SAXSdb — 8v5m

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8v5m
沉积日期 deposition_date	2023-11-30
结构标题 title	Tetramer core subcomplex (conformation 1) of Xenopus laevis DNA polymerase alpha-primase
关键词 keywords	Primase, DNA polymerase, chimeric RNA-DNA primer, RNA/DNA hybrid, DNA replication, DNA synthesis, REPLICATION, TRANSFERASE; REPLICATION, TRANSFERASE
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	47.14 Å
回转半径 Rg (电子) rg_electron	47.16 Å
零角强度 I(0) i0	297255000.00
分子量 molecular_weight	143890.0 kDa
排除体积 excluded_volume	180890 Å³
包络体积 envelope_volume	264090 Å³
水化壳体积 shell_volume	49493 Å³
包络直径 envelope_diameter	160.4 Å
壳层 Rg shell_rg	47.73 Å
包络 Rg envelope_rg	45.79 Å
形状 Rg shape_rg	47.10 Å
总 Rg total_rg	47.42 Å
总原子数 total_atoms	20183
残基数 n_residues	1243
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	159.8 Å
Rg (实空间) rg_real	47.54 Å
Rg 误差 (实空间) rg_real_error	1.54 Å
I(0) (实空间) i0_real	2.9730e+08
I(0) 误差 (实空间) i0_real_error	5.8350e+06
Rg (倒空间) rg_reciprocal	47.15 Å
I(0) (倒空间) i0_reciprocal	297100000.0000
解质量估计 total_estimate	0.7663
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	38.7 Å
偏度 Skewness skewness	0.361
峰度 Kurtosis kurtosis	-0.789
角度范围 angular_range	— – 0.1650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	17350000.0000
实空间数据点数 n_real_points	34
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.727; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.777; Smooth: 0.000

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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 alpha catalytic subunit
分子量 formula_weight	129009.4 kDa
EC 编号 ec_number	2.7.7.7
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
原子数 atom_count	20183

SNAADGSQVFRFYWLDAYEDQYSQPGVVYLFGKVWIESADAYVSCCVSVKNIERTVYLLPRENRVQLSTGKDTGAPVSMMHVYQEFNEAVAEKYKIMKFKSKKVDKDYAFEIPDVPASSEYLEVRYSADSPQLPQDLKGETFSHVFGTNTSSLELFLLSRKIKGPSWLEIKSPQLSSQPMSWCKVEAVVTRPDQVSVVKDLAPPPVVVLSLSMKTVQNAKTHQNEIVAIAALVHHTFPLDKAPPQPPFQTHFCVLSKLNDCIFPYDYNEAVKQKNANIEIALTERTLLGFFLAKIHKIDPDVIVGHDIYGFDLEVLLQRINSCKVPFWSKIGRLRRSVMPKLGGRSGFAERNAACGRIICDIEISAKELIRCKSYHLSELVHQILKAERVVIPPENIRNAYNDSVHLLYMLENTWIDAKFILQIMCELNVLPLALQITNIAGNVMSRTLMGGRSERNEYLLLHAFTENNFIVPDKPVFKKMQQTTVEDNDDMGTDQNKNKSRKKAAYAGGLVLEPKVGFYDKFILLLDFNSLYPSIIQEYNICFTTVHREAPSTQKGEDQDEIPELPHSDLEMGILPREIRKLVERRRHVKQLMKQPDLNPDLYLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTHQGREILLHTKEMVQKMNLEVIYGDTDSIMINTNCNNLEEVFKLGNRVKSEINKSYKLLEIDIDGIFKSLLLLKKKKYAALTVEPTGDGKYVTKQELKGLDIVRRDWCELAKQAGNYVISQILSDQPRDSIVENIQKKLTEIGENVTNGTVPITQYEINKALTKDPQDYPDKKSLPHVHVALWINSQGGRKVKAGDTISYVICQDGSNLSASQRAYAQEQLQKQENLSIDTQYYLSQQVHPVVARICEPIDGIDSALIAMWLGLDPSQFRAHRHYQQDEENDALLGGPSQLTDEEKYRDCERFKFFCPKCGTENIYDNVFDGSGLQIEPGLKRCSKPECDASPLDYVIQVHNKLLLDIRRYIKKYYSGWLVCEEKTCQNRTRRLPLSFSRNGPICQACSKATLRSEYPEKALYTQLCFYRFIFDWDYALEKVVSEQERGHLKKKLFQESENQYKKLKSTVDQVLSRSGYSEVNLSKLFQTLNTIK

来源 Source

来源生物 organism	Xenopus laevis
通用名 common_name	African clawed frog
NCBI 分类编号 ncbi_taxonomy_id	8355
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 polymer

描述 description	DNA polymerase alpha subunit B
分子量 formula_weight	67194.2 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

