SAXSdb — 8u0v

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8u0v
沉积日期 deposition_date	2023-08-29
结构标题 title	S. cerevisiae Pex1/Pex6 with 1 mM ATP
关键词 keywords	Peroxisome AAA-ATPase unfoldase, MOTOR PROTEIN; MOTOR 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	59.42 Å
回转半径 Rg (电子) rg_electron	59.03 Å
零角强度 I(0) i0	5447810000.00
分子量 molecular_weight	628780.0 kDa
排除体积 excluded_volume	789390 Å³
包络体积 envelope_volume	1181200 Å³
水化壳体积 shell_volume	158270 Å³
包络直径 envelope_diameter	184.2 Å
壳层 Rg shell_rg	67.72 Å
包络 Rg envelope_rg	57.63 Å
形状 Rg shape_rg	59.02 Å
总 Rg total_rg	59.23 Å
总原子数 total_atoms	81853
残基数 n_residues	5553
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	167.7 Å
Rg (实空间) rg_real	59.04 Å
Rg 误差 (实空间) rg_real_error	0.79 Å
I(0) (实空间) i0_real	5.4480e+09
I(0) 误差 (实空间) i0_real_error	8.7030e+07
Rg (倒空间) rg_reciprocal	59.72 Å
I(0) (倒空间) i0_reciprocal	5453000000.0000
解质量估计 total_estimate	0.6188
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	77.4 Å
偏度 Skewness skewness	0.106
峰度 Kurtosis kurtosis	-0.537
角度范围 angular_range	— – 0.1300 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	613700000.0000
实空间数据点数 n_real_points	27
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.990; Stabil: 1.000; Sysdev: 0.025; Positv: 1.000; Valcen: 0.995; Smooth: 0.004

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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	Peroxisomal ATPase PEX1
分子量 formula_weight	118654.0 kDa
EC 编号 ec_number	3.6.4.-
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,C,E
原子数 atom_count	81859

MTTTKRLKFENLRIQFSNAIVGNFLRLPHSIINVLESTNYAIQEFGIAVHSHNSDIPIVHLGWDGHDSGSSENVVLINPVLATVYDLNQKSPLVDLYIQRYDHTHLATEVYVTPETSDDWEIIDANAMRFQNGEILHQTRIVTPGETLICYLEGIVTKFKIDRVEPSMKSARITDGSLVVVAPKVNKTRLVKAEYGHSNKTILKNGAIQLLKKVILRSTVCKMDFPKDNLFVVYISDGAQLPSQKGYASIVKCSLRQSKKSDSDNKSVGIPSKKIGVFIKCDSQIPENHIALSSHLWDAFFTHPMNGAKIKLEFLQMNQANIISGRNATVNIKYFGKDVPTKSGDQYSKLLGGSLLTNNLILPTEQIIIEIKKGESEQQLCNLNEISNESVQWKVTQMGKEEVKDIIERHLPKHYHVKETGEVSRTSKDEDDFITVNSIKKEMVNYLTSPIIATPAIILDGKQGIGKTRLLKELINEVEKDHHIFVKYADCETLHETSNLDKTQKLIMEWCSFCYWYGPSLIVLDNVEALFGKPQANDGDPSNNGQWDNASKLLNFFINQVTKIFNKDNKRIRVLFSGKQKTQINPLLFDKHFVSETWSLRAPDKHARAKLLEYFFSKNQIMKLNRDLQFSDLSLETEGFSPLDLEIFTEKIFYDLQLERDCDNVVTRELFSKSLSAFTPSALRGVKLTKETNIKWGDIGALANAKDVLLETLEWPTKYEPIFVNCPLRLRSGILLYGYPGCGKTLLASAVAQQCGLNFISVKGPEILNKFIGASEQNIRELFERAQSVKPCILFFDEFDSIAPKRGHDSTGVTDRVVNQLLTQMDGAEGLDGVYILAATSRPDLIDSALLRPGRLDKSVICNIPTESERLDILQAIVNSKDKDTGQKKFALEKNADLKLIAEKTAGFSGADLQGLCYNAYLKSVHRWLSAADQSEVVPGNDNIEYFSINEHGRREENRLRLKTLLQQDVVHETKTSTSAASELTAVVTINDLLEACQETKPSISTSELVKLRGIYDRFQKDRNGEMPNGENSIDIGSRLSLMGSSDYKDDDDK

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI 分类编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	Peroxisomal ATPase PEX6
分子量 formula_weight	117306.8 kDa
EC 编号 ec_number	3.6.4.-
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

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

MGSSHHHHHHSQDPMKASLTFSLSGIYAPCSISRDIYLEYGDKKAECLYGTIRLPQYGPGCTPGKIVHCVLDDSLPFCSIVVPSKLFGFMPTQPTMDFCYFEPILDNVVPVLDSVTFLINEQLYSKLMDLPQEMQQIQFLHYKYNINSMETVVHSRDILTSGLCQILNCSPFPQGLVDFTETQLILVNDTEQKLSALKYANEDEEYALPKIGTNSALSIDLESLPCTISRDLLRPAPHINDDNSIYAFTDAETLLRLDVTSGSFITVSNMGCVRLVKLFVLLLPNGFKKRTIYAPPKIIASFPDCSVVTISKSNIGHTDIPIANQVFISRVGGWLQSQKCFQNIILTTLKKFFSESKRILCQNDLIPIAFDSSMADLNIAEENDESDDEDELGQYYKNDSLVWFFVTSAELDCFSKDNSHFIIDPNRTKLITTNITNRRPLPLSRSNLQRYYGFAETFYYDLHIFPYVRQLVNILETSFNCSQRGITLNASVLLHSTTNNVGKATMVRFASKYLGIHLLEIDCLSLTSNSRQLDSTSKIIGYIRAKCENVLPYASPAVIFLAHLDSILLDVNANQDPEAIKLQKSINFEMSKLLDDFTFKFPGTTFVGSVNNIDNVPSSFRSHMRFEILVPVPSEAQRLRIFQWYLSSHELNRDVQQKVPVSYMDNISFSSLSSYSAGLTPLDIKSIVETARMTATARFYQESKKCGWLPQSILITQEDLSKATSKARNEFSVSIGAPQIPNVTWDDIGGIDFVKGEILDTIDMPLKHPELFTSGMKKRSGILFYGPPGTGKTLMAKAIATNFSLNFFSVKGPELLNMYIGESEANVRRVFQKAREAKPCVIFFDEIDSVAPKRGNQGDSGGVMDRIVSQLLAELDGMSTDADGVFVIGATNRPDLLDEALLRPGRFDKLLYLGIPDTDTKQLNILEALTRKFVLDNDVKLIELAKLCPFNYTGADFYALCSDAMLNAMSRIARMVEKKVSQHNELTGENISTRRWFDKIATKEDTKVVVKMEDFLKAQEQLTPSVSRAELNHYEAVRANFEGA

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI 分类编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Entity 3 non-polymer

描述 description	ADENOSINE-5'-TRIPHOSPHATE
分子量 formula_weight	507.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	10

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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	3.89 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	106005

fit	/app/data/saxs_computation/u0/8u0v/8u0v.fit
pddf	/app/data/pr_computation/u0/8u0v/8u0v.pr.out
profile	/app/data/saxs_computation/u0/8u0v/8u0v.dat

S. cerevisiae Pex1/Pex6 with 1 mM ATP

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 (3)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)