SAXSdb — 8foe

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8foe
沉积日期 deposition_date	2022-12-30
结构标题 title	Cryo-EM structure of S. cerevisiae DNA polymerase alpha-primase complex bound to a template DNA
关键词 keywords	DNA polymerase, primase, DNA replication, DNA BINDING PROTEIN; DNA 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	53.19 Å
回转半径 Rg (电子) rg_electron	53.04 Å
零角强度 I(0) i0	706974000.00
分子量 molecular_weight	222800.0 kDa
排除体积 excluded_volume	279610 Å³
包络体积 envelope_volume	440010 Å³
水化壳体积 shell_volume	72044 Å³
包络直径 envelope_diameter	171.4 Å
壳层 Rg shell_rg	53.47 Å
包络 Rg envelope_rg	50.65 Å
形状 Rg shape_rg	53.01 Å
总 Rg total_rg	53.14 Å
总原子数 total_atoms	15662
残基数 n_residues	1945
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	172.9 Å
Rg (实空间) rg_real	53.15 Å
Rg 误差 (实空间) rg_real_error	1.79 Å
I(0) (实空间) i0_real	7.0700e+08
I(0) 误差 (实空间) i0_real_error	1.4180e+07
Rg (倒空间) rg_reciprocal	53.20 Å
I(0) (倒空间) i0_reciprocal	707000000.0000
解质量估计 total_estimate	0.8838
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	63.4 Å
偏度 Skewness skewness	0.157
峰度 Kurtosis kurtosis	-0.694
角度范围 angular_range	— – 0.1500 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	29080000.0000
实空间数据点数 n_real_points	31
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.948; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.644

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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	DNA polymerase
分子量 formula_weight	167027.8 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	1
原子数 atom_count	15747

MSSKSEKLEKLRKLQAARNGTSIDDYEGDESDGDRIYDEIDEKEYRARKRQELLHDDFVVDDDGVGYVDRGVEEDWREVDNSSSDEDTGNLASKDSKRKKNIKREKDHQITDMLRTQHSKSTLLAHAKKSQKKSIPIDNFDDILGEFESGEVEKPNILLPSKLRENLNSSPTSEFKSSIKRVNGNDESSHDAGISKKVKIDPDSSTDKYLEIESSPLKLQSRKLRYANDVQDLLDDVENSPVVATKRQNVLQDTLLANPPSAQSLADEEDDEDSDEDIILKRRTMRSVTTTRRVNIDSRSNPSTSPFVTAPGTPIGIKGLTPSKSLQSNTDVATLAVNVKKEDVVDPETDTFQMFWLDYCEVNNTLILFGKVKLKDDNCVSAMVQINGLCRELFFLPREGKTPTDIHEEIIPLLMDKYGLDNIRAKPQKMKYSFELPDIPSESDYLKVLLPYQTPKSSRDTIPSDLSSDTFYHVFGGNSNIFESFVIQNRIMGPCWLDIKGADFNSIRNASHCAVEVSVDKPQNITPTTTKTMPNLRCLSLSIQTLMNPKENKQEIVSITLSAYRNISLDSPIPENIKPDDLCTLVRPPQSTSFPLGLAALAKQKLPGRVRLFNNEKAMLSCFCAMLKVEDPDVIIGHRLQNVYLDVLAHRMHDLNIPTFSSIGRRLRRTWPEKFGRGNSNMNHFFISDICSGRLICDIANEMGQSLTPKCQSWDLSEMYQVTCEKEHKPLDIDYQNPQYQNDVNSMTMALQENITNCMISAEVSYRIQLLTLTKQLTNLAGNAWAQTLGGTRAGRNEYILLHEFSRNGFIVPDKEGNRSRAQKQRQNEENADAPVNSKKAKYQGGLVFEPEKGLHKNYVLVMDFNSLYPSIIQEFNICFTTVDRNKEDIDELPSVPPSEVDQGVLPRLLANLVDRRREVKKVMKTETDPHKRVQCDIRQQALKLTANSMYGCLGYVNSRFYAKPLAMLVTNKGREILMNTRQLAESMNLLVVYGDTDSVMIDTGCDNYADAIKIGLGFKRLVNERYRLLEIDIDNVFKKLLLHAKKKYAALTVNLDKNGNGTTVLEVKGLDMKRREFCPLSRDVSIHVLNTILSDKDPEEALQEVYDYLEDIRIKVETNNIRIDKYKINMKLSKDPKAYPGGKNMPAVQVALRMRKAGRVVKAGSVITFVITKQDEIDNAADTPALSVAERAHALNEVMIKSNNLIPDPQYYLEKQIFAPVERLLERIDSFNVVRLSEALGLDSKKYFRREGGNNNGEDINNLQPLETTITDVERFKDTVTLELSCPSCDKRFPFGGIVSSNYYRVSYNGLQCKHCEQLFTPLQLTSQIEHSIRAHISLYYAGWLQCDDSTCGIVTRQVSVFGKRCLNDGCTGVMRYKYSDKQLYNQLLYFDSLFDCEKNKKQELKPIYLPDDLDYPKEQLTESSIKALTEQNRELMETGRSVVQKYLNDCGRRYVDMTSIFDFMLN