SNAMSVSAKSIAEELKVFDVNFEDEEVPEKMVELCTVHRLKEEDMVNEWMAFSTTRNLPLTVGNLNLLEHEVLNKKSARPRPSLKKEKHCGNRDFNTIQELIEVETAEENLLDSYATPAKGSQKRNLSTPEHPQSKRILSINRSPHVLFSPTSFSPSATPSQKYGSRTNRGEVVTTYGELQGTTWNGGSGSNTNVELFTSLDEPLTKMYKFMFQKLMDIREVVSIKIEELGASLKDHFQIDEFTSVSLPAQETVTVLGQIGCDSNGKLNSKSVILEGDREHSAGMQVPVDLSELKDYSLFPGQVVIMEGTNSTGRRFVPTKLYEGVPLPFHQPSKEFEECPQQMVITACGPFTTSDTITYDALKDLIDIVNRDRPDICILLGPFLDAKHEQIENLQLTVTFEDVFKRCLKMIIEGTRPSGCHLVIVPSLRDVHHDPVYPQPPFSCFEPAKEDKERVHFVADPCTLSVNGVVIGMTSTDLLFHMGAEEISSSAGAPDRFSRILRHILTQRSYYPLYPPNEEINIDYEALYSYTPMPVTPDVFIVPSELRYFIKDVTGCICINPGRLTKGLVGGTYARFLVKSGAMGSEGKRSTCISAQVVRV

来源 Source

来源生物 organism	Xenopus laevis
通用名 common_name	African clawed frog
NCBI 分类编号 ncbi_taxonomy_id	8355
宿主生物 host_organism	Spodoptera frugiperda

Entity 3 polymer

描述 description	DNA primase large subunit
分子量 formula_weight	59673.8 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	C

MLFSRDRKYRHNTRLTGDRKGDLYPSSLQFYQHPPTENISLIEFETFAIERLKLLKAVENLGVSYVKNSEEYSKKLELELRKLKFPYRPLHEEISDDVYDLRRKDHISHFILRLAYCQSEDLRRWFIQQEMDLFKFRFGLLTKESVQEFLKLNDLQYVAISEDEKNMHKEDLMNSSFGLSLTKMEDTEFYKVPFQAALDLVRPRKVFLWRGFAFIPHKDIVSIVLNDFRAKLSKALALSARSLPVVQSDERLQPLLNHLSHSYIGQDFSSQSNTGKISLEQIDGFAAKSFPLCMRQLHKSLRENHHLRHGGRMQYGLFLKGIGLTLEQALQFWRLEFTKGKVDSEKFDKVYAYSIRHNYGKEGKRTDYTPYSCMKVILSNPPSQGDYHGCPFRHSDPELLKQKLQSFKVPSSGINQILELVKGMHYQLACQKYFELTHSVDDCGFSLNHPNQYFAESQKLLTGSREIKKEQTARDSPAVTASQLSSSSSSASIPKSQSSAPEMEDLEQIFSEY

来源 Source

来源生物 organism	Xenopus laevis
通用名 common_name	African clawed frog
NCBI 分类编号 ncbi_taxonomy_id	8355
宿主生物 host_organism	Escherichia coli

Entity 4 polymer

描述 description	DNA primase
分子量 formula_weight	49356.4 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	D

GPHMDLSVYDPASLPDVLPLYYRRLFPFYQYFRWLNYGGVVKNYFQHREFSFTLKDDVYVRYQSFNNQSELEKEMQKMCPYKIDIGAVYSHRPSLHNTVKSGTFQAQEKELVFDIDMTDYDDVRRCCSSADICPKCWTLMTIAVRILDRALAEDFGFKHRLWVYSGRRGVHCWVCDDSARKLSQAERSAVAEYLSVVKGGEETIKKVQLPETIHPFIGKSLKMVERYFEKYALVDQDILENKQCWDKVIALVPEVARESLLREFSKARSSVERWDKLSSCLEATGKDFRRYSNIPKEIMLQFCYPRLDVNVSKGLNHLLKSPFSVHPKTGRISVPIDCKKLDQFDPFSVPTISLICSELDNVSKKEEDEDSAGEGEPEAKKRTRDYKRTSLAPYIKVFEQFLDKLDQSRKGELLNKSDLKKEF

来源 Source

来源生物 organism	Xenopus laevis
通用名 common_name	African clawed frog
NCBI 分类编号 ncbi_taxonomy_id	8355
宿主生物 host_organism	Escherichia coli

Entity 5 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

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7. 引用文献 (2)

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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	9.22 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	64911

fit	/app/data/saxs_computation/v5/8v5m/8v5m.fit
pddf	/app/data/pr_computation/v5/8v5m/8v5m.pr.out
profile	/app/data/saxs_computation/v5/8v5m/8v5m.dat

Tetramer core subcomplex (conformation 1) of Xenopus laevis DNA polymerase alpha-primase

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

来源 Source

Entity 5 non-polymer

7. 引用文献 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)