTMLLDDKSREKPVRDTLDHFVMFSSLIVSGGHLGQANYAFGSTVLEKICERRKRDGLPVTTPQWASIADVGTVALMGTGNETIICRKYPQRFFNVLSVFDFMMSSDNVVTISYVLVEKSMGVAAGEESMVDQVLRAVGKVLGIKDVSSVDGDKEFIDMGVDSLMSVEIKQALERDAGLVISTKDTQLMTFNTLRSMVKGSHVHHHHHH

来源 Source

来源生物 organism	Elysia chlorotica
NCBI 分类编号 ncbi_taxonomy_id	188477
宿主生物 host_organism	Saccharomyces cerevisiae

Entity 2 non-polymer

描述 description	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
分子量 formula_weight	745.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 non-polymer

描述 description	~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] ethanethioate
分子量 formula_weight	400.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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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	3.110 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	3.11 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	93476

fit	/app/data/saxs_computation/ct/9ctn/9ctn.fit
pddf	/app/data/pr_computation/ct/9ctn/9ctn.pr.out
profile	/app/data/saxs_computation/ct/9ctn/9ctn.dat

Modifying region of EcPKS2 - acetylated dataset

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