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	Saccharomyces cerevisiae

Entity 2 polymer

描述 description	DNA primase
分子量 formula_weight	47760.4 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

MTNSVKTNGPSSSDMEYYYKSLYPFKHIFNWLNHSPKPSRDMINREFAMAFRSGAYKRYNSFNSVQDFKAQIEKANPDRFEIGAIYNKPPRERDTLLKSELKALEKELVFDIDMDDYDAFRTCCSGAQVCSKCWKFISLAMKITNTALREDFGYKDFIWVFSGRRGAHCWVSDKRARALTDVQRRNVLDYVNVIRDRNTDKRLALKRPYHPHLARSLEQLKPFFVSIMLEEQNPWEDDQHAIQTLLPALYDKQLIDSLKKYWLDNPRRSSKEKWNDIDQIATSLFKGPKQDSHIIKLRECKEDLVLMTLYPKLDVEVTKQTIHLLKAPFCIHPATGNVCVPIDESFAPEKAPKLIDLQTEMEKNNDVSLTALQPFINQFQAYVSSLLKNELGSVKREREDDDEPASLDF

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	Saccharomyces cerevisiae

Entity 3 polymer

描述 description	DNA primase large subunit
分子量 formula_weight	62305.5 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	B

MFRQSKRRIASRKNFSSYDDIVKSELDVGNTNAANQIILSSSSSEEEKKLYARLYESKLSFYDLPPQGEITLEQFEIWAIDRLKILLEIESCLSRNKSIKEIETIIKPQFQKLLPFNTESLEDRKKDYYSHFILRLCFCRSKELREKFVRAETFLFKIRFNMLTSTDQTKFVQSLDLPLLQFISNEEKAELSHQLYQTVSASLQFQLNLNEEHQRKQYFQQEKFIKLPFENVIELVGNRLVFLKDGYAYLPQFQQLNLLSNEFASKLNQELIKTYQYLPRLNEDDRLLPILNHLSSGYTIADFNQQKANQFSENVDDEINAQSVWSEEISSNYPLCIKNLMEGLKKNHHLRYYGRQQLSLFLKGIGLSADEALKFWSEAFTNNGNMTMEKFNKEYRYSFRHNYGLEGNRINYKPWDCHTILSKPRPGRGDYHGCPFRDWSHERLSAELRSMKLTQAQIISVLDSCQKGEYTIACTKVFEMTHNSASADLEIGEQTHIAHPNLYFERSRQLQKKQQKLEKEKLFNNGNH

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	Saccharomyces cerevisiae

Entity 4 polymer

描述 description	DNA polymerase alpha subunit B
分子量 formula_weight	78865.9 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	C

MSGSIDVITHFGPDADKPEIITALENLTKLHALSVEDLYIKWEQFSNQRRQTHTDLTSKNIDEFKQFLQLQMEKRANQISSSSKVNTSTKKPVIKKSLNSSPLFGLSIPKTPTLKKRKLHGPFSLSDSKQTYNVGSEAETNEKGNSSLKLEFTPGMAEDAVGDSAPLSHAKSSDAKTPGSSTFQTPTTNTPTTSRQNVPAGEILDSLNPENIEISSGNPNVGLLSTEEPSYNQVKVEPFYDAKKYKFRTMRQNLQEASDVLDDQIESFTKIIQNHYKLSPNDFADPTIQSQSEIYAVGRIVPDSPTYDKFLNPESLSLETSRMGGVGRRVRLDLSQVNELSFFLGQIVAFKGKNANGDYFTVNSILPLPYPNSPVSTSQELQEFQANLEGSSLKVIVTCGPYFANDNFSLELLQEFIDSINNEVKPHVLIMFGPFIDITHPLIASGKLPNFPQFKTQPKTLDELFLKLFTPILKTISPHIQTVLIPSTKDAISNHAAYPQASLIRKALQLPKRNFKCMANPSSFQINEIYFGCSNVDTFKDLKEVIKGGTTSSRYRLDRVSEHILQQRRYYPIFPGSIRTRIKPKDVSTKKETNDMESKEEKVYEHISGADLDVSYLGLTEFVGGFSPDIMIIPSELQHFARVVQNVVVINPGRFIRATGNRGSYAQITVQCPDLEDGKLTLVEGEEPVYLHNVWKRARVDLIAS

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	Saccharomyces cerevisiae

Entity 5 non-polymer

描述 description	IRON/SULFUR CLUSTER
分子量 formula_weight	351.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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7. 引用文献 (2)

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分辨率 resolution	5.60 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	176443

fit	/app/data/saxs_computation/fo/8foe/8foe.fit
pddf	/app/data/pr_computation/fo/8foe/8foe.pr.out
profile	/app/data/saxs_computation/fo/8foe/8foe.dat

Cryo-EM structure of S. cerevisiae DNA polymerase alpha-primase complex bound to a template DNA

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

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

来源 Source

Entity 5 non-polymer

7. 引用文献 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)