SAXSdb — 8g9f

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8g9f
沉积日期 deposition_date	2023-02-21
结构标题 title	Complete auto-inhibitory complex 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	46.84 Å
回转半径 Rg (电子) rg_electron	46.24 Å
零角强度 I(0) i0	1007440000.00
分子量 molecular_weight	267150.0 kDa
排除体积 excluded_volume	336090 Å³
包络体积 envelope_volume	477750 Å³
水化壳体积 shell_volume	84822 Å³
包络直径 envelope_diameter	159.5 Å
壳层 Rg shell_rg	52.07 Å
包络 Rg envelope_rg	45.22 Å
形状 Rg shape_rg	46.22 Å
总 Rg total_rg	46.56 Å
总原子数 total_atoms	37540
残基数 n_residues	2321
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	153.3 Å
Rg (实空间) rg_real	46.65 Å
Rg 误差 (实空间) rg_real_error	1.29 Å
I(0) (实空间) i0_real	1.0070e+09
I(0) 误差 (实空间) i0_real_error	2.0280e+07
Rg (倒空间) rg_reciprocal	46.84 Å
I(0) (倒空间) i0_reciprocal	1008000000.0000
解质量估计 total_estimate	0.6625
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	58.6 Å
偏度 Skewness skewness	0.189
峰度 Kurtosis kurtosis	-0.441
角度范围 angular_range	— – 0.1700 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	83050000.0000
实空间数据点数 n_real_points	35
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.890; Stabil: 1.000; Sysdev: 0.021; Positv: 1.000; Valcen: 0.983; Smooth: 0.891

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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 (6)

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	37540

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

Entity 6 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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6. 折叠分类 (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

结构域编号 domain_id	8g9fA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	2820 —

结构域编号 domain_id	8g9fA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	420 — Nucleotidyltransferase; domain 5
同源超家族 H-superfamily homologous superfamily	10 — Ribonuclease H-like superfamily/Ribonuclease H

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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	3.20 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	47277

fit	/app/data/saxs_computation/g9/8g9f/8g9f.fit
pddf	/app/data/pr_computation/g9/8g9f/8g9f.pr.out
profile	/app/data/saxs_computation/g9/8g9f/8g9f.dat

Complete auto-inhibitory complex 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 (6)

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

Entity 6 non-polymer

6. 折叠分类 (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. 引用文献 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)